GARNIER(1e) | EMBOSS Manual for Debian | GARNIER(1e) |
NAME¶
garnier - Predicts protein secondary structure using GOR methodSYNOPSIS¶
garnier
-sequence seqall
-idc integer
-outfile report
garnier
-help
DESCRIPTION¶
garnier is a command line program from EMBOSS (“the European Molecular Biology Open Software Suite”). It is part of the "Protein:2D Structure" command group(s).OPTIONS¶
Input section¶
-sequence seqallAdvanced section¶
-idc integerIn their paper, GOR mention that if you know
something about the secondary structure content of the protein you are
analyzing, you can do better in prediction. 'idc' is an index into a set of
arrays, dharr[] and dsarr[], which provide 'decision constants' (dch, dcs),
which are offsets that are applied to the weights for the helix and sheet
(extend) terms. So, idc=0 says don't use the decision constant offsets, and
idc=1 to 6 indicates that various combinations of dch,dcs offsets should be
used.
Output section¶
-outfile reportBUGS¶
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¶
garnier 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 |