Public Databases: Retrieving and Manipulating Sequences for Beginners
By: Neil Woodford2
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This chapter outlines the basic requirements for finding and exploring sequences of interest in public databases, such as
GenBank. As such, it is not aimed at experienced sequencers, for whom this will be “second nature,” but at the many clinical
bacteriologists who rarely have need of DNA sequences in their usual work, and who would like to develop their interest in
what can appear to be a daunting area. The topics discussed include finding and retrieving sequences from GenBank, identifying
homologous sequences using BLAST searches, resources for accessing microbial genomes, and the Protein Data Bank. Finally,
recommendations are made for useful software (freeware) and online sequence manipulation resources.
Affiliation(s): (2) Antibiotic Resistance Monitoring and Reference Laboratory, Specialist and Reference Microbiology Division, Health Protection Agency-Colindale, London, UK
Series: Methods in Molecular Biology | Volume: 266 | Pub. Date: May-12-2004 | Page Range: 17-28 | DOI: 10.1385/1-59259-763-7:017
Subject: Microbiology
Key Words: Bioinformatics - GenBank database - BLAST search - homology - Protein Data Bank - TIGR - Sanger Institute - freeware - online resources
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