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Simple Tool For Finding Known Regulatory Motifs In A Single (Eukaryotic) Sequence

I'm looking for a motif/regulatory sequence finding tool to recommend to the wet-lab scientists I work with. Are there any simple, user-friendly tools which take a single sequence and find known regulatory motifs (TFBS, TATA-boxes, etc.) within it? The tools I've seen being recommended here all seem to be about de novo discovery using multiple sequences, or involve submitting your own motif file. What I'm really looking for is something similar to BLAST/PFAM and, if possible, applicable to non-model species (namely, Bos taurus). Does such a tool exist?

motif search database
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updated by Biostar Biostar • written by Eric Fournier Eric Fournier

2 answers

If you are at an academic institution, it is free to use the TRANSFAC search tools, like TfBlast to search a sequence against their database. I've recommended this site to wet lab scientists in my lab and they were able to find exactly what they wanted with no problems. The well known MEME suite of tools also has a web interface that would probably be ideal for small jobs.

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written by SES SES

I found HOMER relatively user friendly: http://biowhat.ucsd.edu/homer/ngs/index.html

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written by 14134125465346445 14134125465346445

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