How Do I Generate A -Bfile For Meme?

Question

[a1ultima]

I am using the de-novo transcription binding motif discovery software MEME.

The MEME suite documentation (here) claims you can use the '-bfile' argument to provide MEME with a background Markov model file.

I am asking whether anybody has got suggestions for how to generate such a -bfile, or better still if anybody could point me towards a script that generates such a file given .fasta sequence data.

Here is the description of the -bfile as per MEME Suite documentaiton:

BACKGROUND MODEL -bfile <bfile> — The name of the file containing the background model for sequences. The background model is the model of random sequences used by MEME. The background model is used by MEME during EM as the "null model", for calculating the log likelihood ratio of a motif, for calculating the significance (E-value) of a motif, and, for creating the position-specific scoring matrix (log-odds matrix). By default, the background model is a 0-order Markov model based on the letter frequencies in the training set.

Markov models of any order can be specified in <bfile> by listing frequencies of all possible tuples of length up to order+1. Note that MEME uses only the 0-order portion (single letter frequencies) of the background model for purposes 3) and 4), but uses the full-order model for purposes 1) and 2), above.

Example: To specify a 1-order Markov background model for DNA, <bfile> might contain the following lines. Note that optional comment lines are marked by "#" and are ignored by MEME.

            # tuple   frequency_non_coding
            a       0.324
            c       0.176
            g       0.176
            t       0.324
            # tuple   frequency_non_coding
            aa      0.119
            ac      0.052
            ag      0.056
            at      0.097
            ca      0.058
            cc      0.033
            cg      0.028
            ct      0.056
            ga      0.056
            gc      0.035
            gg      0.033
            gt      0.052
            ta      0.091
            tc      0.056
            tg      0.058
            tt      0.119

Sample -bfile files are given in directory tests: tests/nt.freq (DNA), and tests/na.freq (amino acid).

Answer 1

[UnivStudent]

You can use the fasta-get-markov command to generate a background model.

[a1ultima]

aha! cheers for that