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GARNIER(1e) EMBOSS Manual for Debian GARNIER(1e)


garnier - Predicts protein secondary structure using GOR method


garnier -sequence seqall -idc integer -outfile report

garnier -help


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).


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


Bugs can be reported to the Debian Bug Tracking system (, or directly to the EMBOSS developers (


garnier is fully documented via the tfm(1) system.


Debian Med Packaging Team <>

Wrote the script used to autogenerate this manual page.


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