This is the command oddcompe that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator
PROGRAM:
NAME
oddcomp - Identify proteins with specified sequence word composition
SYNOPSIS
oddcomp -sequence seqall -infile infile -fullwindow toggle -window integer
-ignorebz boolean -outfile outfile
oddcomp -help
DESCRIPTION
oddcomp is a command line program from EMBOSS (“the European Molecular Biology Open
Software Suite”). It is part of the "Protein:Composition" command group(s).
OPTIONS
Input section
-sequence seqall
-infile infile
This is a file in the format of the output produced by 'compseq' that is used to set
the minimum frequencies of words in this analysis.
Required section
-fullwindow toggle
Set this option on (Y) if you want the window size to be set to the length of the
current protein. Otherwise, leave this option unset, in which case you'll be prompted
for a window size to use. Default value: N
-window integer
This is the size of window in which to count. Thus if you want to count frequencies in
a 40 aa stretch you should enter 40 here. Default value: 30
Advanced section
-ignorebz boolean
The amino acid code B represents Asparagine or Aspartic acid and the code Z represents
Glutamine or Glutamic acid. These are not commonly used codes and you may wish not to
count words containing them, just noting them in the count of 'Other' words. Default
value: Y
Output section
-outfile outfile
This is the results file.
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