motif database format for tomtom

Question

[kws15]

Hi everyone,

i have used meme to do some analysis on some sequences and got the output. The next step is to use tomtom to compare the result, i have a database of motifs hundreds files looks like something like this:

Pos A C G T

1 0.150033322225925 0.716511162945685 0.0750583138953682 0.0583972009330223

2 0.0255348955680081 0.0127992868059093 0.948866530820173 0.0127992868059093

3 0.0189260563380282 0.874056841046278 0.106954225352113 6.2877263581488905

4 0.0189260563380282 0.97466046277666 0.00635060362173038 6.28772635814889e-05

How can i make use of these files to compare the output from meme use command line version meme? i know i have to convert the format of these motifs files, i think i have tried all the methods shown in this link http://meme-suite.org/doc/motif_conversion.html, but none of them work . Any help will be appreciated. many thanks

Answer 1

[Girolamo]

The methods do not work because your matrix is not in a standard format. i suggest you, to convert in beeml format. Basically, and put an # at the beginning of the line with a generic name and substitute the 1,2,3,4 at the beginning of the lines with A,C,G,T of and then run again beeml2meme.

[kws15]

Hi Girolamo, thank you very much for your response, i somehow changed the format of my files into something like this in R,

# M0004_1.02

[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8]

A 15 3 2 2 0 6 16 49

C 72 1 87 97 1 63 77 7

G 8 95 11 1 99 14 1 30

T 6 1 0 0 0 18 6 14

---

# M0004_1.02

A 15 3 2 2 0 6 16 49

C 72 1 87 97 1 63 77 7

G 8 95 11 1 99 14 1 30

T 6 1 0 0 0 18 6 14

however beel2meme does not work on both cases, do you know what the problem would be? many thanks

[kws15]

Ah no worries, i think i have worked out why, it s because of the space behind the # , thanks anyways