This is the command garniere that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator
PROGRAM:
NAME
garnier - Predicts protein secondary structure using GOR method
SYNOPSIS
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 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
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