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G-Anchor: a novel approach for whole-genome comparative mapping utilising evolutionary conserved DNA sequences

Lenis, V E; Swain, M; Larkin, D M

Authors

V E Lenis

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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