MOLECULAR BIOLOGY DATABASES

Presentations

• Molecular Biology Databases

Practical lessons

1. Accessing GenBank and EMBL databases by FTP and the WWW
2. The NCBI WWW server and Entrez, part 1
3. The NCBI WWW server and Entrez, part 2
4. Sequence Retrieval System, part 1
5. Sequence Retrieval System, part 2

A selection of Molecular Biology Databases

• NCBI-Nucleotide and EMBL-Nucleotidedatabases. Nucleotide sequence databases, at the NCBI and the EBI, respectively.
• NCBI-Genomes. Genomic sequences database, at the NCBI.
• Ensembl. Eukaryotic genomes database, sponsored by the EBI and the Sanger Center.

• SwissProt and TrEMBL. Protein sequence databases, maintained by the SIB and the EBI, at ExPASy server.
• Prosite. Protein motifs database, at ExPASy.
• PFam. HMM-defined protein families database, at the Sanger Center.
• InterPro. Database of protein families, defined by integrating information about families, domains and motifs from other databases.

• PDB. Protein structure database.
• SCOP. Protein families defined in the context of a hierarchical classification of protein structures.

• KEGG. Kyoto Encyclopedia of Genes and Genomes.

• PubMed. Bibliographic database, at the NCBI.

• Gene Ontology Consortium. Ontology of molecular biology terms.

• NCBI. National Center for Biotechnology Information. Access to GenBank and many other databases  (through the Entrez interface) and tools.
• EBI databases. Access to EMBL databases, other databases and tools.
• SRS. Access to multiple databases and tools, at the EBI.

• The NCBI Handbook. Handbooks about NCBI databases and tools, in PDF format (link).
• NCBI Resources (link).
• Ensembl overview (pdf).
• SwissProt Documentation (link).
• SwissProt Users Manual (link).
• Quick Guide to SwissProt & TrEMBL (pdf).
• SRS: access points, connected databases and available tools (link).
• SRS user's guide (pdf).
• SRS user's guide (link).

Collections of links to Databases

• Molecular Biology Database Collection, NAR 2004. Special issue on databases (link).
• Molecular Biology Database Collection, NAR 2004. Editorial by M.Y.Galperin (pdf).
• Molecular Biology Database Collection, NAR 2004. Database table (html).
• Deambulum Databank Index
• Red Temática del CSIC sobre Bioinformática: Bases de Datos
• Weizmann Institute, Genome and Bioinformatics: Molecular Biology Databases on the Internet

Additional information

• 2can: Bioinformatics Educational Resource: Databases (EBI) (link).

• Introduction to Bioinformatics.Teresa K. Attwood, David J. Parry-Smith. Longman Higher Education, 1999.
• Bioinformatics. A practical guide to the analysis of genes and proteins. Andreas D. Baxevanis and B.F. Francis Ouellete, Eds. Wiley InterScience, 2001.

• François Bry, Peer Kröger (2003),A Computational Biology Database Digest: Data, Data Analysis, and Data Management. Distributed and Parallel Databases 13 (1): 7-42 (pdf).