Last Change: 2018-09-07, 16:50
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garnier − Predicts protein secondary structure
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garnier −sequence seqall −idc integer −outfile report |
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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 (http://bugs.debian.org/emboss), or directly to the EMBOSS developers (http://sourceforge.net/tracker/?group_id=93650&atid=605031).
garnier is fully documented via the tfm(1) system.
Debian−Med Packaging Team <debian−med−packaging@lists.alioth.debian.org>
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Wrote the script used to autogenerate this manual page. |
Copyright © 2007 Debian-Med Packaging Team
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.