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Bioinformatics Advance Access originally published online on June 30, 2005
Bioinformatics 2005 21(17):3461-3468; doi:10.1093/bioinformatics/bti555
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© The Author 2005. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions{at}oupjournals.org

SynBrowse: a synteny browser for comparative sequence analysis

Xiaokang Pan 1, Lincoln Stein 3 and Volker Brendel 1,2,*

1Department of Genetics, Development and Cell Biology, Iowa State University 2112 Molecular Biology Building, Ames, IA 50011-3260, USA
2Department of Statistics, Iowa State University 2112 Molecular Biology Building, Ames, IA 50011-3260, USA
3Cold Spring Harbor Laboratory Cold Spring Harbor, NY 11724, USA

*To whom correspondence should be addressed.

Motivation: The recent efforts of various sequence projects to sequence deeply into various phylogenies provide great resources for comparative sequence analysis. A generic and portable tool is essential for scientists to visualize and analyze sequence comparisons.

Results: We have developed SynBrowse, a synteny browser for visualizing and analyzing genome alignments both within and between species. It is intended to help scientists study macrosynteny, microsynteny and homologous genes between sequences. It can also aid with the identification of uncharacterized genes, putative regulatory elements and novel structural features of a species. SynBrowse is a GBrowse (the Generic Genome Browser) family software tool that runs on top of the open source BioPerl modules. It consists of two components: a web-based front end and a set of relational database back ends. Each database stores pre-computed alignments from a focus sequence to reference sequences in addition to the genome annotations of the focus sequence. The user interface lets end users select a key comparative alignment type and search for syntenic blocks between two sequences and zoom in to view the relationships among the corresponding genome annotations in detail. SynBrowse is portable with simple installation, flexible configuration, convenient data input and easy integration with other components of a model organism system.

Availability: The software is available at http://www.gmod.org

Contact: vbrendel{at}iastate.edu

Received on February 18, 2005; revised on June 15, 2005; accepted on June 25, 2005

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