BACTERIA
ANTIMICROBIAL RESISTANCE |
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| CIPARS | Canadian Integrated Program for Antimicrobial Resistance Surveillance (CIPARS) |
| AMRFinderPlus | Bacterial resistance mechanisms |
| Antimicrobial Drug Database (AMDD) | Bacterial resistance mechanisms |
| ARDB (no longer maintained) | Bacterial resistance mechanisms |
| ARGminer | Bacterial resistance mechanisms |
| BacMet | Bacterial resistance mechanisms |
| Beta-Lactamase Database (BLAD) | Bacterial resistance mechanisms |
| Beta-Lactamase Database (BLDB) | Bacterial resistance mechanisms |
| CBMAR | Bacterial resistance mechanisms |
| The Comprehensive Antibiotic Resistance Database | Bacterial resistance mechanisms |
| FARME | Bacterial resistance mechanisms |
| INTEGRALL | Bacterial resistance mechanisms |
| LacED | Bacterial resistance mechanisms |
| MEGARes | Bacterial resistance mechanisms |
| MUBII-TB-DB | Bacterial resistance mechanisms |
| Mustard Database | Bacterial resistance mechanisms |
| MvirDB | Bacterial resistance mechanisms |
| PathoPhenoDB | Bacterial resistance mechanisms |
| PATRIC database | Bacterial resistance mechanisms |
| RAC: Repository of Antibiotic resistance Cassettes | Bacterial resistance mechanisms |
| ResFinder | Bacterial resistance mechanisms |
| TBDReaMDB | Bacterial resistance mechanisms |
| u-CARE | Bacterial resistance mechanisms |
| VFDB | Bacterial resistance mechanisms |
BACTERIAL PATHOGENS |
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| AMRFinderPlus | A bioinformatic tool that allows users to identify antimicrobial resistance determinants, stress response, and virulence genes in bacterial genomes |
| Antimicrobial Drug Database (AMDD) | An antimicrobial database |
| ARDB (no longer maintained) | A database that tracks antibiotic resistance genes |
| ARGminer | Antibiotic resistance database |
| BacMet | Antibiotic resistance database |
| Beta-Lactamase Database (BLAD) | Structural and phenotypic data on a class of enzymes, beta-lactamase. |
| Beta-Lactamase Database (BLDB) | A database that documents beta-lactamase structure and function. |
| CBMAR | A database focused on the annotation and discovery of novel beta-lactamase genes and proteins in bacteria. |
| EARS-Net | A central and comprehensive database for the European Union that focuses on eight different bacterial pathogens |
| ESAC-Net | A central and comprehensive database for the European Union that focuses on reference data on antimicrobial consumption by 30 countries across Europe. |
| FARME | A database that compiles publicly available DNA elements and predicted proteins that confer antibiotic resistance, regulatory elements and mobile genetic elements. |
| INTEGRALL | Annotated integrons and all other transposable elements that confer resistance to antibiotics in bacteria. |
| LacED | A database that identifies and corrects inconsistencies in already existing databases, namely Beta-lactamases. |
| MEGARes | A hand-curated antibiotic resistance database which incorporates previously published resistance sequences for antimicrobial drugs. |
| MUBII-TB-DB | Highly structured, text-based database focusing on Mycobacterium tuberculosis |
| Mustard Database | Tracks Antimicrobial Resistance Determinants (ARDs) |
| MvirDB | A publicly available database that stores information on toxins, virulence factors and antibiotic resistance genes. |
| PathoPhenoDB | Connects pathogens to their phenotypes |
| PATRIC database | The bacterial bioinformatics resource center |
| RAC | Repository of antibiotic resistance cassettes |
| ResFinder | Antimicrobial resistance genes from whole-genome data sets |
| The Comprehensive Antibiotic Resistance Database | Antibiotic resistance database |
| u-CARE | A database focused on the documentation of multi-drug resistant Escherichia coli (E.coli)[ |
| VFDB | A database that provides scientist quick access to virulence factors in bacterial pathogens |
BACTERIAL TAXONOMY AND BIODIVERSITY |
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| BacDive | Bacterial metadatabase that provides strain-linked information about bacterial and archaeal biodiversity, including taxonomy information |
| NCBI Taxonomy | A taxonomic database operated by NCBI and concentrating on all taxa for which DNA sequences are available (those sequences are stored by GenBank, another database operated by NCBI). |
MICROBIAL BIOCATALYTIC REACTIONS |
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| The University of Minnesota Biocatalysis/Biodegradation Database | Microbial biocatalytic reactions and biodegradation pathways primarily for xenobiotic, chemical compounds. |
CHEMISTRY AND BIOCHEMISTRY
AMINO ACIDS |
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| AAindex | Database of amino acid indices, amino acid mutation matrices, and pair-wise contact potentials |
| AAindex | Amino Acid index database |
| Amino Acids Sequence Database (PRF/SEQDB) | This database consists of amino acid sequences of peptides and proteins, including sequences predicted from genes. You can also search literature in which the sequence is presented.Sequences not included in EMBL, GenBank and SwissProt are also found in PRF/SEQDB since it is constructed on the basis of all amino acid sequences of peptides and proteins reported in literature. |
ALGORITHMS |
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| metalife bioinformatics database | metalife makes available various bioinformatics algorithms, which perform all essential tasks in sequence analysis and sequence-based predictions. |
BIOACTIVE MOLECULES |
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| ChEMBL | Manually curated database of bioactive molecules with drug-like properties. It brings together chemical, bioactivity, and genomic data to aid the translation of genomic information into effective new drugs. |
BIOCHEMICAL REACTIONS |
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| SABIO-RK: database for biochemical reactions and their kinetic properties | Database for biochemical reactions and their kinetic properties |
CARBOHYDRATES |
| SWEET-DB | SWEET-DB offers access to CarbBank entries via graphics-oriented surface. Bibliographic search and similarity-based structure search is possible. 3D structures (optimized by TINKER) of hit entries are displayed and can be saved as PDB files. |
| Carbohydrate-Active Enzymes | This server describes the families of structurally-related catalytic and carbohydrate-binding modules (or functional domains) of enzymes that degrade, modify, or create glycosidic bonds. |
CHEMISTRY |
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| ChemDiv, Inc.: Diverse chemical libraries. Compound collections. Combinatorial chemistry | Chemistry discovery and development services provider: Diversity small molecule organic compounds for bioscreening, combinatorial libraries. |
| CHEMLIBnetBASE | Complements the databases of CHEMnetBASE with dozens of resources, references, and CRC handbooks. |
| CHEMnetBASE | Includes several chemical dictionaries, and the CRC handbook of chemistry & physics. |
| Current chemical reactions | Contains single- and multi-step new synthetic methods. The overall reaction flow is provided for each method, along with a detailed and accurate graphical representation of each reaction step. |
| ProQuest materials science collection | This databases provides access to Materials Research Database with METADEX, ProQuest Materials Science Journals, and deep indexing of over a million tables and figures. |
| Reaxys | Reaxys is a web-based search and retrieval system for chemical compounds, bibliographic data and chemical reactions. |
| SciFinder | SciFinder provides access to several Chemical Abstracts Service databases, including Chemical Abstracts, Registry, CASREACT, CHEMLIST, and CHEMCAT.. |
CYTOCHROME P450 |
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| ADME DB | ADME DB is a database containing information on Human Cytochrome P450 metabolism, kinetics, transporter and structure. The information is organized by category (therapeutic area), drug name, enzyme, reaction, and type. The database includes about 11 000 entries, 5000 reactions, 3000 references and 6500 structures in mol format. |
| BioFrontier / P450 | BioFrontier/P450 is a system, which enables every user to search for information about Human Cytochrome P450. It uses a structure formula or reaction formula as a search query. In addition to the searching function, the system can also predict information about unknown metabolites by analyzing data in the system. |
ENZYMES |
| BRENDA-The Comprehensive Enzyme Information System | BRENDA is the main collection of enzyme functional data available to the scientific community. The enzymes are classified according to the Enzyme Commission list of enzymes. Some 3500 “different” enzymes are covered. |
| Carbohydrate-Active Enzymes | This server describes the families of structurally-related catalytic and carbohydrate-binding modules (or functional domains) of enzymes that degrade, modify, or create glycosidic bonds. |
| Enzymes and Metabolic Pathways | The EMP Project, Inc. was incorporated in 1999 to provide organizational, legal, and financial support for the EMP group projects, such as Enzymes and Metabolic Pathways Database (EMP) and Metabolic Pathways Database (MPW). EMP/MPW is the most comprehensive single source of computerized biochemical data available today. Moreover, this is a powerful tool for metabolic reconstruction and modeling, unmatched in either academia or the genomics industry. Both databases are currently used in a number of public and commercial genomics projects. |
CANCER
CANCER |
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| NCI Database Browser | A WWW browser to the new and enlarged NCI database (250.000 compounds) with all kinds of nifty output features and links to other services for continued processing. |
CANCER GENOME |
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| The Cancer Genome Atlas (TCGA) | Provides data from hundreds of cancer samples obtained using high-throughput techniques such as gene expression profiling, copy number variation profiling, SNP genotyping, genome-wide DNA methylation profiling, microrna profiling, and exon sequencing of at least 1,200 genes |
CANCER IMAGING |
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| The Cancer Imaging Archive (TCIA) | Cancer imaging |
CANCER RESEARCH |
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| Blocks WWW Server | A service for biological sequence analysis at the Fred Hutchinson Cancer Research Center in Seattle, Washington, USA. |
| Healthcare Cost and Utilization Project (HCUP) | The largest collection of hospital care data in the United States. It includes hundreds of millions of inpatient, outpatient, and emergency records. |
| JASPAR | A database of manually curated, non-redundant transcription factor binding profiles. |
| MetOSite | A database about methionine sulfoxidation sites and its functional roles in proteins |
| Oncogenomic databases | A compilation of databases that serve for cancer research |
| RIKEN integrated database of mammals | Integrated database of mammals |
| TDR Targets | A chemogenomics database focused on drug discovery in tropical diseases |
| TRANSFAC | A database about eukaryotic transcription factors, their genomic binding sites and DNA-binding profiles |
CELL
BIOLOGICAL PROCESSES |
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| Biomodels Database | Published mathematical models describing biological processes |
BLAST AND SEQUENCE ALIGNMENT |
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| European Bioinformatics Institute | Tools for bioinformatics. Web based Blast Fasta Clustal. |
