Map 6 to 10-mer motifs in reference genome

[pbarros]

Dear all,

Recently a coleague asked me if it would be possible to map a specific DNA motif of 8-mer size (transcription factor binding site) in a reference genome (rice), i.e. find all the occurrences of this motif in the genome and later filter by location in promoter regions (proximal to CDS sequences) and pattern (usually that TF binds to two motifs separated by aprox. 40bp).

Although I think this is a huge leap of faith, I tried to map this 8bp motif in the genome using BLAT, changing the tileSize and stepSize, but no alignment was generated.

I was wondering if there is any strategy which would alow me to map a small region like this in a genome or in a chromosome...

any thoughts? please don't answer "Chip-seq"

[GenoMax]

You may want to try a "fuzznuc" search with a small "motif" (I assume you want to allow ambiguities) like this rather than blat/blast/alignment. http://emboss.sourceforge.net/apps/c...s/fuzznuc.html

It would be best to install emboss locally for a large search like this: http://emboss.open-bio.org/

[pbarros]

Thanks for the tip GenoMax, it worked!