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