| BLAST/BLAT | Search our genomes for your DNA or protein sequence |
| Blast | Basic Local Alignment Search Tool (BLAST) finds regions of local similarity between sequences |
| Sequence alignment | Align two or more protein sequences with the Clustal Omega program |
CELL LINES (HUMAN AND ANIMAL) |
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| HyperCLDB | HyperCLDB is a hypetext devoted to availability of human and animal cell lines that are available from European collections.More than 4,000 cell lines are recorded.A free text search engine is as well available. |
| Cellosaurus | A knowledge resource on cell lines |
CELL SIGNALING |
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| Cell Signaling Networks Database | Cell Signaling Networks Data base (CSNDB) is a data- and knowledge- base for signaling pathways of human cells. It compiles the information on biological molecules, sequences, structures, functions, and biological reactions which transfer the cellular signals. Signaling pathways are compiled as binary relationships of biomolecules and represented by graphs drawn automatically. |
EXOSOMES |
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| ExoCarta | Database of exosomal proteins, RNA and lipids |
G PROTEINS |
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| GCRDb | G-Protein Coupled Receptor Database. |
HYDROGENASE AND NITROGENASE |
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| Hydrogenase&nitrogenase databases | Hydrogenase and nitrogenase databases. About 4000 references of hydrogen production studies. |
INTERACTION DATABASE |
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| BioGRID | General repository for interaction datasets (Samuel Lunenfeld Research Institute) |
| BIOINFO BANK | Analysis of protein and protein-DNA interactions. |
| IntAct | Open-source database for molecular interactions (EMBL-EBI) |
| NCI-Nature Pathway Interaction Database | Interaction database |
METABOLOME |
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| HMDB | Contains detailed information about small molecule metabolites found in the human body |
| Aging metabolomics | All metabolomes in body fluids in aging |
| Bmi metabolomics | Bmi metabolomic data |
| Disease metabolomics | Disease metabolomic data |
| Gender metabolomics | Gender metabolomic data |
| Geno metabolomics | Geno metabolomic data |
| Golm metabolomics | Golm metabolomic data |
| All metabolomes in body fluids | All body fluid metabolomic data |
| Metabolomic classes | Metabolomic classes data |
| Pharma metabolomics | Metabolomic pharma data |
| Pathway metabolomics | Metabolomic pathway data |
| Yeast metabolomics | Metabolomic yeast data |
| Diurnal metabolomics | Metabolomic diurnal data |
METAL BINDING SITE |
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| Metalloprotein site Database and Browser | An structural database of metal-binding sites in metalloproteins, including an interactive search and visualization interface. |
METAL IONS |
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| The PROMISE Database | The Prosthetic groups and Metal Ions in Protein Active Sites Database. |
MOLECULES |
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| ConsensusPathDB | A molecular functional interaction database, integrating information from 12 other |
| Entrez | National Center for Biotechnology Information |
| Neuroscience Information Framework (University of California, San Diego) | Integrates hundreds of neuroscience relevant resources; many are listed below |
PATHWAYS |
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| BioCyc Database Collection | Collection of thousands of Pathway/Genome Databases (PGDBs), and software tools for exploring them. |
| Reactome | Navigable map of human biological pathways, ranging from metabolic processes to hormonal signalling (Ontario Institute for Cancer Research, European Bioinformatics Institute, NYU Langone Medical Center, Cold Spring Harbor Laboratory) |
| WikiPathways | Pathways |
| BioCyc Database Collection | EcoCyc and MetaCyc are organism specific pathway/genome database |
| KEGG PATHWAY Database | Univ. of Kyoto pathway database |
| Reactome | Navigable map of human biological pathways, ranging from metabolic processes to hormonal signalling (Ontario Institute for Cancer Research, European Bioinformatics Institute, NYU Langone Medical Center, Cold Spring Harbor Laboratory) |
| WikiPathways | Pathways |
PEPTIDE |
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| Peptide search | Find sequences that exactly match a query peptide sequence |
PORPHYRINS |
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| Handbook of Porphyrin Science | Porphyrins, phthalocyanines, and their analogs and derivatives |
RIBOSOMES |
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| Database of ribosomal crosslinks (DRC) | The Database of Ribosomal Cross-links (DRC) provides a complete collection of all the published data produced by cross-linking studies on the Escherichia coli ribosome, as well as on its components and functional ligands. |
SIGNAL TRANSDUCTION |
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| Netpath | Curated resource of signal transduction pathways in humans |
DATA ANALYSIS AND TOOLS
AI |
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| Plotty | Platform for building, deploying, and hyperscaling artificial inteligence (AI) |
BIOINFORMATICS |
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| MANET database | A bioinformatics database that maps evolutionary relationships of protein architectures directly onto biological networks. |
| European Bioinformatics Institute | Tools for bioinformatics. Web based Blast Fasta Clustal. |
BIOINFORMATIC TOOLS |
| Bedtools bedtools.readthedocs.io | Collectively, the bedtools utilities are a swiss-army knife of tools for a wide-range of genomics analysis tasks. The most widely-used tools enable genome arithmetic: that is, set theory on the genome. |
| BioJava biojava.org | The open-source Java framework for bioinformatics. |
| BioPerl bioperl.org | The Bioperl Project is an international association of users & developers of open source Perl tools for bioinformatics, genomics and life science. |
| Biopython biopython.org | Biopython is a set of freely available tools for biological computation written in Python by an international team of developers. |
| ENCODE encodeproject.org | The Encyclopedia of DNA Elements (ENCODE) is a public research project which aims to identify functional elements in the human and mouse genomes. |
| Ensembl ensembl.org | The Ensembl project started in 1999 with the goal to automatically annotate the human genome, integrate this annotation with other available biological data, and make all this publicly available via the web. Since then, many more genomes have been added to Ensembl and the range of available data has expanded to include comparative genomics, variation and regulatory data. |
| FastQC bioinformatics.babraham.ac.uk/projects/fastqc | FastQC aims to provide a simple way to do some quality control checks on raw sequence data coming from high throughput sequencing pipelines. It provides a modular set of analyses which you can use to give a quick impression of whether your data has any problems of which you should be aware before doing any further analysis. |
| Java java.com | Java is a general-purpose computer-programming language that is concurrent, class-based, object-oriented, and specifically designed to have as few implementation dependencies as possible. |
| NCI Database Browser | A WWW browser to the new and enlarged NCI database (250.000 compounds) with all kinds of nifty output features and links to other services for continued processing. |
| OMICtools omictools.com | OmicX is a global benchmark in big biodata analytics. Powered by machine teaching, its unique dynamic analytics ecosystem deciphers and analyses life science data. |
| OWL | OWL is a non-redundant composite of 4 publicly-available primary sources: SWISS-PROT, PIR (1-3), GenBank (translation) and NRL-3D. SWISS-PROT is the highest priority source, all others being compared against it to eliminate identical and trivially-different sequences. The strict redundancy criteria render OWL relatively “small” and hence efficient in similarity searches. |
| Perl perl.org | Perl 5 is a highly capable, feature-rich programming language with over 30 years of development. |
| Python python.org | Python is a programming language that lets you work quickly and integrate systems more effectively. |
| Samtools htslib.org | Samtools is a suite of programs for interacting with high-throughput sequencing data. It consists of three separate repositories - Samtools, BCFtools, HTSlib. |
| UCSC Genome Browser genome.ucsc.edu | The UCSC Genome Browser provides a broad collection of vertebrate and model organism assemblies and annotations, along with a large suite of tools for viewing, analyzing and downloading data. |
CODON USAGE |
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| Codon Usage Database | Codon Usage Database compiled from CUTG. |
DATA PROCESSING AND ANALYSIS SOFTWARE |
| community.tibco.com/products/tibco-statistica | TIBCO Statistica advanced analytics and data science platform helps you to embed analytics everywhere, empower more people and innovate faster. |
| ibm.com/analytics/spss-statistics-software | The IBM SPSS® software platform offers advanced statistical analysis, a vast library of machine-learning algorithms, text analysis, open-source extensibility, integration with big data and seamless deployment into applications. |
| originlab.com | Origin is an industry-leading scientific graphing and data analysis software. |
| products.office.com/en/excel | Microsoft Excel is the industry leading spreadsheet program, a powerful data visualization and analysis tool. |
| systatsoftware.com/products/sigmaplot | SigmaPlot is a software package for scientific graphing and statistical data analysis. |
| systatsoftware.com/products/sigmastat | SigmaStat provides a wide range of powerful yet easy-to-use statistical analyses designed to meet the needs of research scientists and engineers. |
DATA REPOSITORIES |
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| re3data.org : Registry of Research Data Repositories | re3data.org is a worldwide registry of research data repositories in multiple disciplines. |
DNA BAR CODES |
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| Barcode of Life Data Systems | Database of DNA barcodes |
DICTIONARY |
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| Dictionary of Substances & Their Effects (DOSE, 3rd Electronic Edition) | 2005 edition. Comprehensive compilation of peer-reviewed health and environmental data on several thousand chemical substances. Includes biological, ecological and toxicological risks, hazards, and effects data and regulatory limits for the substances. |
CONFERENCE |
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| Conference proceedings citation index. | "Conference Proceedings Citation Index helps researchers access the published literature from ... conferences, symposia, seminars, colloquia, workshops, and conventions worldwide." |
MATHEMATICS |
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| MathSciNet | American Mathematical Society. |
MOLECULAR BIOLOGY SOFTWARE |
| DNAMAN lynnon.com | DNAMAN is a one-for-all software package for molecular biology applications. This package can perform restriction analyses, multiple sequence alignment, PCR primer design, protein sequence analysis, and plasmid drawing. |
| DNAStar dnastar.com/software/molecular-biology | DNASTAR’s Molecular Biology Suite is a comprehensive sequence analysis and alignment software for molecular biology research. The suite provides software solutions for DNA, RNA and protein editing and annotation, Sanger sequence assembly, multiple sequence alignment, virtual cloning, primer design and comprehensive sequence analysis. |
