Logos building from pwm (help)
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5.5 years ago
bpz ▴ 60

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

Logos pwm dna • 5.6k views
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Does anyone knows how the transfac format looks like? Thanks

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The format looks like this:

AC   M00223
XX
ID   V\$STAT_01
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DT   29.11.1995 (created); ewi.
DT   11.03.2003 (updated); dtc.
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NA   STATx
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DE   signal transducers and activators of transcription
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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
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CC   compiled sequences
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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

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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?

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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.

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

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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.

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Hi

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

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Maybe this one although the package documentation seems pretty clear.

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

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5.5 years ago

Try the seqLogo R Bioconductor package.

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4 months ago