Synima: a Synteny imaging tool for annotated genome assemblies

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Synima: a Synteny imaging tool for annotated genome assemblies

Farrer, RA; (2017) Synima: a Synteny imaging tool for annotated genome assemblies. BMC Bioinformatics , 18 , Article 507. 10.1186/s12859-017-1939-7. Green open access

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Abstract

BACKGROUND: Ortholog prediction and synteny visualization across whole genomes are valuable methods for detecting and representing a range of evolutionary processes such as genome expansion, chromosomal rearrangement, and chromosomal translocation. Few standalone methods are currently available to visualize synteny across any number of annotated genomes. RESULTS: Here, I present a Synteny Imaging tool (Synima) written in Perl, which uses the graphical features of R. Synima takes orthologues computed from reciprocal best BLAST hits or OrthoMCL, and DAGchainer, and outputs an overview of genome-wide synteny in PDF. Each of these programs are included with the Synima package, and a pipeline for their use. Synima has a range of graphical parameters including size, colours, order, and labels, which are specified in a config file generated by the first run of Synima - and can be subsequently edited. Synima runs quickly on a command line to generate informative and publication quality figures. Synima is open source and freely available from https://github.com/rhysf/Synima under the MIT License. CONCLUSIONS: Synima should be a valuable tool for visualizing synteny between two or more annotated genome assemblies.

Type:	Article
Title:	Synima: a Synteny imaging tool for annotated genome assemblies
Location:	England
Open access status:	An open access version is available from UCL Discovery
DOI:	10.1186/s12859-017-1939-7
Publisher version:	http://dx.doi.org/10.1186/s12859-017-1939-7
Language:	English
Additional information:	Copyright © The Author(s) 2017. This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
Keywords:	Imaging tool, Orthology, Synteny, Visualization
UCL classification:	UCL UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Life Sciences
URI:	https://discovery.ucl.ac.uk/id/eprint/10039467