| SnapGene snapgene.com | SnapGene offers a fast and easy way to plan, visualize, and document your everyday molecular biology procedures. |
| Vector NTI thermofisher.com/vector-nti-software.html | Vector NTI software is a completely integrated suite of sequence analysis and design tools that help you manage, view, analyze, transform, share, and publish diverse types of molecular biology data, all within one graphically rich analysis environment. |
| Web of science--all databases | Web of Science All Databases indexes (formerly Thomson Reuters Web of Knowledge) indexes core journal articles, conference proceedings, data sets, and other resources in the sciences, social sciences, arts, and humanities. |
MORPHOMETRY |
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| Cell Profiler | Extract quantitative measurements for multiple images |
| FIJI | An extended version of ImageJ with various plugins |
| ImageJ | A free software for image analysis |
| L-measure | Quantitative morphologic measurement |
| Neurostudio | Trace dendritic arbor of neurons |
| PATENTS | |
| Google patents | Comprehensive list of patents |
| Derwent innovations index | The world's most comprehensive database of international patent information. |
PROTOCOLS |
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| Protocol Exchange | Open repository for sharing scientific research protocols. These protocols are posted directly on the Protocol Exchange by authors and are made freely available to the scientific community for use and comment. |
| Springer Nature Experiments | Platform connecting researchers with protocols and methods. |
| jove.com | JoVE creates the ultimate solutions for advancing research and science education by making and publishing videos of scientific experiments from the top laboratories around the globe. |
| cshprotocols.cshlp.org | Cold Spring Harbor Protocols is an interdisciplinary journal providing a definitive source of research methods in cell, developmental and molecular biology, genetics, bioinformatics, protein science, computational biology, immunology, neuroscience and imaging. |
| bio-protocol.org/bio101/Default.aspx | Bio-101 is an online database of life science protocols. Its mission is to make life science research more efficient and reproducible by curating and hosting high-quality, experimentally validated, freely accessible protocols. |
| protocol-online.org | Protocol Online is a database of research protocols in a variety of life science fields. It contains protocols contributed by worldwide researchers as well as links to web protocols hosted by worldwide research labs, biotech companies, personal web sites. |
| Cold Spring Harbor protocols | The database is fully searchable by keyword and subject. |
| Current protocols | Current protocols in bioinformatics; Current protocols in cell biology; Current protocols in immunology; Current protocols in molecular biology; Current protocols in neuroscience; Current protocols in protein science. |
| JoVE. General. | "General" section of the Journal of Visualized Experiments (JoVE), which is an online journal publishing visualized (video-based) biological research studies. |
| Nature Methods | Nature Methods is a forum for the publication of novel methods and significant improvements to tried-and-tested basic research techniques in the life sciences. |
| Nature Protocols | Nature Protocols is an online journal of laboratory protocols for bench researchers. |
| Springer Protocols | Provides access to peer-reviewed biological and biomedical research protocols from the Methods in Molecular Biology, Methods in Molecular Medicine, Neuromethods, Methods in Pharmacology and Toxicology, and Methods in Biotechnology series. |
PRIMER DESIGN TOOLS |
| Array Designer premierbiosoft.com/dnamicroarray | Array Designer is a microarray software that enables fast, efficient design of specific oligos for making whole genome arrays, tiling arrays and resequencing arrays. |
| GenScript Pcr Primer Design | Genscript online PCR primer design tool for perfect PCR and sequencing primers design. |
| NCBI - Primer-BLAST ncbi.nlm.nih.gov/tools/primer-blast | NCBI’s Primer-BLAST tool is for designing PCR primers and checking them for specificity. |
| NIH primer design | Design primers. |
| NIH primer design | Primer blast. |
| ODIN primer design | Primer blast. |
| PCR Primer Design Tool - Eurofins Genomics | The PCR prime rdesgin tool analyses the entered DNA sequence and chooses the optimum PCR primer pairs. |
| PrimeBank-MGH-PGA | Primer Bank is a public resource for PCR primers. |
| Primer Design Tool - Modern Software | Transform Your R&D With Benchling's Cutting-Edge Primer Design Tool. |
| Primer Premier premierbiosoft.com/primerdesign | Primer Premier's search algorithm finds optimal PCR, multiplex and SNP genotyping primers with the most accurate melting temperature using the nearest neighbor algorithm. |
| Primer3Plus - Bioinformatics | The regions of interest can be marked using targets. Returns a list of all possible primers the can be designed on the template sequence. |
| PrimerQuest Tool - Primer Design | Design algorithm includes multiple checks to reduce primer-dimer formation. |
| Real Time PCR Primer Sets | Database of validated primer sets for quantitative PCR. |
PUBLISHING |
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Journal Information |
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| AccessScience | Multimedia encyclopedia and dictionary covering all major scientific disciplines. |
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Citations, abstracts and some full-text of articles published by the Association for Computing Machinery |
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| AGRICOLA | Agriculture, animal sciences, horticulture, hydrology (1970-present). |
| Agricultural & Environmental Science Database | Extensive coverage of environmental science and related disciplines, and including scholarly journals, trade and industry journals, magazines, technical reports, conference proceedings, and government publications. |
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Archival access to all of the Albert Einstein's Complete Papers |
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Contains indexing and abstracts for nearly 800 core English-language, scientific and technical publications back to 1983. |
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The Avery Index to Architectural Periodicals database offers a comprehensive listing of journal articles on architecture and design, including bibliographic descriptions. |
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An index of the web sites included in the 1999-present annual lists issued by the Mars Best of Free Reference Web Sites Committee of the American Library Association |
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Bibliography includes references to scientific and engineering research related to material and operations in a winter battlefield, the nature and impact of cold on facilities and activities, cold-related environmental problems, and the impact of human activity on cold environments. |
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| Biodiversity Heritage Library | Books, journals, and other materials on biodiversity from a worldwide consortium of natural history, botanical, research, and national libraries. Provides free access to hundreds of thousands of volumes from the 15th to the 21st centuries. |
| Biological & Agricultural Index Plus | 1983-present. Agriculture, animal husbandry, botany, cytology, ecology, entomology, environmental science, fishery sciences, food science, forestry, genetics, horticulture, microbiology, plant pathology, soil science, veterinary medicine, zoology. |
| An index with abstracts to periodicals in biology and the life sciences. | |
| BioMed Central | Open-access biomedical electronic journals. Articles are also immediately available on publication thru PubMed Central. |
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Free access to high impact journals published in BioMed Central |
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Collection of full-text, peer-reviewed research journals in biological, ecological and environmental sciences. |
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Pre-publication paper collection |
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| BIOSIS Previews | Comprehensive index to life sciences research literature. Covers journals (5000+), reports, meetings (1500+), reviews, and books in all areas of biology. Weekly email alerts available. |
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The Book Citation Index is designed to enhance the powerful discovery and analysis capabilities of Web of Knowledge by incorporating comprehensive book citation data. Researchers can search for and identify the most relevant and esteemed literature along with peer-reviewed journals. |
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| Botanicus (Missouri Botanical Garden Botanicus Collection) | 1480-1950. Historic botanical literature from the Missouri Botanical Garden Library. |
| Cambridge Scientific Abstracts | Databases in several electronic formats as well as the traditional print journal. They are available through eleven different commercial online hosts and five CD-ROM vendors, while our web-based Internet Database Service (IDS) provides access not only to all of our databases but also to those of several other publishing partners. |
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Archival access to all of the Charles Darwin papers and notes |
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CINAHL provides indexing for close to 3000 journals from the fields of nursing and allied health. |
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Scientific Literature Digital Library hosted by Penn State |
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| Monographs in areas of molecular, cell, and developmental biology, genetics, evolutionary biology, neuroscience, cancer biology, and molecular pathology. | |
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An official publications of the Association of College & Research Libraries, a division of the American Library Association |
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"Current Contents Connect is a current awareness database that provides easy Web access to complete tables of contents, abstracts, bibliographic information, and abstracts from the most recently published issues of leading scholarly journals. |
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Contains cumulative bibliographic citations to statistical books and articles in more than 1,000 journals, with coverage generally extending back to 1974, earlier in some instances. |
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Archival access to all of the Charles Darwin letters |
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Indexes research data, including data studies and data sets, and links them to the scientific literature to track data citation. |
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America’s libraries, archives, and museums |
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Free, full text journals, mostly in the sciences |
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DOAJ is a community-curated online directory that indexes and provides access to high quality, open access, peer-reviewed journals. |
