Interfaces to multiple Databases
- SRS6, at EBI. Sequence Retrieval System at EBI.
- SRS6, at CNB. Sequence Retrieval System at EMBnet/CNB.
- DDBJ. DNA Databank of Japan. National Institute of
Genetics, Japan.
- EBI - Databases. Databases at the European Bioinformatics Institute, EMBL.
- NCBI. National Center for Biotechnology Information. National Library of
Medicine, NIH, US.
DNA sequences and Genomes
- EMBL Nucleotide Sequence and other databases. EBI.
- GenBank. Nucleotide database at NCBI.
- GOLD. Genomes OnLine Database Homepage.
- MOT. Genome Monitoring Table, at EBI.
- EBI Genomes.
- GenoList. Genome Browser at Institut Pasteur.
- GenomeNet. Kyoto University.
- Joint Genome Institute Genome Projects. Department of Energy, US.
- NCBI Genomes
- Sanger Institute Genomes
- TIGR Genomes
- Colibri. Escherichia coli at Institut Pasteur.
- Ensembl. Metazoan genomes at EBI.
- FlyBase. Drosophila Genome Database at Indiana University.
- GeneCards. Human genes at the Weizmann Institute.
- MGI. Mouse Genome Informatics. The Jackson Laboratory, Maine, US.
- SGD. Saccharomyces Genome Database at Stanford University.
- Subtilist. Bacillus subtilis at Institut Pasteur.
- Tuberculist. Mycobacterium tuberculosis at Institut Pasteur.
- Wormbase. Genome and Biology of C. elegans, at CSHL.
Genome analysis and Comparison
- GenomeAtlas. DNA Structural Analysis of
Sequenced Microbial Genomes, at CBS.
- GeneQuiz. Automatic analysis of genomes, at
EBI.
- HAMAP. High-quality automated and manual annotation
of microbial proteomes, at ExPASy.
- INDIGO. Análisis de los genomas de E. coli y B. subtilis
- KEGG. Kyoto Encyclopedia of Genes and Genomes, Kyoto University.
- MBGD. Microbial Genome Database for Comparative Analysis.
- Membrane Transport Systems. Genomic comparisons of membrane transporters.
- PEP. Predictions for Entire Proteomes, at CUBIC.
- PEDANT. Automatic analysis of genomic protein sets,
at MIPS.
- WIT. What Is There? Argonne National Laboratory, US.
SNPs
- dbSNP Home Page. Single Nucleotide Polymorphism database, at NCBI.
- SNP Consortium. The SNP Consortium, at CSHL.
rRNA and tRNA sequences
- Comparative RNA Web Site. Gutell Lab at University of Texas, US.
- Ribosomal Database Project II. Michigan State University, US.
ESTs and cDNAs
- dbEST. Expressed Sequence Tags database at NCBI.
- DGC. Drosophila Gene Collection. Full lenght cDNA sequences.
- EST Links. List of links to EST
resources, at EBI.
- Human cDNA Projects. MIPS.
- HUNT. Human full-length cDNA sequences.
- MGC. Mammalian Gene Collection. Full lenght cDNA sequences.
Microarray expression data
- ArrayExpress. Microarray Expression Data at EBI.
- SMD. Stanford Microarray Database.
Nucleic Acids structure
- NDB. Structural information about Nucleic Acids.
Proteins
- DOLOP. Database of Bacterial Lipoproteins.
- EMP. Enzymes and Metabolic Pathways, at Argonne National Laboratory, US.
- ENZYME. Enzyme nomenclature database, at ExPASy.
- EXProt. Database for proteins with an experimentally verified function, at CMBI.
- PIR. Protein Information Resource, at Georgetown University.
- Proteome BioKnowledge. Protein knowledge database generated by human
experts.
- SWISS-PROT, at EBI. Curated protein sequence database.
- SWISS-PROT and TrEMBL, at ExPASy. Swiss Institute of Bioinformatics.
- TRANSFAC. Transcription Factor Database.
