Vasileios Panagiotis E Lenis1,2, Martin Swain1, Denis M Larkin3. 1. Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, SY23 3DA, UK. 2. School of Biomedical and Healthcare Sciences, Plymouth University Peninsula, Schools of Medicine and Dentistry, Plymouth PL6 8BU, UK. 3. Department of Comparative Biomedical Sciences, Royal Veterinary College, Royal College Street, University of London, London, NW1 0TU, UK.
Abstract
Background: Cross-species whole-genome sequence alignment is a critical first step for genome comparative analyses, ranging from the detection of sequence variants to studies of chromosome evolution. Animal genomes are large and complex, and whole-genome alignment is a computationally intense process, requiring expensive high-performance computing systems due to the need to explore extensive local alignments. With hundreds of sequenced animal genomes available from multiple projects, there is an increasing demand for genome comparative analyses. Results: 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. Conclusions: G-Anchor is a ready-to-use tool for anchoring a pair of vertebrate genomes. It may be used with large genomes that contain a significant fraction of evolutionally conserved DNA sequences and that are not highly repetitive, polypoid, or excessively fragmented. G-Anchor is not a substitute for whole-genome aligning software but can be used for fast and accurate initial genome comparisons. G-Anchor is freely available and a ready-to-use tool for the pairwise comparison of two genomes.
Background: Cross-species whole-genome sequence alignment is a critical first step for genome comparative analyses, ranging from the detection of sequence variants to studies of chromosome evolution. Animal genomes are large and complex, and whole-genome alignment is a computationally intense process, requiring expensive high-performance computing systems due to the need to explore extensive local alignments. With hundreds of sequenced animal genomes available from multiple projects, there is an increasing demand for genome comparative analyses. Results: 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. Conclusions: G-Anchor is a ready-to-use tool for anchoring a pair of vertebrate genomes. It may be used with large genomes that contain a significant fraction of evolutionally conserved DNA sequences and that are not highly repetitive, polypoid, or excessively fragmented. G-Anchor is not a substitute for whole-genome aligning software but can be used for fast and accurate initial genome comparisons. G-Anchor is freely available and a ready-to-use tool for the pairwise comparison of two genomes.
Authors: N Stojanovic; L Florea; C Riemer; D Gumucio; J Slightom; M Goodman; W Miller; R Hardison Journal: Nucleic Acids Res Date: 1999-10-01 Impact factor: 16.971
Authors: Diego Villar; Camille Berthelot; Sarah Aldridge; Tim F Rayner; Margus Lukk; Miguel Pignatelli; Thomas J Park; Robert Deaville; Jonathan T Erichsen; Anna J Jasinska; James M A Turner; Mads F Bertelsen; Elizabeth P Murchison; Paul Flicek; Duncan T Odom Journal: Cell Date: 2015-01-29 Impact factor: 41.582
Authors: Joana Damas; Rebecca O'Connor; Marta Farré; Vasileios Panagiotis E Lenis; Henry J Martell; Anjali Mandawala; Katie Fowler; Sunitha Joseph; Martin T Swain; Darren K Griffin; Denis M Larkin Journal: Genome Res Date: 2016-11-30 Impact factor: 9.043
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