Nucleic Acids Research Advance Access originally published online on November 21, 2007
Nucleic Acids Research 2008 36(Database issue):D469-D474; doi:10.1093/nar/gkm1042
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Nucleic Acids Research, 2008, Vol. 36, Database issue D469-D474
© 2007 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
This article appears in the following Nucleic Acids Research issue: Database issue [View the issue table of contents]
Articles |
GenoList: an integrated environment for comparative analysis of microbial genomes
Plate-forme Intégration et Analyse Génomiques, Pasteur Génopole Ile-de-France, Institut Pasteur, 28 rue du Docteur Roux, 75724 Paris Cedex 15, France
*To whom correspondence should be addressed. Tel: +33 (0)1 44 38 95 35; Fax: +33 (0)1 45 68 84 06; Email: moszer{at}pasteur.fr
Received September 15, 2007. Revised October 30, 2007. Accepted October 31, 2007.
The multitude of bacterial genome sequences being determined has generated new requirements regarding the development of databases and graphical interfaces: these are needed to organize and retrieve biological information from the comparison of large sets of genomes. GenoList (http://genolist.pasteur.fr/GenoList) is an integrated environment dedicated to querying and analyzing genome data from bacterial species. GenoList inherits from the SubtiList database and web server, the reference data resource for the Bacillus subtilis genome. The data model was extended to hold information about relationships between genomes (e.g. protein families). The web user interface was designed to primarily take into account biologists’ needs and modes of operation. Along with standard query and browsing capabilities, comparative genomics facilities are available, including subtractive proteome analysis. One key feature is the integration of the many tools accessible in the environment. As an example, it is straightforward to identify the genes that are specific to a group of bacteria, export them as a tab-separated list, get their protein sequences and run a multiple alignment on a subset of these sequences.
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