DAGchainer: a tool for mining segmental genome duplications and synteny

作者：Brian J. Haas, Arthur L. Delcher, Jennifer R. Wortman, Steven L. Salzberg · 发表于：Bioinformatics · 年份：2004 · DOI：10.1093/bioinformatics/bth397 · 被引用次数：435 · 研究领域：Chromosomal and Genetic Variations、Genomics and Phylogenetic Studies、Plant Disease Resistance and Genetics

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.