DAGchainer: a tool for mining segmental genome duplications and synteny

Authors:
Brian J. Haas;Arthur L. Delcher;Jennifer R. Wortman;Steven L. Salzberg
Affiliations:
The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA;The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA;The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA;The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA
Venue:
Bioinformatics
Year:
2004

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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.