Tools to find Transcription factor binding sites in promoter region in multiple sequences simultaneously

Question

[mirza]

Hi,

I want to find the binding sites of particular transcription factors in promoter region of several gene sequences. All the web based databases like Plant care,plant pan, JASPAR etc. take one sequence at a time. I have hundreds of sequences so it is practically impossible to carrry out the analysis using these. 1. Please suggest me some tools, standalone may be where I can carry out the analysis for multiple sequences at a time.

Answer 1

[Carlo Yague]

Have a look at the MEME suite, especially AME.

AME:

AME identifies known or user-provided motifs that are relatively enriched in your sequences compared with shuffled sequences or your control sequences (sample output from sequences, control and motifs). AME treats motif occurrences the same, regardless of their locations within the sequences.