Syntenator: multiple gene order alignments with a gene-specific scoring function.

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

SUBMITTER: Rodelsperger C 

PROVIDER: S-EPMC2590594 | biostudies-literature | 2008 Nov

REPOSITORIES: biostudies-literature