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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
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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