Question: meme text format
0
gravatar for Assa Yeroslaviz
6.1 years ago by
Assa Yeroslaviz1.3k
Munich
Assa Yeroslaviz1.3k wrote:

Hi I amtrying to run fimo form the meme suite but can't make my sequence file readble.

 

I keep getting the error

>fimo motif ~/fastA.txt

There were no convincing matches to any MEME Suite motif format.
FATAL: No motifs could be read.

I am trying to run fimo with the motif file in text format. From the example file of meme i constructed my motif as a regular expression in such a form:

[ACTG][ACTG]TTC[CT][AG][CT]GAA[ACTG][ACTG]

do I need to add more information to the file

why can't fimo read my file?

 

thanks

Assa

text format meme fimo • 3.0k views
ADD COMMENTlink modified 6.1 years ago by dariober11k • written 6.1 years ago by Assa Yeroslaviz1.3k
2
gravatar for dariober
6.1 years ago by
dariober11k
WCIP | Glasgow | UK
dariober11k wrote:

I think fimo doesn't explicitly take a regular expression. You have to create a meme file format like in this example:

MEME version 4

ALPHABET= ACGT

strands: + -

Background letter frequencies
A 0.303 C 0.183 G 0.209 T 0.306 

MOTIF crp
letter-probability matrix: alength= 4 w= 19 nsites= 17 E= 4.1e-009 
 0.000000  0.176471  0.000000  0.823529 
 0.000000  0.058824  0.647059  0.294118 
 0.000000  0.058824  0.000000  0.941176 
 0.176471  0.000000  0.764706  0.058824 
 0.823529  0.058824  0.000000  0.117647 
 0.294118  0.176471  0.176471  0.352941 
 0.294118  0.352941  0.235294  0.117647 
 0.117647  0.235294  0.352941  0.294118 
 0.529412  0.000000  0.176471  0.294118 
 0.058824  0.235294  0.588235  0.117647 
 0.176471  0.235294  0.294118  0.294118 
 0.000000  0.058824  0.117647  0.823529 
 0.058824  0.882353  0.000000  0.058824 
 0.764706  0.000000  0.176471  0.058824 
 0.058824  0.882353  0.000000  0.058824 
 0.823529  0.058824  0.058824  0.058824 
 0.176471  0.411765  0.058824  0.352941 
 0.411765  0.000000  0.000000  0.588235 
 0.352941  0.058824  0.000000  0.588235 

MOTIF lexA
letter-probability matrix: alength= 4 w= 18 nsites= 14 E= 3.2e-035 
 0.214286  0.000000  0.000000  0.785714 
 0.857143  0.000000  0.071429  0.071429 
 0.000000  1.000000  0.000000  0.000000 
 0.000000  0.000000  0.000000  1.000000 
 0.000000  0.000000  1.000000  0.000000 
 0.000000  0.000000  0.000000  1.000000 
 0.857143  0.000000  0.071429  0.071429 
 0.000000  0.071429  0.000000  0.928571 
 0.857143  0.000000  0.071429  0.071429 
 0.142857  0.000000  0.000000  0.857143 
 0.571429  0.071429  0.214286  0.142857 
 0.285714  0.285714  0.000000  0.428571 
 1.000000  0.000000  0.000000  0.000000 
 0.285714  0.214286  0.000000  0.500000 
 0.428571  0.500000  0.000000  0.071429 
 0.000000  1.000000  0.000000  0.000000 
 1.000000  0.000000  0.000000  0.000000 
 0.000000  0.000000  0.785714  0.214286
ADD COMMENTlink modified 6 months ago by RamRS27k • written 6.1 years ago by dariober11k

But how do I convert my motif into meme format? I don't have any probabilities.

ADD REPLYlink written 6.1 years ago by Assa Yeroslaviz1.3k

I guess you could assign 0 probability to the letters to exclude and equal probs to those to include. E.g. to represent [AG] you would put a row with "0.5 0 0.5 0" (where the alphabet is ACGT).

ADD REPLYlink written 6.1 years ago by dariober11k

Yes this works. Thanks!

What do I do about the background frequencies? How are they being calculated here? Is it a separte background list I need to use or are they calculated from the frequencies of the list?

ADD REPLYlink written 6.1 years ago by Assa Yeroslaviz1.3k
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