Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W626-31.

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

Khatri P, Desai V, Tarca AL, Sellamuthu S, Wildman DE, Romero R, Draghici S.

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Department of Computer Science, Wayne State University, 431 State Hall, Detroit, MI 48202, USA.

Abstract

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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PMCID:: PMC1538776

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