title: New Onto-Tools: Promoter-Express, nsSNPCounter and Onto-Translate.
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.
authors.affiliation: Department of Computer Science, Wayne State University, 431 State Hall, Detroit, MI 48202, USA.
authors.forename: Purvesh
authors.initials: P
authors.lastname: Khatri
authors.forename: Valmik
authors.initials: V
authors.lastname: Desai
authors.forename: Adi L
authors.initials: AL
authors.lastname: Tarca
authors.forename: Sivakumar
authors.initials: S
authors.lastname: Sellamuthu
authors.forename: Derek E
authors.initials: DE
authors.lastname: Wildman
authors.forename: Roberto
authors.initials: R
authors.lastname: Romero
authors.forename: Sorin
authors.initials: S
authors.lastname: Draghici
mesh_terms: D001665:Binding Sites; D030541:Databases, Genetic; D019143:Evolution, Molecular; D020407:Internet; D020641:Polymorphism, Single Nucleotide; D011401:Promoter Regions, Genetic; D011506:Proteins / Q000235:genetics*; D012984:Software; D018511:Systems Integration; D014157:Transcription Factors / Q000378:metabolism*; D014584:User-Computer Interface
chemical_list: D011506:Proteins; D014157:Transcription Factors