title: MEET: motif elements estimation toolkit.
abstract: 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.
authors.affiliation: Institut of BioEngineering of Catalonia, IBEC balidiri REixach 4-6, 08028 Barcelona, Spain. epairo@ibecbarcelona.eu
authors.forename: Erola
authors.initials: E
authors.lastname: Pairó
authors.forename: Joan
authors.initials: J
authors.lastname: Maynou
authors.forename: Montserrat
authors.initials: M
authors.lastname: Vallverdú
authors.forename: Pere
authors.initials: P
authors.lastname: Caminal
authors.forename: Santiago
authors.initials: S
authors.lastname: Marco
authors.forename: Alexandre
authors.initials: A
authors.lastname: Perera
mesh_terms: D000465:Algorithms; D020816:Amino Acid Motifs; D019540:Area Under Curve; D001665:Binding Sites; D019295:Computational Biology / Q000379:methods*; D005800:Genes, Fungal; D016678:Genome; D011336:Probability; D011381:Programming Languages; D011401:Promoter Regions, Genetic; D012372:ROC Curve; D012441:Saccharomyces cerevisiae / Q000235:genetics; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA; D020539:Sequence Analysis, Protein / Q000379:methods; D012984:Software