DAGchainer: a tool for mining segmental genome duplications and synteny

Bioinformatics
Brian J HaasSteven L Salzberg

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.

Associated Software

Nov 14, 2020·Kristian Ullrich
Nov 14, 2020·Kristian Ullrich

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