oddcomp1e
Identify proteins with specified sequence word composition
Usage
oddcomp -sequence
seqall
-infile
infile
-fullwindow
toggle
-window
integer
-ignorebz
boolean
-outfile
outfile
oddcomp -help
Overview
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.
Releases
9 releases since Debian 5.0 (Lenny); the text changed 2 times.