plot_seqlogo
plot_seqlogo generates a sequence logo from aligned sequences in the stream. The bit scores are calculated using Shannon's famous general formula for uncertainty as documentet:
http://www.ccrnp.ncifcrf.gov/~toms/paper/hawaii/latex/node5.html
The maximum bit score is 2 and 4 for nucleotide and protein sequences, respectively.
The sequence logo is output in SVG (Scalable Vector Graphics) and you need a SVG viewer to see the plot such as Firefox or Inskape (Inkscape can also be used to modify the resulting image).
Read more about Inkscape here:
... | plot_seqlogo [options]
[-? | --help] # Print full usage description.
[-x | --no_stream] # Do not emit records.
[-o <file> | --data_out=<file>] # Write result to file.
[-I <file!> | --stream_in=<file!>] # Read input from stream file - Default=STDIN
[-O <file> | --stream_out=<file>] # Write output to stream file - Default=STDOUT
[-v | --verbose] # Verbose output.
To read an alignment from file in FASTA format, use read_fasta and to create a sequence logo pipe the stream to plot_seqlogo:
read_fasta -i align.fna | plot_seqlogo -xo seqlogo.svg
And the result will look like this:
Martin Asser Hansen - Copyright (C) - All rights reserved.
August 2007
GNU General Public License version 2
http://www.gnu.org/copyleft/gpl.html
plot_seqlogo is part of the Biopieces framework.