ODDCOMP(1e) | EMBOSS Manual for Debian | ODDCOMP(1e) |
NAME¶
oddcomp - Identify proteins with specified sequence word compositionSYNOPSIS¶
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 infileThis 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 toggleSet 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 booleanThe 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 outfileThis is the results file.
BUGS¶
Bugs can be reported to the Debian Bug Tracking system (http://bugs.debian.org/emboss), or directly to the EMBOSS developers (http://sourceforge.net/tracker/?group_id=93650&atid=605031).SEE ALSO¶
oddcomp is fully documented via the tfm(1) system.AUTHOR¶
Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>Wrote the script used to autogenerate this
manual page.
COPYRIGHT¶
This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package. It can be redistributed under the same terms as EMBOSS itself.05/11/2012 | EMBOSS 6.4.0 |