Question: seqlogo WebLogo difference
0
gravatar for biotech
2.4 years ago by
biotech540
United States
biotech540 wrote:

I installed Weblogo via command line:

brew install WebLogo

But seems what has been installed is another program:

ls /usr/local/Cellar/weblogo/2.8.2/bin
        seqlogo

seqlogo is a Bioconductor package. Is it the same that the one I installed via brew?

https://www.bioconductor.org/packages/release/bioc/html/seqLogo.html

Thanks

brew • 552 views
ADD COMMENTlink written 2.4 years ago by biotech540
1

Those appear to be two separate programs:

Bembom O (2016). seqLogo: Sequence logos for DNA sequence alignments. R package version 1.40.0.

and

Crooks GE, Hon G, Chandonia JM, Brenner SE WebLogo: A sequence logo generator, Genome Research, 14:1188-1190, (2004)

The executable for the weblogo program appears to be named seqlogo as seen from your ls command.

ADD REPLYlink modified 2.4 years ago • written 2.4 years ago by genomax70k

It's curious an R program has been converted to run in the shell. For seqLogo, just can find the program instructions for R version.

ADD REPLYlink written 2.4 years ago by biotech540

Run /usr/local/Cellar/weblogo/2.8.2/bin/seqlogo -h (or -help) and see what you get. There should be some in-line help. WebLogo is 10+ years older than the R package.

ADD REPLYlink modified 2.4 years ago • written 2.4 years ago by genomax70k
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