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| Dryad | Repository of data underlying scientific publications in the basic and applied biosciences |
| Encyclopedia of Life Sciences | Provides 3000+ peer-reviewed articles, images, a glossary of terms, news, and some multimedia files on a wide variety of life sciences topics. Released 2001, continuously updated. |
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Engineering Village 2 provides access to over 5 million abstracts from Compendex, full text research articles, patents, standards and handbooks, seamlessly. |
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Citation, abstracts, and some full text of unpublished and difficult-to-find technical reports from several different U.S. government agencies |
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Free databases |
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| FSTA Direct | Published by IFIS Publishing, the FSTA. – Food Science and Technology Abstracts. database is the largest and most respected database in its field, covering all aspects of food science, food technology and food-related human nutrition. The entire FSTA. database is now available directly from IFIS Publishing for the first time in a web-searchable form as FSTA Direct.. |
| Gale OneFile: Agriculture | Nearly 200 titles focused on agriculture and its related fields: from practical aspects of farming to cutting edge scientific research in horticulture. |
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"Garden, Landscape & Horticulture Index (GLHI) is the premier resource for access to articles about plants and gardens. |
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General science full text features bibliographic indexes (coverage starting 1984), full text (starting 1995), plus graps, charts, diagrams, photos, and illustrations. |
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| GigaDB | Repository of large scale datasets underlying scientific publications in the biological and biomedical research |
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Handbook of paleoanthropology / Winfried Henke, Ian Tattersall (eds.) |
"Comprehensive handbook that takes a multifaceted and multidisciplinary approach to palaeoanthropology |
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Provides web access to more than three-million full-text documents from some of the world's most highly cited publications in electrical engineering, computer science and electronics. |
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Summarizes studies relating to all aspects of immune systems in man and animals, in normal functions and disorders. |
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Free access to citations and abstracts to articles from over 20,000 journals in a variety of subject areas |
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| IntechOpen | IntechOpen offers peer-reviewed books to the academic and scientific community on an open-access platform. |
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Index of organism’s names |
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JCR is a comprehensive, and unique resource tool for Journal Citation and Article Counts; Impact Factor; Immediacy Index; Cited Half-Life; Citing Half-Life; Source Data Listing, etc. |
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Provides image and full-text online access to back issues of selected scholarly journals in history, economics, political science, demography, mathematics and other fields of the humanities and social sciences. |
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| MEDLINE (via EBSCOHost) is the U.S. National Library of Medicine® (NLM) premier bibliographic database that contains more than 22 million references to journal articles in life sciences with a concentration on biomedicine. | |
| MEDLINE (via the National Library of Medicine) is the U.S. National Library of Medicine® (NLM) premier bibliographic database that contains more than 22 million references to journal articles in life sciences with a concentration on biomedicine. | |
| Presents an extensive selection of medical dictionaries, encyclopedias, glossaries, directories, and links to news and information regarding health topics and drug information for the general public. | |
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Download PDFs in education, science, and medicine |
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| National Science Digital Library | Education and research in science, technology, engineering, mathematics. |
| Nature Journals Online | Online access to the journal Nature and its sister publications in Biotechnology, Cell Biology, Genetics, Immunology, Medicine, Neuroscience, and Structural Biology. 1996-present (varies by title). |
| NCBI (National Center for Biotechnology Information) | Platform for biomedical and genomic databases. |
| NCBI Bookshelf | National Center for Biotechnology Information e-books. |
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A collection of biomedical books that can be searched directly by concept. National Center for Biotechnology Information. |
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An index to the worldwide technical literature pertaining to marine and brackish water environments. |
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Online, full-text handbooks covering topics in physics. |
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The Public Library of Science provides free access to the full-text of all of their highly rated journals |
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| PLOS (Public Library of Science) | Provides open-access peer-reviewed scientific and medical journal articles and journals. |
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Retired on September 1, 2019, the Popline database contained "more than 400,000 records" and "provided students and researchers worldwide with access to journal articles, reports, books, unpublished resources, and full-text documents to users in low- and middle-income countries." |
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Searchable and browsable database of dissertations and theses from around the world. |
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| PubMed | References and abstracts on life sciences and biomedical topics |
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PubMed / a service of the National Library of Medicine and the National Institutes of Health |
Provides access to over 16 million citations from MEDLINE and other life science journals for biomedical articles back to the 1950s. Includes links to many sites providing full text articles and other related resources. |
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Major headlines in all science disciplines |
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| Science Direct | Science journals database. |
| Science Magazine | Science publishing |
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Behind-the-scenes look at the scientists, journals, institutions, nations |
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| Science.gov | A gateway to government science information and research results. Searches over 55 scientific databases and 200 million pages of science information with just one query, and is a portal to over 2100 scientific Websites. [Free] |
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Over 55 databases and over 2100 selected websites from 13 federal agencies, offering 200 million pages of authoritative U.S. government science information |
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An electronic virtual library of scholarly journals published in Latin America. |
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| SciFinder | Combined access to Chemical Abstracts CAPlus, Registry, CASREACT, CHEMLIST, CHEMCAT databases, and Medline. |
| SciFindern | Next generation SciFinder interface that includes the latest datasets, search features, and mobile support. |
| Provides indexing, abstracting of and citation linking to journals in biology ,physics, chemistry, geosciences, agriculture, medicine, business, social work, and the social sciences. | |
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Statistical sources at Cornell University |
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| Web of Science: Core Collection | Access the world’s leading scholarly literature in the sciences, social sciences, arts, and humanities and examine proceedings of international conferences, symposia, seminars, colloquia, workshops, and conventions. |
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Worldwide catalog of over 100 million books |
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| Zoological record |
Bibliographical references from more than 6,000 international journals, review annuals, monographs, meeting proceedings, books and reports, representing research in all major areas of zoology, including: behavior, ecology, evolution, genetics, habitat, nutrition, parasitology, reproduction, taxonomy, zoogeography. |
PUBLISHING TOOLS |
| EndNote endnote.com | EndNote is a reference management software that not only frees you from the tedious work of manually collecting and curating your research materials and formatting bibliographies, but also gives you greater ease and control in coordinating with your colleagues. |
| Mendeley mendeley.com | Mendeley is a free reference manager and academic social network that can help you organize your research, collaborate with others online, and discover the latest research. |
| NoteExpress inoteexpress.com/index.htm | NoteExpress is designed to help you organize research notes and bibliographic references, generate bibliographies automatically, and search and capture bibliographic data from Internet with efficiency and ease. |
SEQUENCE ANALYSIS |
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| Blocks WWW Server | A service for biological sequence analysis at the Fred Hutchinson Cancer Research Center in Seattle, Washington, USA. |
SEMANTIC SEARCH |
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| WikiProfessional | A web-based research environment for semantic searching, providing an intuitive tool for analyzing and relating concepts. |
SCIENCE SEARCH TOOLS |
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| Web of Science: All Databases | Provides cross-search of multiple Web of Science databases. |
| WorldWideScience.org: The Global Science Gateway | WorldWideScience.org searches dozens of open access science databases. |
| Zoological Record | Extensive coverage of the world's zoological and animal science literature, covering research from biochemistry to veterinary medicine. |
| WolframAlpha | Provides scientific information for questions |
SEQUENCE ANALYSIS |
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| Blocks WWW Server | A service for biological sequence analysis at the Fred Hutchinson Cancer Research Center in Seattle, Washington, USA. |
RECODE |
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| RECODE | The RECODE database is a compilation of ‘programmed’ translational recoding events taken from the scientific literature and personal communications. The database deals with programmed ribosomal frameshifting, codon redefinition and translational bypass occurring in a variety of organisms. |
| Recorder-2000 – The naturalists database | Recorder-2000 – the main database used by recorders/naturalists/ecologists working to National Biodiversity Network (NBN) standards. |
SOFTWARE |
