Question: Simple Tool For Finding Known Regulatory Motifs In A Single (Eukaryotic) Sequence
0
gravatar for Eric Fournier
7.4 years ago by
Eric Fournier1.4k
Quebec, Canada
Eric Fournier1.4k wrote:

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 database search • 3.0k views
ADD COMMENTlink modified 6.3 years ago by Biostar ♦♦ 20 • written 7.4 years ago by Eric Fournier1.4k
6
gravatar for SES
7.4 years ago by
SES8.3k
Vancouver, BC
SES8.3k wrote:

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.

ADD COMMENTlink modified 7.4 years ago • written 7.4 years ago by SES8.3k
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gravatar for 14134125465346445
7.4 years ago by
United Kingdom
141341254653464453.5k wrote:

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

ADD COMMENTlink written 7.4 years ago by 141341254653464453.5k
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