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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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