DAGchainer: a tool for mining segmental genome duplications and synteny.
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.
Haas
Brian J
BJ
The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA. bhaas@tigr.org <bhaas@tigr.org>
Delcher
Arthur L
AL
Wortman
Jennifer R
JR
Salzberg
Steven L
SL
D000465:Algorithms; D017360:Arabidopsis / Q000235:genetics; D002874:Chromosome Mapping / Q000379:methods*; D017124:Conserved Sequence; D020440:Gene Duplication; D016415:Sequence Alignment / Q000379:methods*; D017422:Sequence Analysis, DNA / Q000379:methods*; D012689:Sequence Homology, Nucleic Acid; D012984:Software