HOME HELP FEEDBACK SUBSCRIPTIONS ARCHIVE SEARCH TABLE OF CONTENTS		QUICK SEARCH:   [advanced] Author: Keyword(s): Year:  Vol:  Page:

This Article Full Text Full Text (PDF) Alert me when this article is cited Alert me if a correction is posted Citation Map Services Email this article to a friend Similar articles in this journal Similar articles in PubMed Alert me to new issues of the journal Download to citation manager Citing Articles Citing Articles via HighWire Citing Articles via CrossRef Citing Articles via Google Scholar Google Scholar Articles by Chetouani, F. Articles by Kunst, F. Search for Related Content PubMed PubMed Citation Articles by Chetouani, F. Articles by Kunst, F. Agricola Articles by Chetouani, F. Articles by Kunst, F.

FindTarget: software for subtractive genome analysis

Laboratoire Génomique des Microorganismes Pathogènes, Institut Pasteur, Département de Biologie Moléculaire, 25 rue du Dr Roux, 75724 Paris Cedex 15, France¹

Author for correspondence: Farid Chetouani. Tel: +33 1 45 68 87 48. Fax: +33 1 45 68 87 86. e-mail: fchetou{at}pasteur.fr

In silico subtractive/differential genome analysis is a powerful approach for identifying genus- or species-specific genes, or groups of genes that are responsible for a unique phenotype. By this method, one searches for genes present in one group of bacteria and absent in another group. A software package has been developed, named FindTarget, that has a user-friendly web interface to facilitate differential genome analysis. The user chooses the genomes to compare, the similarity criteria and the thresholds to decide if a gene has a counterpart in another genome. The searches are based on BLASTP comparisons of proteomes. FindTarget also includes access to sequences, coloured multiple alignments, phylogenetic trees of conserved proteins and links to public annotated databases which provide a means for validation of the results. To illustrate this approach, a FindTarget search for genes putatively involved in the specificity of cell envelope synthesis of Gram-negative bacteria is presented. The results show that most of the identified genes are clearly involved in cell wall processes, underlining the power of such an approach in general and that of FindTarget in particular.

Keywords: comparative genomics, bioinformatics, software, differential genome analysis

This article has been cited by other articles:

				P. Lechat, L. Hummel, S. Rousseau, and I. Moszer GenoList: an integrated environment for comparative analysis of microbial genomes Nucleic Acids Res., January 11, 2008; 36(suppl_1): D469 - D474. [Abstract] [Full Text] [PDF]

				T. Rossignol, P. Lechat, C. Cuomo, Q. Zeng, I. Moszer, and C. d'Enfert CandidaDB: a multi-genome database for Candida species and related Saccharomycotina Nucleic Acids Res., January 11, 2008; 36(suppl_1): D557 - D561. [Abstract] [Full Text] [PDF]