DAGchainer: a Tool for Mining Segmental Genome Duplications and Synteny

Overview

Journal Bioinformatics

Publisher Oxford University Press

Specialty Biology

Date 2004 Jul 13

PMID 15247098

Citations 193

Authors

Brian J Haas

Arthur L Delcher

Jennifer R Wortman

Steven L Salzberg

Affiliations

Soon will be listed here.

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.

Citing Articles

Constraint of accessible chromatins maps regulatory loci involved in maize speciation and domestication.

Liu Y, Gao X, Liu H, Yang X, Liu X, Xu F Nat Commun. 2025; 16(1):2477.

PMID: 40075057 PMC: 11903877. DOI: 10.1038/s41467-025-57932-1.

GenomeDecoder: inferring segmental duplications in highly repetitive genomic regions.

Zhang Z, Gupta I, Pevzner P Bioinformatics. 2025; 41(2).

PMID: 39908455 PMC: 11842051. DOI: 10.1093/bioinformatics/btaf058.

Pandagma: a tool for identifying pan-gene sets and gene families at desired evolutionary depths and accommodating whole-genome duplications.

Cannon S, Lee H, Weeks N, Berendzen J Bioinformatics. 2024; 40(9).

PMID: 39180716 PMC: 11377846. DOI: 10.1093/bioinformatics/btae526.

Chromosome segregation during spermatogenesis occurs through a unique center-kinetic mechanism in holocentric moth species.

Hockens C, Lorenzi H, Wang T, Lei E, Rosin L PLoS Genet. 2024; 20(6):e1011329.

PMID: 38913752 PMC: 11226059. DOI: 10.1371/journal.pgen.1011329.

The genomic and cellular basis of biosynthetic innovation in rove beetles.

Kitchen S, Naragon T, Bruckner A, Ladinsky M, Quinodoz S, Badroos J Cell. 2024; 187(14):3563-3584.e26.

PMID: 38889727 PMC: 11246231. DOI: 10.1016/j.cell.2024.05.012.