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ALMOB
2008

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

11 years 9 months ago
Syntenator: Multiple gene order alignments with a gene-specific scoring function
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 th...
Christian Rödelsperger, Christoph Dieterich
Added 08 Dec 2010
Updated 08 Dec 2010
Type Journal
Year 2008
Where ALMOB
Authors Christian Rödelsperger, Christoph Dieterich
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