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Bioinformatics Advance Access published online on October 31, 2006
Bioinformatics, doi:10.1093/bioinformatics/btl556
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© The Author (2006). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org
Received August 1, 2006
Revised October 17, 2006
Accepted October 23, 2006

Applications note

GECO - linear visualization for comparative genomics

C. T. Kuenne 1 *, R. Ghai 1, T. Chakraborty 1, and T. Hain 1

1 Institute of Medical Microbiology, Justus-Liebig-University, Frankfurter Strasse 107, D-35392 Giessen, Germany

* To whom correspondence should be addressed.
C. T. Kuenne, E-mail: Carsten.Kuenne{at}mikrobio.med.uni-giessen.de


  Abstract

Summary: In order to understand and interpret phylogenetic and functional relationships between multiple prokaryotic species, qualitative and quantitative data must be correlated and displayed. GECO allows linear visualization of multiple genomes using a client/server based approach by dynamically creating .png- or .pdf-formatted images. It is able to display ortholog relations calculated using BLASTCLUST by color coding ortholog representations. Irregularities on the genomic level can be identified by anomalous G/C composition. Thus, this software will enable researchers to detect horizontally transferred genes, pseudogenes and insertions/deletions in related microbial genomes.

Availability: http://bioinfo.mikrobio.med.uni-giessen.de/geco2/GecoMainServlet.

Associate Editor: Alex Bateman
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