Synima: a Synteny imaging tool for annotated genome assemblies

Rhys A Farrer* (Corresponding Author)

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

28 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 languageEnglish
Article number507
Number of pages4
JournalBioMed Central Bioinformatics
Volume18
Issue number1
DOIs
Publication statusPublished - 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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