Automated denovo motif analysis

Question

[swttalyan]

Dear all, I have a question-

I have thousands(2-3 thousand ) bed files, for which I would like to derive denovo motifs.

Which package would you suggest such that it is done the fastest? I am more interested in percentile frequencies rather than graphical output.

best

Abhi

Answer 1

[ddiez]

Personally, I would probably use the meme program in the MEME suite for motif discovery and analyze the results in R. If you want to keep the whole analysis in R a possibility is the rGADEM Bioconductor package for motif discovery. Take a look also to the package MotIV for further motif analyses.