garnier1e
Predicts protein secondary structure using gor method
Usage
garnier -sequence
seqall
-idc
integer
-outfile
report
garnier -help
Overview
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 seqall
Advanced section
-
-idc integer -
In 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 report
Releases
9 releases since Debian 5.0 (Lenny); the text changed 2 times.