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Motif analysis

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?

jaspar motif meme homer analysis
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updated by lieven.sterck lieven.sterck • written by sk_24 • sk_24

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.

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updated by lieven.sterck lieven.sterck • written by b.contreras.moreira • b.contreras.moreira

1 answer

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)

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written by lieven.sterck lieven.sterck

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