Identification of motifs and TF in promoter sequences common in different groups (eukaryotes and prokaryotes)

[Diego Figueredo]

Hello. I am carrying out an analysis of promoter sequences of the conserved gene in eukaryotic ( 3 species) and prokaryotic (2 species). My goal is to identify conserved regular sequences or to identify transcription factor binding sites. 

In addition to identifying the common sequences in the promoters of the 5 species, I would like to know which transcription factors bind to these sequences. So, I would like to get help from the team to know the best tool for my question.

Thanks.

Diego.

[cegrant]

I’d suggest starting with XSTREME. This will run STREME, MEME, SEA, Tomtom, and FIMO on your input sequences. STREME and MEME are de novo motif discovery tools. They should identify any motifs shared by your sequences. SEA  looks for enrichment of the discovered motifs in your sequences, and additionally searched for enrichment of known motifs. You can select from a variety of standard motif collections that we make available on the MEME Suite web site. Tomtom is a motif comparison tool that will compare the discovered motifs to libraries of standard motifs, identifying similarities between the discovered motifs and known motifs. Finally FIMO will scan your sequences with the Position Weight Matrix for the discovered motifs and identify all sequence matches to the motifs.

Documentation for XSTREME 

Sample XSTREME output

Don’t hesitate to let us know if you have further questions.