DAGchainer: A Tool for Mining Segmental Genome Duplications and Synteny

Bioinformatics. 2004 Dec 12;20(18):3643-6. doi: 10.1093/bioinformatics/bth397. Epub 2004 Jul 9.

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.

Publication types

  • Evaluation Study
  • Research Support, U.S. Gov't, P.H.S.

MeSH terms

  • Algorithms*
  • Arabidopsis / genetics
  • Chromosome Mapping / methods*
  • Conserved Sequence
  • Gene Duplication*
  • Sequence Alignment / methods*
  • Sequence Analysis, DNA / methods*
  • Sequence Homology, Nucleic Acid*
  • Software*