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Bioinformatics Advance Access originally published online on July 9, 2004
Bioinformatics 2004 20(18):3643-3646; doi:10.1093/bioinformatics/bth397
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Bioinformatics vol. 20 issue 18 © Oxford University Press 2004; all rights reserved.

Applications Note

DAGchainer: a tool for mining segmental genome duplications and synteny

Brian J. Haas *,{dagger}, Arthur L. Delcher {dagger}, Jennifer R. Wortman and Steven L. Salzberg

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

Received on May 26, 2004; accepted on June 29, 2004
Advance Access Publication July 9, 2004

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.

Contact: bhaas{at}tigr.org

* To whom correspondence should be addressed.

{dagger} The authors wish it to be known that, in their opinion, the first two authors should be regarded as joint First Authors.


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