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MAPPER - Multi-genome Analysis of Positions and Patterns of Elements of Regulation (RRID:SCR_003077)Copy Citation Copied
URL: http://genome.ufl.edu/mapper/
Proper Citation: MAPPER - Multi-genome Analysis of Positions and Patterns of Elements of Regulation (RRID:SCR_003077)
Description: A platform composed of three modules: the Database, the Search Engine, and rSNPs, for the computational identification of transcription factor binding sites (TFBSs) in multiple genomes, that combines TRANSFAC and JASPAR data with the search power of profile hidden Markov models (HMMs). The Database contains putative TFBSs found in the upstream sequences of genes from the human, mouse and D.melanogaster genomes. For each gene, they scanned the region from 10,000 base pairs upstream of the transcript start to 50 base pairs downstream of the coding sequence start against all their models. Therefore, the database contains putative binding sites in the gene promoter and in the initial introns and non-coding exons. Information displayed for each putative binding site includes the transcription factor name, its position (absolute on the chromosome, or relative to the gene), the score of the prediction, and the region of the gene the site belongs to. If the selected gene has homologs in any of the other two organisms, the program optionally displays the putative TFBSs in the homologs. The Search Engine allows the identification, visualization and selection of putative TFBSs occurring in the promoter or other regions of a gene from the human, mouse, D.melanogaster, C.elegans or S.cerevisiae 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. rSNPs MAPPER is designed to identify Single Nucleotide Polymorphisms (SNPs) that may have an effect on the presence of one or more TFBSs.
Abbreviations: MAPPER, MAPPER 2,
Synonyms: Multi-genome Analysis of Positions and Patterns of Elements of Regulation, MAPPER 2 - Multi-genome Analysis of Positions and Patterns of Elements of Regulation, MAPPER database
Resource Type: data or information resource, database, service resource
Defining Citation: PMID:15608292, PMID:15799782
Keywords: transcription factor binding site, gene promoter, intron, non-coding exon, transcription factor, chromosome, gene, homolog, rsnp, single nucleotide polymorphism, search engine
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