Hello,
as suggested here in a previous question (here), I used TRANSFAC2MEME to convert a minimal TRANSFAC PSSM into a MEME one. Since I generate by my self the TRANSFAC matrices, I cannot provide the program additional information beside the name of the matrix and the matrix itself. The MEME format is more informative than a TRANSFAC, and I feel this to be related on my failure.
From MS-DOS Prompt I obtain this:
C:\Documents and Settings\Standard\Desktop>perl transfac2meme.pl rax.txt MEME version 3.0
ALPHABET= ACGT
strands: + -
Background letter frequencies (from dataset with add-one prior applied): A 0.250000 C 0.250000 G 0.250000 T 0.250000
Converted 0 motifs. Skipped 0 motifs.
1 answer
All fixed. TRANSFAC2MEME does not support the minimal TRANSFAC PSSM. Matrices have to be provided with this format:
A sample TRANSFAC Matrix:
ID Example
PO A C G T
01 6 4 4 6 N
02 4 9 3 4 N
03 12 4 3 1 A
04 6 1 11 2 R
05 3 2 11 4 G
06 3 3 4 10 N
XX
The consensus line, at right, can be made quikly using a series of N.
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