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MEET: Motif Elements Estimation Toolkit
Pairó Castiñeira, Erola; Maynou Fernández, Joan; Vallverdú Ferrer, Montserrat; Caminal Magrans, Pere; Marco Colás, Santiago; Perera Lluna, Alexandre
Universitat Politècnica de Catalunya. Departament d'Enginyeria de Sistemes, Automàtica i Informàtica Industrial; Universitat Politècnica de Catalunya. SISBIO - Senyals i Sistemes Biomèdics
MEET is an R package that integrates a set of algorithms for the detection of transcription factor binding sites(TFBS). The MEET R package includes five motif searching algorithms: MEME/MAST(Multiple Expectation-Maximization for Motif Elicitation), Q-residuals, MDscan (Motif Discovery scan), ITEME (Information Theory Elements for Motif Estimation)and MATCH. In addition MEET allows the user to work with different alignment algorithms: MUSCLE (Multiple Sequence Comparison by Log-Expectation), ClustalW and MEME. The package can work in two modes, training and detection. The training mode allows the user to choose the best parameters of a detector. Once the parameters are chosen, the detection mode allows to analyze a genome looking for binding sites. Both modes can combine the different alignment and detection methods, offering multiple possibilities. Combining the alignments and the detection algorithms makes possible the comparison between detection models at the same level, without having to care about the differences produced during the alignment process. The MEET R package can be downloaded from http://sisbio.recerca.upc.edu/R/MEET_1.0. tar.gz
Àrees temàtiques de la UPC::Enginyeria biomèdica::Electrònica biomèdica
Biomedical engineering
Enginyeria biomèdica
Attribution-NonCommercial-NoDerivs 3.0 Spain
http://creativecommons.org/licenses/by-nc-nd/3.0/es/
info:eu-repo/semantics/submittedVersion
info:eu-repo/semantics/conferenceObject
         

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