Convert a DNA sequence to MEME format

Question

[tianshenbio]

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?

[GenoMax]

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.