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syntenator multiple gene order alignments with a gene-specific scoring functionsyntenator多个基因顺序排列gene-specific得分函数.pdf

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syntenator multiple gene order alignments with a gene-specific scoring functionsyntenator多个基因顺序排列gene-specific得分函数

Algorithms for Molecular Biology BioMed Central Software article Open Access Syntenator: Multiple gene order alignments with a gene-specific scoring function Christian Rödelsperger1,2 and Christoph Dieterich*1 Address: 1Department of Evolutionary Biology, Max Planck Institute for Developmental Biology, Spemannstrasse 35, Tübingen, Germany and 2Institute of Medical Genetics, Charité University Hospital, Berlin, Germany Email: Christian Rödelsperger - christian.roedelsperger@charite.de; Christoph Dieterich* - christoph.dieterich@tuebingen.mpg.de * Corresponding author Published: 6 November 2008 Received: 20 June 2008 Accepted: 6 November 2008 Algorithms for Molecular Biology 2008, 3:14 doi:10.1186/1748-7188-3-14 This article is available from: /content/3/1/14 © 2008 Rödelsperger and Dieterich; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. 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 t