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This article is part of the supplement: Proceedings of the Ninth Annual Research in Computational Molecular Biology (RECOMB) Satellite Workshop on Comparative Genomics

Open Access Proceedings

Identification of conserved gene clusters in multiple genomes based on synteny and homology

Anasua Sarkar1*, Hayssam Soueidan2 and Macha Nikolski1

Author Affiliations

1 LaBRI, CNRS/Université Bordeaux 1, 351 crs Libération, 33405 Talence, France

2 Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands

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BMC Bioinformatics 2011, 12(Suppl 9):S18  doi:10.1186/1471-2105-12-S9-S18

Published: 5 October 2011

Abstract

Background

Uncovering the relationship between the conserved chromosomal segments and the functional relatedness of elements within these segments is an important question in computational genomics. We build upon the series of works on gene teams and homology teams.

Results

Our primary contribution is a local sliding-window SYNS (SYNtenic teamS) algorithm that refines an existing family structure into orthologous sub-families by analyzing the neighborhoods around the members of a given family with a locally sliding window. The neighborhood analysis is done by computing conserved gene clusters. We evaluate our algorithm on the existing homologous families from the Genolevures database over five genomes of the Hemyascomycete phylum.

Conclusions

The result is an efficient algorithm that works on multiple genomes, considers paralogous copies of genes and is able to uncover orthologous clusters even in distant genomes. Resulting orthologous clusters are comparable to those obtained by manual curation.