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Bioinformatics Advance Access published online on June 30, 2005
Bioinformatics, 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@oupjournals.org
Received February 18, 2005
Revised June 15, 2005
Accepted June 25, 2005

Article

SynBrowse: a synteny browser for comparative sequence analysis

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

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

* To whom correspondence should be addressed.
Volker Brendel, E-mail: vbrendel{at}iastate.edu


  Abstract

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 macro-synteny, micro-synteny and homologous genes between sequences. It can also aid with 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.synbrowser.org/download.html.


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