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4 - Databases

Published online by Cambridge University Press:  05 March 2012

Alan J. Bleasby ,
Jon C. Ison  and
Peter M. Rice
Alan J. Bleasby
Affiliation:
European Bioinformatics Institute, Hinxton
Jon C. Ison
Affiliation:
European Bioinformatics Institute, Hinxton
Peter M. Rice
Affiliation:
European Bioinformatics Institute, Hinxton
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Summary

General database configuration

Sequence database support

EMBOSS provides excellent database support. All the common sequence formats you are likely to come across are supported. See the EMBOSS User’s Guide.

A variety of indexing and access methods are supported. For example, EMBL entries can be read from :

  • A non-indexed EMBL-format flatfile held locally

  • Original EMBL flatfiles using the CD-ROM, Staden or EMBOSS indexes

  • Original EMBL flatfiles using local SRS indexes

  • A file indexed for use with BLAST version 2 indexes

  • GCG database format

  • A query to the EMBL-EBI DBFETCH service

  • A query to the EMBL-EBI web server

  • A query to the Entrez web server

  • A query to any MRS web server

  • A query to any SRS web server (local or remote)

  • A relational database such as Sybase or Oracle by calling a local application.

Type
Chapter
Information
EMBOSS Administrator's Guide
Bioinformatics Software Management
 , pp. 92 - 132
Publisher: Cambridge University Press
Print publication year: 2011

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