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 |