DAGchainer: a tool for mining segmental genome duplications and synteny.

by: BJ Haas, AL Delcher, JR Wortman, SL Salzberg

Bioinformatics, Vol. 20, No. 18. (12 December 2004), pp. 3643-3646.

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Abstract

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.

@article{citeulike:197234, abstract = {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.}, address = {The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA. bhaas@tigr.org <bhaas@tigr.org>}, author = {Haas, B. J. and Delcher, A. L. and Wortman, J. R. and Salzberg, S. L. }, citeulike-article-id = {197234}, issn = {1367-4803}, journal = {Bioinformatics}, keywords = {algorithm, genome, synteny}, month = {December}, number = {18}, pages = {3643--3646}, posted-at = {2007-11-29 11:41:34}, priority = {2}, title = {DAGchainer: a tool for mining segmental genome duplications and synteny.}, url = {http://view.ncbi.nlm.nih.gov/pubmed/15247098}, volume = {20}, year = {2004} }

RIS record

TY - JOUR ID - citeulike:197234 L3 - citeulike-article-id:197234 TI - DAGchainer: a tool for mining segmental genome duplications and synteny. JF - Bioinformatics VL - 20 IS - 18 SP - 3643 EP - 3646 AD - The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA. bhaas@tigr.org <bhaas@tigr.org> SN - 1367-4803 N2 - 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. KW - algorithm KW - genome KW - synteny AU - Haas, BJ AU - Delcher, AL AU - Wortman, JR AU - Salzberg, SL PY - 2004/12/12/ UR - http://view.ncbi.nlm.nih.gov/pubmed/15247098 ER -

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