Bioinformatics. 2004 Dec 12;20(18):3643-6. Epub 2004 Jul 9.

DAGchainer: a tool for mining segmental genome duplications and synteny.

Haas BJ, Delcher AL, Wortman JR, Salzberg SL.

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The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA. bhaas@tigr.org <bhaas@tigr.org>

Abstract

SUMMARY: Given the positions of protein-coding genes along genomic sequence and probability values for protein alignments between genes, DAGchainer identifies chains of gene pairs sharing conserved order between genomic regions, by identifying paths through a directed acyclic graph (DAG). These chains of collinear gene pairs can represent segmentally duplicated regions and genes within a single genome or syntenic regions between related genomes. Automated mining of the Arabidopsis genome for segmental duplications illustrates the use of DAGchainer.

PMID:: 15247098; [PubMed - indexed for MEDLINE]

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R01-LM007938/LM/NLM NIH HHS/United States

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