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Bioinformatics Advance Access published online on July 9, 2004
Bioinformatics, doi:10.1093/bioinformatics/bth397
Bioinformatics © Oxford University Press 2004; all rights reserved
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Received May 26, 2004
Accepted June 29, 2004

Applications note

DAGchainer: A tool for mining segmental genome duplications and synteny

Brian J. Haas 1*, Arthur L. Delcher 1, Jennifer R. Wortman 1, Steven L. Salzberg 1

1 The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, Maryland 20850, USA

* To whom correspondence should be addressed. E-mail: bhaas{at}tigr.org.


  Abstract

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.


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