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Bioinformatics Advance Access published online on May 18, 2006
Bioinformatics, doi:10.1093/bioinformatics/btl193
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© The Author (2006). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org
Received March 4, 2006
Revised May 12, 2006
Accepted May 14, 2006

Applications note

Combo: a whole genome comparative browser

Reinhard Engels 1 *, Tamara Yu 1, Chris Burge 2, Jill P. Mesirov 1, David DeCaprio 1, and James E. Galagan 1

1 The Broad Institute of MIT and Harvard, 320 Charles Street, Cambridge, Massachusetts 02142, USA
2 Department of Biology Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA

* To whom correspondence should be addressed.
Reinhard Engels, E-mail: reinhard{at}broad.mit.edu


  Abstract

Summary: Combo is a comparative genome browser that provides a dynamic view of whole genome alignments along with their associated annotations. Combo provides two different visualization perspectives. The perpendicular (dotplot) view provides a dotplot of genome alignments synchronized with a display of genome annotations along each axis. The parallel view displays two genome annotations horizontally, synchronized through a panel displaying local alignments as trapezoids. Users can zoom to any resolution, from whole chromosomes to individual bases. They can select, highlight, and view detailed information from specific alignments and annotations. Combo is organism agnostic and can import data from a variety of file formats.

Availability: Combo is integrated as part of the Argo Genome Browser which also provides single-genome browsing and editing capabilities. Argo is written in Java, runs on multiple platforms, and is freely available for download at http://www.broad.mit.edu/annotation/argo/.

Associate Editor: Alfonso Valencia
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