- TrEMBL. Computer annotated, translated EMBL sequences, at EBI.
- Verified Protein
Starts. E. coli proteins with verified start.
Protein similarity and Families
- CluSTr. SWISS-PROT and TrEMBL proteins classified into groups of related
proteins, at EBI.
- COGs. Clusters of Orthologous Groups of proteins, at NCBI.
- InParanoid. Database of pairwise orthologs, at CGB, Karolinska Institute, Sweden.
- ProtoMap. Hierarchical
classification of all proteins in SWISSPROT and TrEMBL.
- SYSTERS. Clusters of similar proteins, at CMB, Max Plank Institute.
Patterns, Profiles and Families
- Blocks. Multiple alignments of the most highly conserved regions of groups of proteins documented in InterPro.
- InterPro. Integrated view of commonly used motif databases.
- MetaFam Protein Family Database. Comprehensive database of protein family information.
- Pfam, at Sanger. Multiple sequence alignments and HMMs of protein domains and families, at Sanger Institute.
- Pfam, at Saint Louis
- Pfam, at Karolinska
- Pfam, at INRA
- PRINTS. Database of groups of conserved motifs, or protein fingerprints.
- ProDom. Protein domain families automatically generated from SWISS-PROT and TrEMBL.
- PROSITE. Database of protein families and domains, defined by patterns and profiles, at ExPASy.
- SMART. Simple Modular Architecture Research Tool, at EMBL.
Protein structure and Families
- Amino Acid Properties and Structures. Institute of Chemistry, FU, Berlin..
- Amino Acid Properties and Structures. PROWL, Rockefeller University.
- CATH Database of Structural Domains. Hierarchical classification of protein domain structures
- DSSP. Database of Secondary Structure in Proteins.
- HOMSTRAD. Aligned three-dimensional structures of homologous proteins.
- HSSP. Database of homology-derived secondary structure of proteins.
- FSSP. Fold classification based on Structure-Structure alignment of Proteins.
- OCA. Integrated access to several protein databases.
- PDB. Protein Databank: single international repository for 3-D macromolecular structure data.
- PDBsum. Summaries and structural analyses of PDB data files.
- Protein Loop Classification Index. Computational clustering of loops in the PDB SELECT database.
- RCSB - Databases. Databases of the Research Collaboratory for Structural Bioinformatics, home of PDB.
- SCOP. Structural Classification of Proteins.
- Superfamily. Groups of proteins identified with HMM profiles from superfamilies defined in SCOP.
- TOPS. Protein Topology.
Molecular Interactions
- BIND. Biomolecular Interaction Network Database.
- DIP. Database of Interacting Proteins, at UCLA.
- PIMRider. Protein-protein
interactions, at Hybrigenics.
- Interact. Protein-Protein Interaction
database, at UMBER.
- Molecular Interaction Links. From BIND website.
Metabolism
- EMP. Enzymes and Metabolic Pathways at Argonne National Laboratory, US.
- WIT. What Is There?. Argonne National Laboratory, US.
- KEGG. Kyoto Encyclopedia of Genes and Genomes. Kyoto University.
Literature
- PubMed. Database of biomedical literature at NCBI.
Gene Ontology
- Gene Ontology Consortium. Controlled and hierarchical vocabulary to
organize biological knowledge.
- Gene Ontology Annotation. Assignments of gene products to the Gene
Ontology, at EBI.
- AmiGO. HTML-based browser for The Gene Ontology.
- Quickgo. Fast web based viewer for the Gene Ontology, et EBI.
Taxonomy
NEWT. Taxonomy database at EBI..
Taxonomy Browser.
Taxonomy browser at NCBI.
Database lists
- DataBase
Bookmarks for Bioinformatics. Klaus P. Schafer. University of Konstanz, Germany.
- Deambulum
Databank Index. Deambulum, Infobiogen, France.
- Molecular Biology Database
Collection: 2003 update. A. D. Baxevanis.
- Molecular Biology Databases on the Internet. Weizmann Institute, Genome and Bioinformatics.
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