DAGchainer: A tool for mining segmental genome duplications and synteny

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

doi:10.1093/bioinformatics/bth397

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 journal › Article › peer-review

230 Scopus citations

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.

Original language	English (US)
Pages (from-to)	3643-3646
Number of pages	4
Journal	Bioinformatics
Volume	20
Issue number	18
DOIs	https://doi.org/10.1093/bioinformatics/bth397
State	Published - Dec 12 2004
Externally published	Yes

ASJC Scopus subject areas

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

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10.1093/bioinformatics/bth397

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title = "DAGchainer: A tool for mining segmental genome duplications and synteny",

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.",

author = "Haas, {Brian J.} and Delcher, {Arthur L.} and Wortman, {Jennifer R.} and Salzberg, {Steven L.}",

note = "Funding Information: This research was supported in part by NIH grant R01-LM007938 to S.L.S.",

year = "2004",

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doi = "10.1093/bioinformatics/bth397",

language = "English (US)",

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AU - Haas, Brian J.

AU - Delcher, Arthur L.

AU - Wortman, Jennifer R.

AU - Salzberg, Steven L.

N1 - Funding Information: This research was supported in part by NIH grant R01-LM007938 to S.L.S.

PY - 2004/12/12

Y1 - 2004/12/12

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.

AB - 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.

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DAGchainer: A tool for mining segmental genome duplications and synteny

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