MAPPER: A Search Engine for the Computational Identification of Putative Transcription Factor Binding Sites in Multiple Genomes

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MAPPER: A Search Engine for the Computational Identification of Putative Transcription Factor Binding Sites in Multiple Genomes

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dc.contributor.author Marinescu, Voichita D
dc.contributor.author Riva, Alberto
dc.contributor.author Kohane, Isaac Samuel
dc.date.accessioned 2011-04-08T16:19:14Z
dc.date.issued 2005
dc.identifier.citation Marinescu, Voichita D., Isaac S. Kohane, and Alberto Riva. 2005. MAPPER: A search engine for the computational identification of putative transcription factor binding sites in multiple genomes. BMC Bioinformatics 6: 79. en_US
dc.identifier.issn 1471-2105 en_US
dc.identifier.uri http://nrs.harvard.edu/urn-3:HUL.InstRepos:4817623
dc.description.abstract Background: Cis-regulatory modules are combinations of regulatory elements occurring in close proximity to each other that control the spatial and temporal expression of genes. The ability to identify them in a genome-wide manner depends on the availability of accurate models and of search methods able to detect putative regulatory elements with enhanced sensitivity and specificity. Results: We describe the implementation of a search method for putative transcription factor binding sites (TFBSs) based on hidden Markov models built from alignments of known sites. We built 1,079 models of TFBSs using experimentally determined sequence alignments of sites provided by the TRANSFAC and JASPAR databases and used them to scan sequences of the human, mouse, fly, worm and yeast genomes. In several cases tested the method identified correctly experimentally characterized sites, with better specificity and sensitivity than other similar computational methods. Moreover, a large-scale comparison using synthetic data showed that in the majority of cases our method performed significantly better than a nucleotide weight matrix-based method. Conclusion: The search engine, available at , allows the identification, visualization and selection of putative TFBSs occurring in the promoter or other regions of a gene from the human, mouse, fly, worm and yeast genomes. In addition it allows the user to upload a sequence to query and to build a model by supplying a multiple sequence alignment of binding sites for a transcription factor of interest. Due to its extensive database of models, powerful search engine and flexible interface, MAPPER represents an effective resource for the large-scale computational analysis of transcriptional regulation. en_US
dc.language.iso en_US en_US
dc.publisher BioMed Central en_US
dc.relation.isversionof doi:10.1186/1471-2105-6-79 en_US
dc.relation.hasversion http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1131891/pdf/ en_US
dash.license LAA
dc.title MAPPER: A Search Engine for the Computational Identification of Putative Transcription Factor Binding Sites in Multiple Genomes en_US
dc.type Journal Article en_US
dc.description.version Version of Record en_US
dc.relation.journal BMC Bioinformatics en_US
dash.depositing.author Kohane, Isaac Samuel
dc.date.available 2011-04-08T16:19:14Z
dash.affiliation.other HMS^Countway Library of Medicine en_US
dash.affiliation.other HMS^Medicine-Brigham and Women's Hospital en_US
dash.affiliation.other HMS^Pediatrics-Children's Hospital en_US

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