Identification of motifs in repetitive sequences

[Claudia34]

Hello,

I'd like to identify small DNA motifs in sequences from highly repetitive genomic regions. We performed Illumina sequencing (36 nt reads) after ChIP-seq and I filtered reads coming from regions of interest. I'd like to know if our protein binds specific small motifs (between 6 and 9 nucleotides). I am currently using "dreme" tool but I don't know if it's the best way to do it. I have tried to run dreme independently on input filtered sequences and ChIPed filtered sequences but identified motifs are so different that I can't perform any enrichment analysis.
Did anyone perform such analyses? Are there any other tools for these kinds of analysis? Do you have any suggestions?

Thanks a lot,
Claudia

[llgama7]

I think you can use BCRANK, this tool can accept the sequences who have your interesting motifs, so you can feed it with the sequences that contain your motif

http://bioconductor.org/packages/release/bioc/vignettes/BCRANK/inst/doc/BCRANK_intro_fig1.pdf

[llgama7]

I think you can use BCRANK, this tool can accept the sequences who have your interesting motifs, so you can feed it with the sequences that contain your motif

http://bioconductor.org/packages/rel...intro_fig1.pdf