Problems With Transfac2Meme

Question

[Anima Mundi]

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.

Answer 1

[Anima Mundi]

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.