Jean‐Loup Risler, Génome et Informatique, Evry, France
Alexandra Louis, Infobiogen, Evry, France
Published online: September 2005
DOI: 10.1038/npg.els.0005313
The exhausting pace at which new genomic sequences are deposited with the databanks makes it essential to put efficient retrieval systems at the scientific community's disposal. Entrez and SRS are two such programs, freely accessible from the Web, that enable powerful simple and Boolean queries.
Keywords: sequence; databases; retrieval; entrez; SRS
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Figure 1. Screenshot of an Entrez query showing how to use the ‘Preview’ item in order to add terms in a query and perform Boolean searches.
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Figure 2. Screenshot of a Sequence Retrieval System (SRS) ‘simple query’: here all the ABC transporter sequences from human and mouse in the European Molecular Biology Laboratory (EMBL) databank were requested.
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Figure 3. Screenshot of an SRS ‘extended query’, showing that various items can be selected from the Feature table.
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| References | |
| Apweiler R, Attwood TK, Bairoch A, et al. (2001) The InterPro database, an integrated documentation resource for protein families, domains and functional sites. Nucleic Acids Research 29: 37–40. | |
| Baxevanis AD (2001a) The Molecular Biology Database Collection: an updated compilation of biological database resources. Nucleic Acids Research 29: 1–10. | |
| book Baxevanis AD (2001b) "Information retrieval from biological databases". In: Baxevanis AD and Ouelette BF (eds.) Bioinformatics, a Practical Guide to the Analysis of Genes and Proteins, pp. 155–185. New York, NY: John Wiley & Sons. | |
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| Etzold T, Ulyanov A and Argos P (1996) SRS: information retrieval system for molecular biology data banks. Methods in Enzymology 266: 114–128. | |
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| Further Reading | |
| book Database Issue. Nucleic Acids Research. [The first issue each January is a special volume on databanks.] | |
| Putnam NC (1998) Searching MEDLINE free on the Internet using the National Library of Medicine's PubMed. Clinical Excellence for Nurse Practitioners 2: 314–316. | |
| Samson C (2000) Database searching with DNA and protein sequences: an introduction. Briefings in Bioinformatics 1: 22–32. | |
| The Gene Ontology Consortium (2000) Gene ontology: tool for the unification of biology. Nature Genetics 25: 25–29. | |
| The Gene Ontology Consortium (2001) Creating the gene ontology resource: design and implementation. Genome Research 11: 1425–1433. | |
| Web Links | |
| ePath European Bioinformatics Institute (EBI) http://www.ebi.ac.uk | |
| ePath Entrez the query system at NCBI http://www.ncbi.nlm.nih.gov/Entrez | |
| ePath International Nucleotide Sequence Database (INSD) http://www.ncbi.nlm.nih.gov/collab | |
| ePath SRS the query system at EBI http://srs.ebi.ac.uk | |
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