Logos building from pwm (help)

Question

[bpz]

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

[bpz]

Does anyone knows how the transfac format looks like? Thanks

[Alex Reynolds]

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

[bpz]

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.

[pld]

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.

[bpz]

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

[Jean-Karim Heriche]

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.

[bpz]

Hi

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

[Alex Reynolds]

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

[Jean-Karim Heriche]

Maybe this one although the package documentation seems pretty clear.

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

Answer 1

[Jean-Karim Heriche]

Try the seqLogo R Bioconductor package.

Answer 2

[Paul A. Gagniuc]

Try:

MAKE LOGO FROM MATRICES version 1

MAKE LOGO FROM MATRICES version 2

MAKE LOGO FROM MATRICES version 3