TRANSFAC motif format

Any valid TRANSFAC format file is acceptable.

For MEME SUITE purposes, the essential portions of the TRANSFAC motif format are:

• ID <motif name>
• BF <species name>
• P0 <a₁> ... <a_n>
• 01 <c_1,1> ... <c_1,n> <consensus letter>
• 02 <c_2,1> ... <c_2,n> <consensus letter> ...
• nn <c_nn,1> ... <c_nn,n> <consensus letter>
• XX
• //

The P0 row labels the columns with the letters of the sequence alphabet. The numbered rows (01...nn) contain counts for each letter in the sequence alphabet for that position in the motif. These counts should give the number of times each letter appears in known examples of the motif at the given position. The counts in each numbered row should add up to the same total count. The last column in each count row gives the consensus letter for that position in the motif, and is ignored by MEME SUITE programs.

Here is an example of a TRANSFAC format motif file containing two motifs suitable for MEME SUITE programs:

      ID any_old_name_for_motif_1
      BF species_name_for_motif_1
      P0      A      C      G      T
      01      1      2      2      0      S
      02      2      1      2      0      R
      03      3      0      1      1      A
      04      0      5      0      0      C
      05      5      0      0      0      A
      06      0      0      4      1      G
      07      0      1      4      0      G
      08      0      0      0      5      T
      09      0      0      5      0      G
      10      0      1      2      2      K
      11      0      2      0      3      Y
      12      1      0      3      1      G
      XX
      //
      ID any_old_name_for_motif_2
      BF species_name_for_motif_2
      P0      A      C      G      T
      01      2      1      2      0      R
      02      1      2      2      0      S
      03      0      5      0      0      C
      04      3      0      1      1      A
      05      0      0      4      1      G
      06      5      0      0      0      A
      07      0      1      4      0      G
      08      0      0      5      0      G
      09      0      0      0      5      T
      10      0      2      0      3      Y
      11      0      1      2      2      K
      12      1      0      3      1      G
      XX
      //