DAGchainer: a tool for mining segmental genome duplications and synteny

Abstract

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.

Keywords

SyntenyGenomeGeneSegmental duplicationBiologyGeneticsComputational biologyGene predictionGene family

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Publication Info

Year: 2004
Type: article
Volume: 20
Issue: 18
Pages: 3643-3646
Citations: 412
Access: Closed

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APA Style

                            
                                
                                    Brian J. Haas, 
                                
                                    Arthur L. Delcher, 
                                
                                    Jennifer R. Wortman
                                
                                et al.
                            
                            (2004). 
                            DAGchainer: a tool for mining segmental genome duplications and synteny. 
                            Bioinformatics
                            , 20
                            (18)
                            , 3643-3646.
                            https://doi.org/10.1093/bioinformatics/bth397
                        

Identifiers

DOI: 10.1093/bioinformatics/bth397