Convert a DNA sequence to MEME format
0
0
Entering edit mode
10 weeks ago
tianshenbio ▴ 110

Hi,

I am trying to search a simple DNA sequence motif, TATCTA, in a large fasta file using FIMO. First I need to generate a meme file to use for that. So I tried:

iupac2meme TATCTA >motif.meme

Then I got the file:

MEME version 4

ALPHABET= ACGT

strands: + -

Background letter frequencies (from uniform background):
A 0.25000 C 0.25000 G 0.25000 T 0.25000 

MOTIF TATCTA TAGATA

letter-probability matrix: alength= 4 w= 6 nsites= 20 E= 0
  0.000000    0.000000    0.000000    1.000000  
  1.000000    0.000000    0.000000    0.000000  
  0.000000    0.000000    0.000000    1.000000  
  0.000000    1.000000    0.000000    0.000000  
  0.000000    0.000000    0.000000    1.000000  
  1.000000    0.000000    0.000000    0.000000

I noticed that the 'motif' here includes both the forward and reverse sequences, is that a problem since I only want to search the forward one?

FIMO fasta motif MEME-suite format conversion • 251 views
ADD COMMENT
0
Entering edit mode

FIMO help page says

If a motif has the strand feature set to +/- (rather than +), then FIMO will search both strands for occurrences.

So you may simple need to remove - to search only forward strand.

ADD REPLY

Login before adding your answer.

Traffic: 1291 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