V E Lenis
G-Anchor: a novel approach for whole-genome comparative mapping utilising evolutionary conserved DNA sequences
Lenis, V E; Swain, M; Larkin, D M
Authors
M Swain
D M Larkin
Abstract
Here we introduce G-Anchor, a new, fast, and efficient pipeline that uses a strictly limited but highly effective set of local sequence alignments to anchor (or map) an animal genome to another species’ reference genome. G-Anchor makes novel use of a databank of highly conserved DNA sequence elements. We demonstrate how these elements may be aligned to a pair of genomes, creating anchors. These anchors enable the rapid mapping of scaffolds from a de novo assembled genome to chromosome assemblies of a reference species. Our results demonstrate that G-Anchor can successfully anchor a vertebrate genome onto a phylogenetically related reference species genome using a desktop or laptop computer within a few hours, and with comparable accuracy to that achieved by a highly accurate whole-genome alignment tool such as LASTZ. G-Anchor thus makes whole-genome comparisons accessible to researchers with limited computational resources.
Citation
Lenis, V. E., Swain, M., & Larkin, D. M. (in press). G-Anchor: a novel approach for whole-genome comparative mapping utilising evolutionary conserved DNA sequences. GigaScience, 7(5), https://doi.org/10.1093/gigascience/giy017
Journal Article Type | Article |
---|---|
Acceptance Date | Apr 1, 2018 |
Deposit Date | Apr 10, 2018 |
Publicly Available Date | Apr 10, 2018 |
Journal | GigaScience |
Electronic ISSN | 2047-217X |
Publisher | Oxford University Press |
Peer Reviewed | Peer Reviewed |
Volume | 7 |
Issue | 5 |
DOI | https://doi.org/10.1093/gigascience/giy017 |
Public URL | https://rvc-repository.worktribe.com/output/1387810 |
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