Convert Fasta format to MEME-motif format

[Kashif Nawaz]

I know repeats can be scan through FIMO, for their location in whole genome. But FIMO required MEME-motif file as an input, which mainly contain "letter-probability matrix".

I have read the MEME motif format (http://meme-suite.org/doc/meme-format.html) in detail. I have problem in understanding the concept behind generating the "letter-probability matrix" in MEME-motif format. I am unable to find any software/script which directly converts fasta format to MEME-motif.

So, I have two questions regarding this:

• How to convert single fasta file into this MEME-motif file?
• In case I have multiple copy of fasta file of tandem repeats which are varying at few nucleotide positions only, how to convert these fasta files into one MEME-motif file?

[CharlesEGrant]

Assuming you have the MEME suite installed on your computer, you
have access to the scripts here: http://meme-suite.org/doc/motif_conversion.html

None does exactly what you want, but 'sites2meme' is close.
You also have access to 'fasta-grep' ( http://meme-suite.org/doc/fasta-grep.html )

This will do what you want (assuming you have a Mac or *nix computer)

    mkdir temp
    fasta-grep '.+' -dna -o < motif_sites.fasta > temp/motif_name.txt
    sites2meme temp > motif_name.meme