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

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

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