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 availa...
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| Format: | Article |
| Language: | English |
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BMC
2017-11-01
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| Series: | BMC Bioinformatics |
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| Online Access: | http://link.springer.com/article/10.1186/s12859-017-1939-7 |
| _version_ | 1818911756986089472 |
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| author | Rhys A. Farrer |
| author_facet | Rhys A. Farrer |
| author_sort | Rhys A. Farrer |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-12-19T23:03:46Z |
| format | Article |
| id | doaj.art-0c31cc5eb21c4df180a4f4ed2651b1f0 |
| institution | Directory Open Access Journal |
| issn | 1471-2105 |
| language | English |
| last_indexed | 2024-12-19T23:03:46Z |
| publishDate | 2017-11-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Bioinformatics |
| spelling | doaj.art-0c31cc5eb21c4df180a4f4ed2651b1f02022-12-21T20:02:26ZengBMCBMC Bioinformatics1471-21052017-11-011811410.1186/s12859-017-1939-7Synima: a Synteny imaging tool for annotated genome assembliesRhys A. Farrer0Department of Infectious Disease Epidemiology, Imperial College LondonAbstract 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.http://link.springer.com/article/10.1186/s12859-017-1939-7SyntenyImaging toolOrthologyVisualization |
| spellingShingle | Rhys A. Farrer Synima: a Synteny imaging tool for annotated genome assemblies BMC Bioinformatics Synteny Imaging tool Orthology Visualization |
| title | Synima: a Synteny imaging tool for annotated genome assemblies |
| title_full | Synima: a Synteny imaging tool for annotated genome assemblies |
| title_fullStr | Synima: a Synteny imaging tool for annotated genome assemblies |
| title_full_unstemmed | Synima: a Synteny imaging tool for annotated genome assemblies |
| title_short | Synima: a Synteny imaging tool for annotated genome assemblies |
| title_sort | synima a synteny imaging tool for annotated genome assemblies |
| topic | Synteny Imaging tool Orthology Visualization |
| url | http://link.springer.com/article/10.1186/s12859-017-1939-7 |
| work_keys_str_mv | AT rhysafarrer synimaasyntenyimagingtoolforannotatedgenomeassemblies |