DAGchainer: A tool for mining segmental genome duplications and synteny

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

Research output: Contribution to journalArticlepeer-review

230 Scopus citations


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.

Original languageEnglish (US)
Pages (from-to)3643-3646
Number of pages4
Issue number18
StatePublished - Dec 12 2004
Externally publishedYes

ASJC Scopus subject areas

  • Statistics and Probability
  • Biochemistry
  • Molecular Biology
  • Computer Science Applications
  • Computational Theory and Mathematics
  • Computational Mathematics


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