Creating Sequence Logos From The Command Line

Question

[Qdjm]

What's your favourite way to create sequence logos from the command line or programmatically?

This is in response to a question at StackOverflow on making sequence logos in ggplot2. I looked here and was surprised that couldn't find the answer.

Ideally, the package would be easy to use but flexible enough to show different logo representations (e.g. scale height by frequency or by information content) and different alphabets (DNA, RNA, and amino acids).

We have our own way of doing this in the lab, and being a PI, I don't know what it is, but I would like to hear other options.

[Timtico]

if you want i can provide the sourcecode of my way of doing it (see my answer). However it might be a bif different of our approach as I use Perl scripts to build position weight matrices.

Answer 1

[Jeremy Leipzig]

There are some well-known problems with sequence logos, namely that the most frequent nucleotide gets top billing even if it is only a fraction more frequent than the runner-up.

Charles Berry developed an alternative that mitigates some of these issues.

An example is in this paper:

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1664696/

I can ask the programmer there to dig up the R code although it shouldn't be hard to replicate.

[Jeremy Leipzig]

OK here it is: https://github.com/leipzig/berryLogo

[Gww]

That is a really neat way to present sequence logos!

[Timtico]

would be really interested to obtain the R code, did you have any luck with that?

[Qdjm]

I agree with Timtico, this is cool, and I would like the code as well. We'll try it out. But not quite what I was looking for.

[Jeremy Leipzig]

i'll cook up some code that uses ggplot

[Timtico]

thanks for that, i will try it out asap!

Answer 2

[Timtico]

Use R and the packages seqLogo and Biostrings.

I used to use them to make perfect vectorised sequencelogos in PDF format.

Answer 3

[by0]

Check out RWebLogo. It's an R wrapper for the WebLogo python library. It can be downloaded from CRAN: http://cran.r-project.org/web/packages/RWebLogo/index.html

and is hosted on github: https://github.com/omarwagih/RWebLogo

Answer 4

[Casey Bergman]

We have tried WebLogo and SeqLogo, but ultimately wrote our own routines in R for maximal flexibility in terms of layout of plots and figures.

Answer 5

[puthier]

I would suggest RSAT that can also be used as a stand-alone application and which implements lots of unix commands for position weight matrix analysis.

http://rsat.ulb.ac.be/

Answer 6

[Paul A. Gagniuc]

Try an independent implementation from the motif set to the Sequence logo, or a direct offline application here: Make a Sequence Logo in your browser by using native Javascript