Synima: a Synteny imaging tool for annotated genome assemblies

Rhys A Farrer

doi:10.1186/s12859-017-1939-7

Synima: a Synteny imaging tool for annotated genome assemblies

Rhys A Farrer^* (Corresponding Author)

^*Corresponding author for this work

Medical Sciences

Research output: Contribution to journal › Article › peer-review

29 Citations (Scopus)

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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.

Original language	English
Article number	507
Number of pages	4
Journal	BioMed Central Bioinformatics
Volume	18
Issue number	1
DOIs	https://doi.org/10.1186/s12859-017-1939-7
Publication status	Published - 21 Nov 2017

Bibliographical note

Acknowledgements
I would like to thank Chris Desjardins and Brian Haas for assistance and
contributions to the ortholog prediction code and pipeline, and José Muñoz
and anonymous reviewer 1 for code testing.

Funding
This work was supported by an MIT / Wellcome Trust Fellowship.

Availability of data and materials
Synima is open source and freely available from https://github.com/rhysf/
Synima under the MIT License. The download includes all example data
presented in this manuscript.

Keywords

Synteny
imaging tool
orthology
visualization

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10.1186/s12859-017-1939-7Licence: CC BY

Synima: a Synteny imaging tool for annotated genome assemblies
© The Author(s). 2017 Open Access 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.
Final published version, 1.49 MBLicence: CC BY

Cite this

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title = "Synima: a Synteny imaging tool for annotated genome assemblies",

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.",

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note = "Acknowledgements I would like to thank Chris Desjardins and Brian Haas for assistance and contributions to the ortholog prediction code and pipeline, and Jos{\'e} Mu{\~n}oz and anonymous reviewer 1 for code testing. Funding This work was supported by an MIT / Wellcome Trust Fellowship. Availability of data and materials Synima is open source and freely available from https://github.com/rhysf/ Synima under the MIT License. The download includes all example data presented in this manuscript.",

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N2 - 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.

AB - 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.

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Synima: a Synteny imaging tool for annotated genome assemblies

Abstract

Bibliographical note

Keywords

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