How to graphically represent a known DNA motif in a list of DNA sequences

Question

[Student]

Hello.

I was using FIMO to search a known motif in a list of genes. FIMO gives me a list of motif occurences, that is the matched sequence, the p-value, the q-value and also the start nucleotide position of the motif and end nucleotide position in the gene sequence. Do you know if there is a way to represent them graphically with MEME suite tool or using other softwares ? I would like to do the same of this post or something like the graphs shown by MEME when it shows de novo sequence motifs (like this) in oder to understand if the motif has the biological meaning that I thought (for example, the TATA sequence is at 25 bp from the site of transcription initiation, thus I expect it to be upstream of the genes. If it is not there, it is not the transcription factor binding site). I would like to have it on a graph to visually see better it and use it in my report.

I do not consider the post of the first link because the answers of that post have not helped me.

Thank you in advance.

Answer 1

[Alex Reynolds]

You could convert the positions from BED coordinates to aligned sequence via samtools faidx (example with convenience Perl script for multiple, stranded inputs). Alignment here is defined by strand-specific start position from FIMO hits.

You could then run these aligned sequences through WebLogo or seqlogo packages (Python | R) to generate a sequence logo representing information content over the hits.