Syntenator: Multiple gene order alignments with a gene-specific scoring function

doi:10.1186/1748-7188-3-14

Algorithms for Molecular Biology

Volume 3

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Software article

Syntenator: Multiple gene order alignments with a gene-specific scoring function

Christian Rödelsperger¹^,2 and Christoph Dieterich¹

¹Department of Evolutionary Biology, Max Planck Institute for Developmental Biology, Spemannstrasse 35, Tübingen, Germany

²Institute of Medical Genetics, Charité University Hospital, Berlin, Germany

author email corresponding author email

Algorithms for Molecular Biology 2008, 3:14doi:10.1186/1748-7188-3-14


Published:	6 November 2008

Abstract

Background

Identification of homologous regions or conserved syntenies across genomes is one crucial step in comparative genomics. This task is usually performed by genome alignment softwares like WABA or blastz. In case of conserved syntenies, such regions are defined as conserved gene orders. On the gene order level, homologous regions can even be found between distantly related genomes, which do not align on the nucleotide sequence level.

Results

We present a novel approach to identify regions of conserved synteny across multiple genomes. Syntenator represents genomes and alignments thereof as partial order graphs (POGs). These POGs are aligned by a dynamic programming approach employing a gene-specific scoring function. The scoring function reflects the level of protein sequence similarity for each possible gene pair. Our method consistently defines larger homologous regions in pairwise gene order alignments than nucleotide-level comparisons. Our method is superior to methods that work on predefined homology gene sets (as implemented in Blockfinder). Syntenator successfully reproduces 80% of the EnsEMBL man-mouse conserved syntenic blocks. The full potential of our method becomes visible by comparing remotely related genomes and multiple genomes. Gene order alignments potentially resolve up to 75% of the EnsEMBL 1:many orthology relations and 27% of the many:many orthology relations.

Conclusion

We propose Syntenator as a software solution to reliably infer conserved syntenies among distantly related genomes. The software is available from http://www2.tuebingen.mpg.de/abt4/plone webcite.