motif database format for tomtom
1
0
Entering edit mode
6.7 years ago
kws15 ▴ 40

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

meme suite tomtom • 1.7k views
ADD COMMENT
0
Entering edit mode
6.7 years ago
Girolamo ▴ 140

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.

ADD COMMENT
0
Entering edit mode

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

ADD REPLY
0
Entering edit mode

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

ADD REPLY

Login before adding your answer.

Traffic: 1317 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6