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| acdlabs.com/resources/freeware/chemsketch | ACD/ChemSketch Freeware is a drawing package that allows you to draw chemical structures including organics, organometallics, polymers, and Markush structures. It also includes features such as calculation of molecular properties (e.g., molecular weight, density, molar refractivity etc.), 2D and 3D structure cleaning and viewing, functionality for naming structures (fewer than 50 atoms and 3 rings), and prediction of logP. |
| adobe.com/products/illustrator.html | Adobe Illustrator is a vector graphics editor developed and marketed by Adobe Inc. |
| adobe.com/products/photoshop.html | Adobe Photoshop is an imaging and graphic design software developed and published by Adobe Inc. for macOS and Windows. |
| Edraw Max edrawsoft.com | Edraw Max is a 2D business technical diagramming software which helps create flowcharts, organizational charts, mind map, network diagrams, floor plans, workflow diagrams, business charts, and engineering diagrams. |
| Image Pro Plus mediacy.com/imageproplus | Image-Pro Plus image analysis software makes it easy to acquire images, count, measure and classify objects, and automate your work. |
| LYSANDRASOFT | LYSANDRA – a software for creating keys and database on different groups of living organisms. By present day we finished completely creating the first key and catalogue on the beetles of the genus Cryptocephalus (Chrysomelidae, Coleoptera) for the Palearctic Region and here we propose the work on CD to your. On our site you can learn all about this work and if it will interest to you, you can order and acquire this work on CD. |
| Morpheus | Converts microarray or qPCR results to heatmaps |
THERMODYNAMIC |
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| DiProDB | A database to collect and analyse thermodynamic, structural and other dinucleotide properties |
VIDEO |
| Alexander Street Video | Streaming videos and documentaries. |
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WESTERN BLOTTING |
| Western Blotting | Provides scientific information for Western Blotting |
DNA
DNA REPOSITORY |
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| DDBJ | DDBJ (DNA Data Bank of Japan) is the sole DNA data bank in Japan, which is officially certified to collect DNA sequences from researchers and to issue the internationally recognized accession number to data submitters. We collect data mainly from Japanese researchers, but of course accept data and issue the accession number to researchers in any other countries. |
DNA VARIATION |
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| PolymiRTS | A database of DNA variations in putative microRNA target sites |
NUCLEOTIDES |
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| GSDB | The Genome Sequence DataBase (GSDB) is a database of publicly available nucleotide sequences and their associated annotation maintained by NCGR. GSDB acquires most of its sequence data from the International Nucleotide Sequence Database Collaboration (IC, comprising DDBJ, EMBL, and GenBank databases) on a nightly basis. Each sequence record is parsed and stored in a relational database representation. |
| DNA Data Bank of Japan (National Institute of Genetics) | DNA databank |
| EMBL (European Bioinformatics Institute) | DNA databank |
| Ensembl |
provides automatic annotation databases for human, mouse, other vertebrate and eukaryote genomes |
| Ensembl Genomes |
provides genome-scale data for bacteria, protists, fungi, plants and invertebrate metazoa, through a unified set of interactive and programmatic interfaces (using the Ensembl software platform) |
| GenBank (National Center for Biotechnology Information) | DNA databank |
| 23andMe's |
A direct-to-consumer genetic testing service in which customers provide a saliva sample that is laboratory analysed, using single nucleotide polymorphism genotyping. |
| HapMap |
A haplotype map (HapMap) of the human genome |
| OMIM |
Online Mendelian Inheritance in Man of inherited diseases |
| RefSeq |
An open access, annotated and curated collection of publicly available nucleotide sequences (DNA, RNA) and their protein products. |
| 1000 Genomes Project |
The genomes of more than a thousand anonymous participants from a number of different ethnic groups were analyzed and made publicly available. |
| EggNOG Database |
A hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses. It provides multiple sequence alignments and maximum-likelihood trees, as well as broad functional annotation. |
NUCLEOSOME |
| Nucleosome positioning region database | Nucleosome positioning |
SEQUENCE REPEATS |
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| BIOEXPLORER | The database of simple sequence repeats in the human genome |
| SSRD: A Simple Sequence Repeats Database of the Human Genome | The database of simple sequence repeats in the human genome(SSRD), is a comprehensive resource for information about Simple Sequence Repeats in the human genome. The 501 SSRs, contained in SSRD, are divided into k-mer repeats, where k ranges from one to six, i.e. monomer repeats to hexamer repeats. |
SNP |
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| SNPedia | Database of SNPs |
EPIGENOME
EPIGENETICS |
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| Chromatin structure | Structure of chromatin |
| Genome analysis | Methods for analysis of genome |
| Epigenetic tools | Databases of epigenetics |
| iMETHYL database | Methylome data |
| Methbank database | A database of DNA methylomes across a variety of species |
| Metbase database | A database of DNA methylomes |
METHYLOME |
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| MethBase | Database of DNA methylation data visualized on the UCSC Genome Browser |
GENES
GENES |
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| AmiGO 2 | AmiGO 2 is a project to create the next generation of AmiGO--the current official web-based set of tools for searching and browsing the Gene Ontology database |
| Assembly Converter | Map (liftover) your data's coordinates to the current assembly. |
| BioGPS | BioGPS is a gene portal built with two guiding principles in mind -- customizability and extensibility |
| Biolinks | A subdivision of www.bioplanet.com. This site contains a comprehensive list of genetic related database links. |
| BioMart | Use this data-mining tool to export custom datasets from Ensembl. |
| BLAST/BLAT | Search our genomes for your DNA or protein sequence. |
| Data Slicer | Get a subset of data from a BAM or VCF file. |
| DECIPHER | DECIPHER (DatabasE of genomiC varIation and Phenotype in Humans using Ensembl Resources) is an interactive web-based database which incorporates a suite of tools designed to aid the interpretation of genomic variants |
| Ensembl | DNA sequences and assemblies |
| File Chameleon | Convert Ensembl files for use with other analysis tools |
| Gene Wiki | Describe the relationships and functions of all human genes. |
| GTR® | Genetic Testing Registry (GTR®) provides a central location for voluntary submission of genetic test information by providers |
| HGNC | Gene nomenclature |
| ID History Converter | Convert a set of Ensembl IDs from a previous release into their current equivalents. |
| Linkage Disequilibrium Calculator | Calculate LD between variants using genotypes from a selected population. |
| Monarch | An integrative data and analytic platform connecting phenotypes to genotypes across species, bridging basic and applied research with semantics-based analysis |
| NDEx query | Examine gene(s) for their properties, relevant pathways (curated and experimentally derived), protein interactions (PPI network), gene associations (including drugs, disease and gene association networks), pathway figures (node only networks) and INDRAgo (machine curated pathways) |
| OMIM | OMIM is a comprehensive, authoritative compendium of human genes and genetic phenotypes |
| Post-GWAS | Upload GWAS summary statistics and highlight likely causal gene candidates. |
| TiGER | Genes |
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Variant Effect Predictor |
Analyse your own variants and predict the functional consequences of known and unknown variants via our Variant Effect Predictor (VEP) tool. |
| Variant Recoder | Translate a variant identifier, HGVS notation or genomic SPDI notation to all possible variant IDs, HGVS, VCF format and genomic SPDI. |
| VCF to PED converter | Parse a vcf file to create a linkage pedigree file (ped) and a marker information file, which together may be loaded into ld visualization tools like Haploview. |
| WikiProfessional | Gene Wiki |
GENE DISEASE DATABASE |
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| Gene Disease Database | A database of diseased genes |
GENE-DISEASE INTERACTION |
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| CTD (Comparative Toxicogenomics Database) | Describes chemical-gene-disease interactions |
GENETICS |
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| Biolinks | A subdivision of www.bioplanet.com. This site contains a comprehensive list of genetic related database links. |
GENE NOMENCLATURE |
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| HGNC | a resource for approved human gene nomenclature |
| International Human Epigenome Consortium | Integrates epigenomic reference data from well-known national endeavors such as the Canadian CEEHRC, European Blueprint, European Genome-phenome Archive (EGA), US ENCODE and NIH Roadmap, German DEEP, Japanese CREST, Korean KNIH, Singapore's GIS and China's EpiHK |
GENES, PROTEINS AND DISEASES |
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| GeneCards | A database of human genes, proteins and diseases |
PROMOTERS |
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| EPD Eukaryotic Promoter Database | A database of eukaroytic promoters |
REFERENCE GENES |
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| Housekeeping and Reference Transcript Atlas (HRT Atlas) | Web-based tool for searching cell specific candidate reference genes/transcripts suitable for qPCR experiment normalization. HRT Atlas also describes a complete list of human and mouse housekeeping genes and transcripts |
GENOME
COFFEE GENOMICS |
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| CoffeeDNA is a public domain database for coffee genomics comprising comprehensive information on coffee germplasm, Coffea specific Microsatellites, Transposons, SNPs, Expressed Sequence Tag sequences and Gene profiling | |
DNA DATABASES |
| 1000 Genomes Project | The genomes of more than a thousand anonymous participants from a number of different ethnic groups were analyzed and made publicly available. |
| 23andMe's database | Database |
| DNA Data Bank of Japan | National Institute of Genetics |
| EMBL | European Bioinformatics Institute |
| Ensembl | Provides automatic annotation databases for human, mouse, other vertebrate and eukaryote genomes |
| Ensembl Genomes | Provides genome-scale data for bacteria, protists, fungi, plants and invertebrate metazoa, through a unified set of interactive and programmatic interfaces (using the Ensembl software platform) |
| GenBank | National Center for Biotechnology Information |
| HapMap | A haplotype map (HapMap) of the human genome |
| RefSeq | An open access, annotated and curated collection of publicly available nucleotide sequences (DNA, RNA) and their protein products. |
GENOMICS |
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| Bioinformatic Harvester | Bioinformatic database |
| ArrayExpress | Archive of functional genomics data; stores data from high-throughput functional genomics experiments from EMBL |
| Personal Genome Project | Human genomes of 100,000 volunteers from around the world |
| Gene Expression Omnibus (GEO) | A public functional genomics data repository from the U.S. National Cancer Institute (NCI), which supports array- and sequence-based data. Tools for querying and downloading gene expression profiles are provided. |
