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

Question

[Eric Fournier]

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?

Answer 1

[SES]

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.

Answer 2

[14134125465346445]

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