Question: How toconvert a set of motif consensus sequences in IUPAC to meme format?
0
gravatar for ilovesuperheroes1993
8 weeks ago by
ilovesuperheroes19930 wrote:

I am trying to run FIMO from MEME Suite to to search for occurrences of a list of motifs in my DNA sequences. The list of motifs are present in IUPAC format, given by their consensus sequences. I have a text file containing the motif name followed by its consensus sequence or Sequence logo as given below:

>AHR_HUMAN.H11MO.0.B
dKhGCGTGh
>ALX1_HUMAN.H11MO.0.B
vTRATYGnATTA
>ANDR_HUMAN.H11MO.0.A
WKThYYddbhTRTTTRYh
>ANDR_HUMAN.H11MO.1.A
dGnACWbTbWGTdCYb

and so on.

I am trying to run FIMO, which expects the motifs in meme format as input.

Can anyone tell me how to convert all the motifs to meme format in one step? I have about 100 motifs I need to scan, and I don't want to scan one motif at a time.

In the online server of Meme Suite, I can just paste the list of motifs (as given above) and it works. But that is awfully slow and I want to run it on my own server.

ADD COMMENTlink modified 8 weeks ago by shenwei3565.6k • written 8 weeks ago by ilovesuperheroes19930
1
gravatar for jared.andrews07
8 weeks ago by
jared.andrews077.9k
Memphis, TN
jared.andrews077.9k wrote:

They have a utility for that and converting from just about any other format as well..

ADD COMMENTlink written 8 weeks ago by jared.andrews077.9k

Yes there is the iupac2meme utility.

iupac2meme Usage: iupac2meme [options] <consensus_sequence>+ It works fine if I type in a single motif sequence at a time. How do I use this for multiple motifs in one go?

ADD REPLYlink written 8 weeks ago by ilovesuperheroes19930
1

Using a for or while loop. See this stackoverflow answer for details.

ADD REPLYlink written 8 weeks ago by jared.andrews077.9k
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