| Chromatin structure | Structure of chromatin |
| Genome analysis | Methods for analysis of genome |
GENOME MAP (HUMAN) |
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| The Unified Database | An integrated Human Genome mapping database. |
IMMUNITY
ANTIBODIES |
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| Antibodies | MSRS Primary Antibody Database – lists 125,000+ primary antibodies from 600+ companies worldwide. Each search lists all the antibodies found according to criteria and are sortable in 10 fields including: antibody, host, antigen species, label, form, clone number, isotype, unit, product number and company. The database is regularly update and we accept antibody listings from companies, laboratories, and individuals without any charge. |
IG AND TCR RECEPTORS |
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| IMGT server | IMGT is a database specializing in Immunoglobulins (Ig), T cell receptors (TcR) and Major Histocompatibility Complex (MHC) molecules of all vertebrate species, created in 1989 by Marie-Paule Lefranc. |
IMMUNOLOGY SOCIETIES AND JOURNALS |
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| Russian Immunology | This searchable Web Site was created in 2001 by Russian Journal of Immunology in collaboration with Russian Society of Immunology. The “Russian Immunology” contains information about immunological societies and journals, regional Russian institutes and laboratories, as well as constantly updated list of conferences and courses in immunology and adjacent fields. |
PEPTIDE SEQUENCES BINDING MHC MOLECULES |
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| MHCPEP | MHCPEP is a database comprising over 13000 peptide sequences known to bind MHC molecules. Entries were compiled from published reports as well as from direct submissions of experimental data. Each entry contains the peptide sequence, its MHC specificity and, when available, experimental method, observed activity, binding affinity, source protein, anchor positions, and publication references. |
RUSSIAN IMMUNOLOGY |
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| Russian Immunology | This searchable Web Site was created in 2001 by Russian Journal of Immunology in collaboration with Russian Society of Immunology. The “Russian Immunology” contains information about immunological societies and journals, regional Russian institutes and laboratories, as well as constantly updated list of conferences and courses in immunology and adjacent fields. |
MEDICINE
ACQUATIC |
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| ProQuest aquatic science collection | A resource for researchers studying conservation, aquatic pollution, environmental quality, oceanography, policy and legislation, and more. |
| ProQuest atmospheric science collection | This collection includes the Meteorological & Geoastrophysical Abstracts database, full-text ProQuest Atmospheric Science Journals, and deep indexing to uncover hidden data. |
| Water resources abstracts | Provides citations and abstracts to the technical and scientific literature on water-related topics. |
| WATERnetBASE | Comprehensive multidiscipline resource providing access to reference works on drinking water, ground water, hydrogeology, hydrology, storm water, surface water, waste water, water pollution and wetlands. Also includes the current edition of Water encyclopedia. |
ANATOMY |
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| Anatomage TableOnCloud Interactive Anatomy Software | Virtual anatomy dissection software. |
| ANTHROPOLOGY | |
| Anthropology Index Online | An index to anthropological journals. |
| Anthropology online | This site provides the largest, most comprehensive resource for the study of human culture and behavior. |
| AnthropologyPlus . | Anthropology Plus combines Anthropological Literature. |
| AnthroSource / a service of the American Anthropological Association in partnership with University of California Press. | Current issues of American Anthropological Association's journals and bulletins. |
ENVIRONMENT |
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| Environment abstracts | Allows users to search abstracts of thousands of journal articles and conference papers and link to selected full text. |
| Environment complete | "Environment Complete offers deep coverage in applicable areas of agriculture, ecosystem ecology, energy, renewable energy sources, natural resources, marine & freshwater science, geography, pollution & waste management, environmental technology, and environmental law. |
| ENVIROnetBASE | Provides access to environmental handbooks published by CRC Press. |
| Environmental & Ecology Databases on EBSCOhost | Collection of three major environmental collections. |
| GeoRef | Indexes references and selected abstracts to the world's literature in geology, including journal articles, books, maps, conference papers, reports, theses, and references to all publications of the U.S. Geological Survey. |
| GreenFILE | "GreenFILE offers well-researched but accessible information covering all aspects of human impact on the environment. |
| Sustainability science abstracts | "The Sustainability database explores the management of human use and conservation of the natural resource base, ensuring the attainment and continued satisfaction of human needs in the present as well as maintaining the potential to meet the needs and aspirations of future generations. |
| GEOLOGY | |
| GeoRef | Indexes references and selected abstracts to the world's literature in geology. |
| GeoScienceWorld | Serves as a comprehensive resource for research and communications in the geological and earth sciences. |
| HEALTH | |
| WHO (World Health Organization) | United Nations information on health topics. |
| ASFA | The ASFA series is the premier reference in the field of aquatic resources. |
| HEALTH STATISTIC | |
| Health, United States | Health, United States is an annual report on trends in health statistics. |
| HISTORY OF SCIENCE | |
| History of science, technology, and medicine | History of science and technology and allied historical fields. |
| HUMAN BEHAVIOR | |
| Ethnographic video online and anthropology online | Intended to be a visual encyclopedia of human behavior and culture, online in streaming video. |
INHERITED DISORDERS |
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| FINDbase | The Frequency of INherited Disorders database |
| INFECTIOUS DISEASE | |
| CDC (Centers for Disease Control) | The U.S. government's Infectious Diseases Center Page, with information, news releases and links to bioterrorism and emergency preparedness resources. |
| Center for Biosecurity-UPMC | This is a premier source for bioterrorism and biodefense links and information. |
MALARIA |
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| UCSC Malaria Genome Browser | Genome of malaria causing species (Plasmodium falciparum and others) |
MEDICAL EQUIPMENT |
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| Medical Equipment directory world-wide | Index and directory medical equipment, biotechnology, biochemistry and pharmaceutical industry world-wide |
| MEDICAL IMAGING | |
| Internet Pathology Laboratory for Medical Education | The WebPath® educational resource contains over 2700 images with text that illustrate gross and microscopic pathologic findings along with radiologic imaging associated with human disease conditions. |
| MEDICINE | |
| AccessMedicine | Access Medicine from McGraw-Hill Medical is a comprehensive online medical resource that provides a complete spectrum of knowledge from the best minds in medicine, with essential information accessible anywhere. |
MENDELIAN INHERITANCE DATABASE |
| OMIM (Online Mendelian Inheritance in Man): inherited diseases | Online Mendelian Inheritance in Man of inherited diseases |
NEUROIMAGING |
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| Neuroimaging Informatics Tools and Resources Clearinghouse | Neuroimaging |
ORGANISMS |
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| Lifemapsc.com | Navigate the universe of biological entities |
ORTHOLOGY RESOURCES |
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| EggNOG Database | A hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses. It provides multiple sequence alignments and maximum-likelihood trees, as well as broad functional annotation. |
PATHOGEN-HOST INTERACTION |
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| PHI-base | Pathogen-host interaction database. It links gene information to phenotypic information from microbial pathogens on their hosts. Information is manually curated from peer reviewed literature. |
PHARMACOLOGY, TOXICOLOGY |
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| TOXLINE | Covers journal articles, monographs, technical reports, theses, and other literature in all areas of toxicology, including chemicals and pharmaceuticals, pesticides, environmental pollutants, and mutagens and teratogens. Covers 1999-present. |
| TOXNET | Toxicology data, citations and abstracts for the toxicology literature, Toxic Release Information and chemical information. |
| United States Pharmacopeia: The National Formulary | Compendium of drug information for the United States published annually by the United States Pharmacopeial Convention. |
PHYLOGENETIC TREE ANALYSIS |
| Mega megasoftware.net | MEGA is an integrated tool for conducting automatic and manual sequence alignment, inferring phylogenetic trees, mining web-based databases, estimating rates of molecular evolution, and testing evolutionary hypotheses. |
| TREE-PUZZLE tree-puzzle.de | TREE-PUZZLE is a computer program to reconstruct phylogenetic trees from molecular sequence data by maximum likelihood. |
| FigTree tree.bio.ed.ac.uk/software/figtree | FigTree is designed as a graphical viewer of phylogenetic trees and as a program for producing publication-ready figures. |
| DNASTAR - MegAlign dnastar.com/software/molecular-biology | MegAlign is DNASTAR’s software application providing both DNA and protein sequence alignment using a range of pairwise sequence alignment and multiple alignment methods. Use bootstrapping to test for consistency and robustness of phylogenetic trees created using one of the Clustal methods. |
PLANTS AND AGRICULTURE |
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| International Plant Names Index - IPNI | Database of the names and associated basic bibliographical details of all seed plants. |
| AGRICOLA | Agricultural engineering and marketing, animal breeding, entomology, environmental pollution, farm mangagement, foods and feeds, pesticides, rural sociology, social sciences, veterinary medicine, and water resources. |
RADIOLOGY |
| The Cancer Imaging Archive (TCIA) | Radiology archives |
| Neuroimaging Informatics Tools and Resources Clearinghouse | Radiology resources and clearinghouse |
SAMPLES AND SPECIMENS |
| Specimens | Gross and microscopic images of pathology specimens. All should have Creative Commons Attribution (CC-BY) licenses. |
TOXICOLOGY |
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| TOXNET | toxicology data network / National Library of Medicine. |
VISUAL DATABASE OF HUMAN BODY |
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| Visible Body | Visible Body is an interactive visual database of the human body, with thousands of 3D models, animations, CTI & MRI scans, definitions, pronunciations, and more. Instructors can use Courseware for assignments and tracking students' progress. |
PROTEINS
CYTOKINES |
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| Cytokine Family Database | The Cytokine Family Database (dbCFC) is a collection of EST (Expressed Sequence Tag) records of cytokines deposited in the NCBI GenBank. It provides information about the identification of EST records to cytokine members and related data contained in other databases. |
