Question: Is it possible to convert Minimal MEME Motif Format to PFMatrix
0
gravatar for guandongshang
17 months ago by
guandongshang0 wrote:

Hi,Guys I am wondering whehter I can convert the result of MEME sutie like

MEME version 4.4

ALPHABET= ACGT

strands: + -

Background letter frequencies (from file `../../promoter_background/Ath.bg'):
A 0.33230 C 0.16770 G 0.16770 T 0.33230

MOTIF AT1G01060 MP00119

letter-probability matrix: alength= 4 w= 10 nsites= 599 E= 4.8e-803
  0.854758      0.001669      0.051753      0.091820   
  0.000000      0.000000      1.000000      0.000000   
  1.000000      0.000000      0.000000      0.000000   
  0.000000      0.000000      0.000000      1.000000   
  0.996661      0.003339      0.000000      0.000000   
  0.000000      0.013356      0.008347      0.978297   
  0.005008      0.000000      0.005008      0.989983   
  0.085142      0.010017      0.000000      0.904841   
  0.287145      0.076795      0.056761      0.579299   
  0.188648      0.240401      0.195326      0.375626   

URL http://planttfdb.cbi.pku.edu.cn/tf.php?sp=Ath&did=AT1G01060.1#bind_motif

to convert the PFMatrix like

Background: 
   A    C    G    T 
0.25 0.25 0.25 0.25 
Matrix: 
  [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8]
A   14    0   14    0    4    1    0    3
C    1    0    0    0    6    8    0    6
G    0   15    1    0    0    0    9    4
T    0    0    0   15    5    6    6    2

I search many site,but only I can find is that How to convert other fomart to MEME suite result. So I am wondering whether I can reverse change.

pfm meme motif • 496 views
ADD COMMENTlink modified 17 months ago by Mensur Dlakic9.1k • written 17 months ago by guandongshang0
1
gravatar for Mensur Dlakic
17 months ago by
Mensur Dlakic9.1k
USA
Mensur Dlakic9.1k wrote:

It is a matter of writing a simple script. You have all the information in MEME output such as background frequencies, motif width (10) and the number of sites (599). It would look something like this:

Background: 
   A    C    G    T 
0.33 0.17 0.17 0.33 
Matrix: 
  [,1] [,2] [,3]
A  512    0  599
C    1    0    0
G   31  599    0
T   55    0    0

I have done only the first three out of 10 positions, but you can do the rest by simple calculation.

EDIT: In case it is not obvious, we multiply each number in the letter matrix (say, 0.854758) by the number of sites (599) and round it to the nearest integer (512).

ADD COMMENTlink modified 17 months ago • written 17 months ago by Mensur Dlakic9.1k

Thanks!That's very clear.

ADD REPLYlink written 17 months ago by guandongshang0
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