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Bioinformatics Advance Access published online on September 11, 2006
Bioinformatics, doi:10.1093/bioinformatics/btl471
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© The Author (2006). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org
Received June 1, 2006
Revised August 29, 2006
Accepted August 31, 2006

Applications note

SPEED: a molecular-evolution-based database of mammalian orthologous groups

Eric J. Vallender 1 4, Justin E. Paschall 2 4, Christine M. Malcom 3, Bruce T. Lahn 1, and Gerald J. Wyckoff 2 *

1 Howard Hughes Medical Institute, Department of Human Genetics, and Committee on Genetics, University of Chicago, 920 E. 58th St, Chicago, IL 60637
2 Division of Molecular Biology and Biochemistry, University of Missouri- Kansas City, 5007 Rockhill Rd, Kansas City, MO 64110
3 Howard Hughes Medical Institute, Department of Human Genetics, and Committee on Genetics, University of Chicago, 920 E. 58th St, Chicago, IL 60637; Department of Anthropology, University of Chicago, 920 E. 58th St, Chicago, IL 60637

* To whom correspondence should be addressed.
Gerald J. Wyckoff, E-mail: wyckoffg{at}umkc.edu


  Abstract

Motivation: The abundance of nucleotide sequence information available has expanded horizons of inquiry for molecular evolution; however the full potential of whole-genome analysis has not been realized because of inadequate tools. Here we present one of the first toolkits to aid multidisciplinary high-throughput analysis.

Summary: SPEED was created to integrate molecular evolutionary data with existing genetic resources and provide a straightforward user interface to 17352 orthologous gene groups, containing representatives from eight mammalian species and an avian outgroup.

Availability: See http://bioinfobase.umkc.edu/speed/) for access.

Supplementary Information: A larger version of the data model and a site map are available online.

Associate Editor: Chris Stoeckert

4 These authors contributed equally to the work


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