HOMOLOGOUS PROTEIN DOMAIN |
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| DOMO | DOMO is a database of homologous protein domain families. It was obtained from successive sequence analysis steps including similarity search, domain delineation, multiple sequence alignment and motif construction. 83054 non redundant protein sequences from SWISSPROT and PIR have been analysed yielding a database of 99058 domains clustered into 8877 multiple sequence alignments. |
PROTEIN DATABASES |
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| A Library of Protein Family Cores | Structural alignments of protein families and computed average core structures for each family. The core structures can be divided into residues with low spatial variation and those with high spatial variation. Amino acids with low spatial variance occupy essentially the same relative position in all family members. This library is useful for building models, threading, and exploratory analysis. It is also a useful mechanism for summarizing variability in NMR structures. |
| Assembly Converter | Map (liftover) your data's coordinates to the current assembly |
| BioGPS biogps.org | BioGPS is a gene portal built with two guiding principles in mind - customizability and extensibility. |
| CATH | Protein Structure Classification database |
| CiteAb citeab.com | CiteAb’s antibody and biochemical search engine provides a simple way for researchers to find reagents that work. |
| Data Slicer | Get a subset of data from a BAM or VCF file |
| Database of Interacting Proteins | Univ. of California |
| Interact | An Object Oriented Database for Protein-Protein Interactions. |
| DisProt | Database of experimental evidences of disorder in proteins (Indiana University School of Medicine, Temple University, University of Padua) |
| ExPASy Molecular Biology Server | This is the ExPASy proteomics server of the Swiss Institute of Bioinformatics (SIB). This server is dedicated to the analysis of protein sequences and structures as well as 2-D PAGE. |
| File Chameleon | Convert Ensembl files for use with other analysis tools |
| guidetopharmacology.org | This website is intended to become a “one-stop shop” portal to pharmacological information. The searchable database provides quantitative information on drug targets and the prescription medicines and experimental drugs that act on them. It aims to offer accurate information on the basic science underlying drug action. |
| ID History Converter | Convert a set of Ensembl IDs from a previous release into their current equivalents |
| InterPro | InterPro provides functional analysis of proteins by classifying them into families and predicting domains and important sites. |
| Linkage Disequilibrium Calculator | Calculate LD between variants using genotypes from a selected population |
| locate.imb.uq.edu.au | LOCATE is a curated database that houses data describing the membrane organization and subcellular localization of proteins from the RIKEN FANTOM4 mouse and human protein sequence set. |
| mips.helmholtz-muenchen.de/corum | Protein complexes are key molecular entities that integrate multiple gene products to perform cellular functions. The CORUM database is a collection of experimentally verified mammalian protein complexes. |
| MobiDB | Database of intrinsic protein disorder annotation (University of Padua) |
| ModBase | Database of comparative protein structure models (Sali Lab, UCSF) |
| NCBI | Protein sequence and knowledgebase (National Center for Biotechnology Information) |
| neXtProt | A human protein-centric knowledge resource |
| PaxDB pax-db.org | PaxDB is a comprehensive absolute protein abundance database, which contains whole genome protein abundance information across organisms and tissues. |
| Pfam | Protein families database of alignments and HMMs (Sanger Institute) |
| PIR – Protein Information Resource | The Protein Information Resource (PIR), in collaboration with the Munich Information Center for Protein Sequences(MIPS) and the Japanese International Protein Sequence Database (JIPID) maintains the PIR-International Protein Sequence Database – a comprehensive, annotated, and non-redundant set of protein sequence databases in which entries are classified into family groups and alignments of each group are available. |
| PIR-NREF | The PIR-NREF is a Non-redundant REFerence protein database designed to provide a timely and comprehensive collection of all protein sequence data, keeping pace with the genome sequencing projects and containing source attribution and minimal redundancy. |
| PMD | The Protein Mutant Database (PMD) covers natural as well as artificial mutants, including random and site-directed ones, for all proteins except members of the globin and immunoglobulin families. The PMD is based on literature, not on proteins. That is, each entry in the database corresponds to one article which may describe one, several or a number of protein mutants. |
| PRINTS | A compendium of protein fingerprints from (Manchester University) |
| ProDom | The Protein Domain database. |
| PROSITE | PROSITE is a database of protein families and domains. It consists of biologically significant sites, patterns and profiles that help to reliably identify to which known protein family (if any) a new sequence belongs. |
| Protein Data Bank | Worldwide repository for the processing and distribution of 3-D biological macromolecular structure data. |
| Protein Data Bank (PDB) | Protein database |
| Protein Databases | Proteins, also known as the essential building blocks of a human body are a vital part of living organisms. Studies regarding the structure and... |
| Protein Information Resource | Georgetown University Medical Center [GUMC]) |
| Retrieve/ID mapping | Batch search with UniProt IDs or convert them to another type of database ID (or vice versa) |
| Structural Classification of Proteins (SCOP) | Structural classification |
| Swiss-model | Server and repository for protein structure models |
| Swiss-Prot | Protein knowledgebase (Swiss Institute of Bioinformatics) |
| Text Search | Search by the name of protein |
| thebiogrid.org | BioGRID is an interaction repository with data compiled through comprehensive curation efforts. The index searches publications for protein and genetic interactions, chemical associations and post translational modifications from major model organism species. |
| UniProt uniprot.org | The mission of UniProt is to provide the scientific community with a comprehensive, high-quality and freely accessible resource of protein sequence and functional information. |
| unihi.org | Users can enter gene or protein identifiers from different organisms to obtain physical and regulatory interaction partners in the human interactome. |
| Uniprot | UniProt Knowledgebase |
| UniprotKB | UniProt Knowledgebase |
| UnifRef | Provides clustered sets of sequences |
| UniParc | A comprehensive and non-redundant database of publicly available protein sequences |
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Variant Effect Predictor |
Analyse your own variants and predict the functional consequences of known and unknown variants via our Variant Effect Predictor (VEP) tool |
| Variant Recoder | Translate a variant identifier, HGVS notation or genomic SPDI notation to all possible variant IDs, HGVS, VCF format and genomic SPDI |
| VCF to PED converter | Parse a vcf file to create a linkage pedigree file (ped) and a marker information file, which together may be loaded into ld visualization tools like Haploview |
| wwpdb.org | Since 1971, the Protein Data Bank archive (PDB) has served as the single repository of information about the 3D structures of proteins, nucleic acids, and complex assemblies. |
PROTEIN ATLAS |
| Human protein atlas | A public database with expression profiles of human protein coding genes both on mRNA and protein level in tissues, cells, subcellular compartments, and cancer tumors. |
| proteinatlas.org | The Human Protein Atlas aims to map all the human proteins in cells, tissues and organs using integration of various omics technologies, including antibody-based imaging, mass spectrometry-based proteomics, transcriptomics and systems biology. |
| Human Protein Atlas: aims at mapping all the human proteins in cells, tissues and organs | Aims at mapping all the human proteins in cells, tissues and organs |
PROTEIN CRYSTALLIZATION |
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| Crystal TB | Crystal T.B. is a database containing information on Protein Crystallization Conditions, which was carefully selected by experts in this field. The database greatly helps researchers in setting conditions for protein crystallization, by comparing information found in the database, thus contributing to reducing the time to analyze protein structures. |
PROTEIN DOMAINS |
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| Protein Domains | Proteomics is known as the study of protein structures and these structural units are distinguished as protein domains. The overall functional role of a... |
| CDD | A Conserved Domain Database and Search Service. |
PROTEIN-PROTEIN OR DNA INTERACTION |
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| Cytoscape | Protein-protein and Protein-DNA interactions |
| NDEx | Protein-protein and Protein-DNA interactions |
| String | Protein-protein interaction networks, functional enrichment analysis |
PROTEIN SIMILARITY |
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| Similarity Matrix of Proteins (SIMAP) | Database of protein similarities computed using FASTA |
PROTEOME |
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| Proteomes | Set of proteins thought to be expressed by an organism |
PEPTIDE MOFITS |
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| Minimotif Miner | Database of short contiguous functional peptide motifs |
POLYGLUTAMIN REPEATS |
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| PolyQ | Database of polyglutamine repeats in disease and non-disease associated proteins |
PROTEIN SEQUENCES |
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| MIPS | Munich Information Centre for Proteins Sequences (Germany). |
PROTEIN-PROTEIN INTERACTION |
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| Interact | An Object Oriented Database for Protein-Protein Interactions. |
PROTEOMICS |
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| Human Protein Atlas (HPA) | A public database with expression profiles of human protein coding genes both on mRNA and protein level in tissues, cells, subcellular compartments, and cancer tumors. |
RNA
MICROARRAY |
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| ArrayExpress at EBI | Any curated MIAME or MINSEQE compliant transcriptomics data |
| ArrayTrack | ArrayTrack hosts both public and private data, including MAQC benchmark data, with integrated analysis tools |
| caArray at NCI | Cancer data, prepared for analysis on caBIG |
| EBI | ArrayExpress |
| Gene Expression Omnibus (GEO) | Any curated MIAME compliant molecular abundance study |
| GeneNetwork system | Open access standard arrays, exons arrays, and RNA-seq data for genetic analysis (eQTL studies) with analysis suite |
| Genevestigator | Gene expression search engine based on manually curated, well annotated public and proprietary microarray and RNA-seq datasets |
| ImmGen database | Open access across all immune system cells; expression data, differential expression, coregulated clusters, regulation |
| MUSC database | The database is a repository for DNA microarray data generated by MUSC investigators as well as researchers in the global research community. |
