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. 2006 Jul 1;34(Web Server issue):W626-31.
doi: 10.1093/nar/gkl213.

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

Purvesh Khatri  1 , Valmik Desai, Adi L Tarca, Sivakumar Sellamuthu, Derek E Wildman, Roberto Romero, Sorin Draghici
Affiliations

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

Purvesh Khatri et al. Nucleic Acids Res. .

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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Figures

Figure 1
Figure 1
Example of a typical module. The black thick lines are two upstream sequences to be analyzed. The thin shorter color-coded segment between them are the elements common to both, and the thick color-coded segments are the elements that together form a module. The gap X is approximately equal to gap ∼X and gap Y is approximately equal to gap ∼Y.
Figure 2
Figure 2
The output provided by Promoter-Express for a selected module. The figure also shows some of the possible data manipulations and interactions with the GUI.
Figure 3
Figure 3
Input (left panel) and output (right panel) for nsSNPCounter.
Figure 4
Figure 4
A comparison between the performance of Onto-Translate (OT) and MatchMiner (MM). The figures show the percentage of successful translations from probe IDs to gene symbols, for a number of sets of genes corresponding to popular Affymetrix human (left) and mouse (right) arrays.
See this image and copyright information in PMC

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