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.
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DAGchainer operates with homologous gene pairs found within complete genome sequences, combining them into chains of syntenic genes.
“It operates with homologous gene pairs found within complete genome sequences, combining them into chains of syntenic genes.”
From halSynteny: a fast, easy-to-use conserved synteny block construction method for multiple whole-genome alignments (2020) · cites this paper as [4]
The DAG-based method DAGchainer was previously implemented for constructing synteny from BLAST alignments of gene annotations.
“The DAG-based method DAGchainer [4] was previously implemented for constructing synteny from the BLAST [29] alignments of gene annotations.”
From halSynteny: a fast, easy-to-use conserved synteny block construction method for multiple whole-genome alignments (2020) · cites this paper as [4]
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- Authors
- Haas, B. J., Delcher, A. L., Wortman, J. R., & Salzberg, S. L.
- Affiliations
- The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA
- Corresponding author
- Haas, Brian J.
- Venue
- Bioinformatics
- Publisher
- Oxford University Press (OUP)
- Published
- 2004-07-09
- Volume
- 20
- Issue
- 18
- Pages
- 3643-3646
- ISSN
- 1367-4803 (ISSN-L)
- 1367-4811
- OpenAlex
- W2149517531
- Cited by
- 381
- References
- 0
- Citations by year
- 2026: 16 · 2025: 18 · 2024: 36 · 2023: 13 · 2022: 17 · 2021: 17 · 2020: 24 · 2019: 23 · 2018: 26 · 2017: 24 · 2016: 14 · 2015: 13 · 2014: 24 · 2013: 17 · 2012: 12
- FWCI
- 3.14
- Type
- journal article
- Language
- en
- Open access
- closed
- Locations
- Bioinformatics (publishedVersion)
- PubMed (publishedVersion)
- Funders
- National Institutes of Health
- U.S. National Library of Medicine (R01LM007938)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genome Rearrangement Algorithms
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Agricultural and Biological Sciences › Plant Science › Chromosomal and Genetic Variations
- Keywords
- synteny, directed acyclic graphs, protein-coding genes, Arabidopsis genome, comparative genomics
- MeSH terms
- Algorithms, Chromosome Mapping, Sequence Homology, Nucleic Acid, Software, Sequence Alignment, Conserved Sequence, Arabidopsis, Sequence Analysis, DNA, Gene Duplication
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