| NCI mAdb | Hosts NCI data with integrated analysis and statistics tools |
| NextBio | Microarrays analysis |
| Stanford Microarray database | private and published microarray and molecule abundance database (now defunct) |
| The Cancer Genome Atlas (TCGA) | collection of expression data for different cancers |
| UNC Microarray database | provides the service for microarray data storage, retrieval, analysis, and visualization |
| UNC modENCODE Microarray database | Nimblegen customer 2.1 million array |
| UPenn RAD database | MIAME compliant public and private studies, associated with ArrayExpress |
| UPSC-BASE | data generated by microarray analysis within Umeå Plant Science Centre (UPSC). |
miRNA |
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| miRBase | The microRNA database |
| PolymiRTS | A database of DNA variations in putative microRNA target sites |
ncRNA |
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| ncRNA | Noncoding RNAs Database. |
RNA |
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| Database of RNA-binding Protein Specificities | This University of Toronto site page provides a database of RNA-binding protein specificities where you can browse by domain such as RNA Recognition Motif, K Homology, CCCH Zinc Finger and more. Also you can browse by species such as Homo Sapiens, Mus Musculus, Drosophila Melanogaster and Caenorhabditis Elegans. |
| Extracellular RNA Atlas - GenboreeKB | Extracellular RNA Atlas |
| ExtracellularRNA datasets | Extracellular RNA dataset |
| ExtracellularRNA snapshot | Extracellular RNA snapshot |
| NAR Database Summary Paper Category List | Oxford Journals site contains a list of excellent collections of Nucleotide sequence databases, RNA sequence databases, Protein sequence databases, Structure databases, Genomics databases, Metabolic and signaling pathways, Human & other vertebrate genomes, Human genes and diseases, Microarray data & gene expression databases, Protemics resources, Molecular biology databases, Organelle databases, plant databases, Immunological databases and cell biology. |
| Noncoding RNA Database v2.0 | lncRNAdb.org site has a searchable database which provides comprehensive annotations of eukaryotic long non-coding RNAs (lncRNAs). All entries are manually curated from referenced literature and each entry contains references information about the RNA including: Nucleotide sequences, Genomic context, Gene expression data derived from the Illumina Body Atlas, Structural information, Subcellular localization, Conservation, Function with referenced literature. |
| RNA Databases | RNA stands for Ribonucleic acid. The RNA is a polymeric molecule which when teamed with proteins and carbohydrates are considered as three essential macromolecules... |
| RNA STRAND | This site contains known RNA secondary structures of any type and organism. The ultimate goal of this database is to incorporate a comprehensive collection of known RNA secondary structures, and to provide the scientific community with simple yet powerful ways of analyzing, searching and updating the proposed database. |
| RNABase | RNABase is an annotated database of all publicly available RNA structures. |
| RNA-binding protein database | RNA-binding protein database |
| RNAcentral | RNACentral.com is a new resource that provides unified access to the ncRNA sequence data supplied by the Expert Databases. |
| The RNA Modification Database | The RNA modification database provides a comprehensive listing of post transcriptionally modified nucleosides from RNA. |
rRNA |
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| rRNA database | The European ribosomal RNA database. |
| Ribosomal Database Project II | The Ribosomal Database Project (RDP) provides ribosome related data services to the scientific community, including online data analysis, rRNA derived phylogenetic trees, and aligned and annotated rRNA sequences. |
| 5S ribosomal RNA Database | The purpose of this database is to provide information on nucleotide sequences of 5S rRNAs and their genes. The sequences for particular organisms can be retrieved as single files using a taxonomic browser or in multiple sequence structural alignments. |
siRNA |
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| siRNA Database | Database of siRNA target sequences and other resources for RNA interference studies. |
Small RNA |
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| Small RNA database | Small RNAs are broadly defined as the RNAs not directly involved in protein synthesis. Small RNAs are usually in the 75-400 nucleotides range, although some are as long as thousand base pairs. They are synthesized by either RNA Polymerase I, II or III. The sequences reported here are based on actual sequence determinations and not on the basis of oligonucleotide catalogs. |
tRNA |
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| AARS DataBase | Aminoacyl-tRNA Synthetase Data Bank. |
| GtRDB: The Genomic tRNA Database | This genomic tRNA database contains tRNA identifications made by the program tRNAscan-SE on complete or nearly complete genomes. |
uRNA |
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| The uRNA Database | The uRNADB is a tool in the study of the structures and functions of various U RNAs. It provides aligned, annotated and phylogenetically ordered sequences. The alignments of the sequences represent conserved secondary structure elements where each base pair is proven by comparative sequence analysis. |
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SPECIES |
| Encyclopedia of Life | Open-access resource of detailed information about species of organisms. |
| Catalogue of Life | A meta-database of all species on earth |
ARABIDOPSIS |
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| The Arabidopsis thaliana Database (AtDB) Project provides genomic and related data about Arabidopsis. | |
BACTERIA |
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| SubtiWiki | Integrated database for the model bacterium Bacillus subtilis[4] |
FLIES |
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| FlyBase | FlyBase is a comprehensive database for information on the genetics and molecular biology of Drosophila. It includes data from the Drosophila Genome Projects and data curated from the literature. |
BIRDS |
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| Birds of the World | Online database of over 10,000 bird species globally. |
HUMANS |
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| Personal Genome Project | Human genomes of 100,000 volunteers from around the world |
LEGUME |
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| Legume Information System (LIS) | Genomic database for the legume family |
MOUSE |
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| Edinburgh Mouse Atlas | Mouse gene expression data |
MODEL ORGANISM DATABASE |
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| Model Organism Databases | A database of model organisms |
ORGANISMS |
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| Superfamily | Library of HMMs representing superfamilies and database of (superfamily and family) annotations for all completely sequenced organisms |
PARASITE |
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| Parasites - Centers for Disease Control & Prevention | Introduction to medically important parasites. |
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PATHOGEN |
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| PHI-base | Pathogen-host interaction database. It links gene information to phenotypic information from microbial pathogens on their hosts. Information is manually curated from peer reviewed literature. |
PRIMATE |
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| All the world's primates | All the World's Primates is the comprehensive and authoritative resource. |
PROKARYOTES |
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| EzTaxon-e | Database for the identification of prokaryotes based on 16S ribosomal RNA gene sequences |
RAT |
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| RGD Rat Genome Database | Genomic and phenotype data for Rattus norvegicus |
SACCHAROMYCES CERVISIAE |
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| Saccharomyces Genome Database | genome of the yeast model organism |
| SCPD | The Promoter Database of Saccharomyces cerevisiae. |
Schizosaccharomyces pombe |
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| Schizosaccharomyces pombe | manually curated phenotypic data for the yeast |
SOYBEAN |
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| SoyBase Database (SoyBase) | USDA soybean genetics and genomic database (Soybean) |
VIRUS |
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| Virus database on-line (ICTVdB) | ICTVdB provides access to the ICTV (International Committee on Taxonomy of Viruses), the Index Virum, a catalogue of all ICTV approved virus names, the universal virus database containg the descriptions of viruses and to an picture gallery of viruses. All databses have links to other prominent websites available around the world which are devoted to information about viruses, along with short, clear descriptions of each of them. |
WORM |
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| Caenorhabditis elegans | C elegans genome |
| Wormbase | Genome of the model organism Caenorhabditis elegans and WormBase ParaSite for parasitic species |
XENOPUS |
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| Xenbase | Genome of the model organism Xenopus tropicalis and Xenopus laevis |
YEAST |
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| PomBase | Manually curated phenotypic data for the yeast Schizosaccharomyces pombe |
ZEBRAFISH |
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| Zebrafish Information Network | Genome of this fish model organism |
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Transcription factor knockout |
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ATACdb: a comprehensive human chromatin accessibility database |
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ENdb: an experimentally supported enhancer database for human and mouse |
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A comprehensive human gene expression profile database with TF knockdown/knockout (KnockTF), which provides a large number of available resources of human gene expression profile datasets associated with TF knockdown/knockout and annotates TFs and their target genes in a tissue/cell type-specific manner. |
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LncSEA: a comprehensive human lncRNA sets resource and enrichment analysis platform. |
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SEanalysis: a web tool for super-enhancer associated regulatory analysis |
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SEdb: the comprehensive human Super-Enhancer database |
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Users can obtain the number of datasets per knock-method |
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Users can submit a gene list to extract a transcriptional regulatory subnetwork. |
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Users can submit a gene list and set (FDR adjusted) P-value to perform TF enrichment. |
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TRCirc: a resource for transcriptional regulation information of circRNAs |
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TRlnc: a comprehensive database of human transcriptional regulation of lncRNAs |
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VARAdb: a variation annotation database for human |
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