Question: Logos building from pwm (help)
0
gravatar for bpz
12 weeks ago by
bpz0
Mexico
bpz0 wrote:

Hello everyone

Maybe this is very simple, but I can't find a way to do it. I need to build a logos from a position weight matrix (pwm), I am trying to use WEBLOGO, the manual says it accepts MSAs and PWMs, but I can only find the way to upload alignments. I just have a pwm:

Frequencies: A, C, G, T E-value: 2.49E-05

X   
0.0096 0.9712 0.0096 0.0096 
0.9712 0.0096 0.0096 0.0096 
0.0096 0.9712 0.0096 0.0096 
0.9712 0.0096 0.0096 0.0096 
0.0096 0.9712 0.0096 0.0096 
0.9712 0.0096 0.0096 0.0096 
0.1695 0.5861 0.1254 0.119  
0.4977 0.1948 0.1401 0.1674

Can anyone point me to the right direction? Thanks

dna logos pwm • 342 views
ADD COMMENTlink modified 11 weeks ago • written 12 weeks ago by bpz0

Does anyone knows how the transfac format looks like? Thanks

ADD REPLYlink written 12 weeks ago by bpz0

The format looks like this:

AC   M00223
XX
ID   V$STAT_01
XX
DT   29.11.1995 (created); ewi.
DT   11.03.2003 (updated); dtc.
CO   Copyright (C), Biobase GmbH.
XX
NA   STATx
XX
DE   signal transducers and activators of transcription
XX
BF   T01575 STAT1alpha; Species: mouse, Mus musculus.
BF   T01492 STAT1alpha; Species: human, Homo sapiens.
BF   T01573 STAT1beta; Species: human, Homo sapiens.
XX
PO      A      C      G      T
01      0      0      0     14      T
02      0      0      0     14      T
03      2     12      0      0      C
04      0     12      0      2      C
05      0      9      2      3      C
06      4      2      8      0      G
07      0      0      8      6      K
08     13      1      0      0      A
09     14      0      0      0      A
XX
BA   14 genomic sequences of 14 different genes
XX
CC   compiled sequences
XX
RN   [1]; RE0003481.
RX   PUBMED: 7774815.
RA   Horvath C. M., Wen Z., Darnell jr J. E.
RT   A STAT protein domain that determines DNA sequence recognition suggests a novel DNA-binding domain
RL   Genes Dev. 9:984-994 (1995).
XX
ADD REPLYlink modified 12 weeks ago • written 12 weeks ago by Alex Reynolds17k

Mmm, I only have the pwm as I showed it. Does anyone knows how can I convert it into transfac format? or how can I get a logos from the data I have?

Thanks in advance.

ADD REPLYlink written 11 weeks ago by bpz0

http://meme-suite.org/doc/transfac-format.html

The transfac format looks fairly simple, I'd just convert it by hand unless you have a huge number of motifs to process.

ADD REPLYlink written 11 weeks ago by pld4.4k

I have 48 motifs to prepare. I think I can convert them by hand.

ADD REPLYlink written 11 weeks ago by bpz0

Have you tried my suggestion i.e. the seqLogo package ? It does exactly this: make a sequence logo from a position weight matrix. If this is not what you want, please clarify.

ADD REPLYlink written 11 weeks ago by Jean-Karim Heriche7.9k

Hi

Yes, that is exactly what I want. I will check seqlogo. Can you recommend a tutorial for it?

ADD REPLYlink written 11 weeks ago by bpz0
1

http://davetang.org/muse/2013/01/30/sequence-logos-with-r/

ADD REPLYlink written 11 weeks ago by Alex Reynolds17k

Maybe this one although the package documentation seems pretty clear.

EDIT: Just realized this is the same link as above.

ADD REPLYlink modified 11 weeks ago • written 11 weeks ago by Jean-Karim Heriche7.9k
0
gravatar for Jean-Karim Heriche
12 weeks ago by
EMBL Heidelberg, Germany
Jean-Karim Heriche7.9k wrote:

Try the seqLogo R Bioconductor package.

ADD COMMENTlink written 12 weeks ago by Jean-Karim Heriche7.9k
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