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transcription factor binding sites

My ultimate goal is to locate the binding sites of a specific transcription factor. Is there a program that will allow me to search based on the factor's name or by the consensus binding site (it's only 7 nucleotides long). I've tried working with NestedMICA but am now having trouble opening the xms file that results. The manual for NestedMICA suggests using the MotifExplorer tool, but that does not seem to exist anymore? Thanks for any helpful insights!

rna-seq nestedmica
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updated by Denise CS Denise CS • written by sursan • sursan

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You can get that information from the Ensembl Regulation database in BioMart. Let's suppose you are interested in TF USF-1. With BioMart you can find the location of the binding motifs associated with this TF at a genome wide level. You can choose USF-1 as Feature type in FILTERS; and binding matrix, chr, start, end, and score for example in ATTRIBUTES) . If you've got the Binding Matrix ID (e.g. MA0003.1) you can use that as FILTERS instead of the feature type (i.e. TF name). Check the links for more info on BioMart and the Ensembl Regulatory Build.

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written by Denise CS Denise CS

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