Motif analysis

Question

[sk_24]

I have a motif sequence for a transcription factor. I want to scan the promoter regions of the genome using the motif information to get the potential binding sites. Which tool would be ideal for this?

[b.contreras.moreira]

Motif usually means a consensus sequence, which can be in matrix format or IUPAC string, which you can scan along some genomic sequences. I would suggest RSAT as it will help you:

1. Cut the promoter sequences from selected organisms; note there are instances for Metazoa, Plant, Fungi, Prokaryots and Protists, you can contact the RSAT team if your genome is not supported.
2. Scan string motifs with Pattern-matching -> dna-pattern
3. Scan matrix motifs in several formats with Pattern-matching -> matrix-scan-quick

There are also tutorials to run RSAT locally on Docker, Apptainer and conda.

Answer 1

[lieven.sterck]

Motif Scan? MotifSuite ? just to name some ...

or search for 'motif' on bio.tools or simply using google

EDIT: or RSAT thus indeed (was kinda looking for that one but could not get the name immediately)