Hello,

I would like to convert automatically a PSSM from TRANSFAC to MEME format.

Here there is an example of a set of lines related to a matrix:

MEME version 4.0

ALPHABET= ACGT

strands: + -

Background letter frequencies (from dataset without add-one prior applied): A 0.276 C 0.224 G 0.224 T 0.276

MOTIF 2

BL MOTIF 2 width=26 seqs=23 letter-probability matrix: alength= 4 w= 26 nsites= 23 E= 1

In particular, I do not know: a) how to deal with the "Background letter frequencies" lines (as I start from a TRANSFAC); b) how to deal with E value (just set it to 0?).

This helps, thanks.

Can it also convert Jaspar matrices to MEME format? thanks!