Introduction

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.

Publications

  1. DAGchainer: a tool for mining segmental genome duplications and synteny.
    Cite this
    Haas BJ, Delcher AL, Wortman JR, Salzberg SL, 2004-12-01 - Bioinformatics (Oxford, England)

Credits

  1. Brian J Haas
    Developer

  2. Arthur L Delcher
    Developer

  3. Jennifer R Wortman
    Developer

  4. Steven L Salzberg
    Investigator

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Summary
AccessionBT000424
Tool TypeApplication
Category
PlatformsLinux/Unix
TechnologiesC++, Perl
User InterfaceTerminal Command Line
Download Count0
Submitted BySteven L Salzberg