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Nucleic Acids Research 2006 34(Web Server issue):W626-W631; doi:10.1093/nar/gkl213
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© The Author 2006. Published by Oxford University Press. All rights reserved
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions@oxfordjournals.org

Article

New Onto-Tools: Promoter-Express, nsSNPCounter and Onto-Translate

Purvesh Khatri, Valmik Desai, Adi L. Tarca1, Sivakumar Sellamuthu, Derek E. Wildman1, Roberto Romero1 and Sorin Draghici*

Department of Computer Science, Wayne State University 431 State Hall, Detroit, MI 48202, USA 1 Perinatology Research Branch NIH/NICHD, 4 Brush, 3990 John R, Detroit, MI 48201, USA

*To whom correspondence should be addressed. Email: sorin{at}wayne.edu

Received February 14, 2006. Revised March 24, 2006. Accepted March 24, 2006.

The Onto-Tools suite is composed of an annotation database and eight complementary, web-accessible data mining tools: Onto-Express, Onto-Compare, Onto-Design, Onto-Translate, Onto-Miner, Pathway-Express, Promoter-Express and nsSNPCounter. Promoter-Express is a new tool added to the Onto-Tools ensemble that facilitates the identification of transcription factor binding sites active in specific conditions. nsSNPCounter is another new tool that allows computation and analysis of synonymous and non-synonymous codon substitutions for studying evolutionary rates of protein coding genes. Onto-Translate has also been enhanced to expand its scope and accuracy by fully utilizing the capabilities of the Onto-Tools database. Currently, Onto-Translate allows arbitrary mappings between 28 types of IDs for 53 organisms. Onto-Tools are freely available at http://vortex.cs.wayne.edu/Projects.html.


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