
                                  garnier 



Function

   Predicts protein secondary structure

Description

   This is an implementation of the original Garnier Osguthorpe Robson
   algorithm (GOR I) for predicting protein secondary structure.

   Secondary structure prediction is notoriously difficult to do
   accurately. The GOR I alogorithm is one of the first semi-successful
   methods.

   The Garnier method is not regarded as the most accurate prediction,
   but is simple to calculate on most workstations.

   The accuracy of any secondary structure prediction program is not much
   better than 70% to 80% at best. This is an early algorithm and will
   probably not predict with much better than about 65% accuracy.

   The Web servers for PHD, DSC, and others are generally preferred.

   Do not rely on this (or any other) program alone to make your
   predictions with. Use several programs and take a consensus of the
   results.

Usage

   Here is a sample session with garnier


% garnier 
Predicts protein secondary structure
Input sequence(s): tsw:amic_pseae
Output report [amic_pseae.garnier]: 

   Go to the input files for this example
   Go to the output files for this example

Command line arguments

   Standard (Mandatory) qualifiers:
  [-sequence]          seqall     Sequence database USA
  [-outfile]           report     Output report file name

   Additional (Optional) qualifiers: (none)
   Advanced (Unprompted) qualifiers:
   -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.

   Associated qualifiers:

   "-sequence" associated qualifiers
   -sbegin1             integer    Start of each sequence to be used
   -send1               integer    End of each sequence to be used
   -sreverse1           boolean    Reverse (if DNA)
   -sask1               boolean    Ask for begin/end/reverse
   -snucleotide1        boolean    Sequence is nucleotide
   -sprotein1           boolean    Sequence is protein
   -slower1             boolean    Make lower case
   -supper1             boolean    Make upper case
   -sformat1            string     Input sequence format
   -sdbname1            string     Database name
   -sid1                string     Entryname
   -ufo1                string     UFO features
   -fformat1            string     Features format
   -fopenfile1          string     Features file name

   "-outfile" associated qualifiers
   -rformat2            string     Report format
   -rname2              string     Base file name
   -rextension2         string     File name extension
   -rdirectory2         string     Output directory
   -raccshow2           boolean    Show accession number in the report
   -rdesshow2           boolean    Show description in the report
   -rscoreshow2         boolean    Show the score in the report
   -rusashow2           boolean    Show the full USA in the report

   General qualifiers:
   -auto                boolean    Turn off prompts
   -stdout              boolean    Write standard output
   -filter              boolean    Read standard input, write standard output
   -options             boolean    Prompt for standard and additional values
   -debug               boolean    Write debug output to program.dbg
   -verbose             boolean    Report some/full command line options
   -help                boolean    Report command line options. More
                                  information on associated and general
                                  qualifiers can be found with -help -verbose
   -warning             boolean    Report warnings
   -error               boolean    Report errors
   -fatal               boolean    Report fatal errors
   -die                 boolean    Report deaths


   Standard (Mandatory) qualifiers Allowed values Default
   [-sequence]
   (Parameter 1) Sequence database USA Readable sequence(s) Required
   [-outfile]
   (Parameter 2) Output report file name Report output file
   Additional (Optional) qualifiers Allowed values Default
   (none)
   Advanced (Unprompted) qualifiers Allowed values Default
   -idc 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. Integer from 0 to 6 0

   The meaning and use of the parameter 'idc' is currently being
   investigated. The original author, Bill Pearson writes:

   "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. I don't remember what they are, but I must
   have gotten the values from their paper."

Input file format

   garnier read any protein sequence USA.

  Input files for usage example

   'tsw:amic_pseae' is a sequence entry in the example protein database
   'tsw'

  Database entry: tsw:amic_pseae

ID   AMIC_PSEAE     STANDARD;      PRT;   384 AA.
AC   P27017;
DT   01-AUG-1992 (Rel. 23, Created)
DT   01-DEC-1992 (Rel. 24, Last sequence update)
DT   15-DEC-1998 (Rel. 37, Last annotation update)
DE   ALIPHATIC AMIDASE EXPRESSION-REGULATING PROTEIN.
GN   AMIC.
OS   Pseudomonas aeruginosa.
OC   Bacteria; Proteobacteria; gamma subdivision; Pseudomonas group;
OC   Pseudomonas.
RN   [1]
RP   SEQUENCE FROM N.A., AND SEQUENCE OF 1-18.
RC   STRAIN=PAC;
RX   MEDLINE; 91317707.
RA   WILSON S.A., DREW R.E.;
RT   "Cloning and DNA sequence of amiC, a new gene regulating expression
RT   of the Pseudomonas aeruginosa aliphatic amidase, and purification of
RT   the amiC product.";
RL   J. Bacteriol. 173:4914-4921(1991).
RN   [2]
RP   X-RAY CRYSTALLOGRAPHY.
RX   MEDLINE; 92106343.
RA   WILSON S.A., CHAYEN N.E., HEMMINGS A.M., DREW R.E., PEARL L.H.;
RT   "Crystallization of and preliminary X-ray data for the negative
RT   regulator (AmiC) of the amidase operon of Pseudomonas aeruginosa.";
RL   J. Mol. Biol. 222:869-871(1991).
RN   [3]
RP   X-RAY CRYSTALLOGRAPHY (2.1 ANGSTROMS).
RX   MEDLINE; 95112789.
RA   PEARL L.H., O'HARA B., DREW R.E., WILSON S.A.;
RT   "Crystal structure of AmiC: the controller of transcription
RT   antitermination in the amidase operon of Pseudomonas aeruginosa.";
RL   EMBO J. 13:5810-5817(1994).
CC   -!- FUNCTION: NEGATIVELY REGULATES THE EXPRESSION OF THE ALIPHATIC
CC       AMIDASE OPERON. AMIC FUNCTIONS BY INHIBITING THE ACTION OF AMIR
CC       AT THE PROTEIN LEVEL. IT BINDS TO AMIR. IT EXHIBITS PROTEIN KINASE
CC       ACTIVITY.
CC   -!- SUBUNIT: HOMODIMER.
CC   -!- DOMAIN: CONSISTS OF TWO BETA-ALPHA-BETA DOMAINS WITH A CENTRAL
CC       CLEFT IN WHICH THE AMIDE BINDS.
CC   --------------------------------------------------------------------------
CC   This SWISS-PROT entry is copyright. It is produced through a collaboration
CC   between  the Swiss Institute of Bioinformatics  and the  EMBL outstation -
CC   the European Bioinformatics Institute.  There are no  restrictions on  its
CC   use  by  non-profit  institutions as long  as its content  is  in  no  way
CC   modified and this statement is not removed.  Usage  by  and for commercial
CC   entities requires a license agreement (See http://www.isb-sib.ch/announce/
CC   or send an email to license@isb-sib.ch).
CC   --------------------------------------------------------------------------
DR   EMBL; X13776; CAA32024.1; -.
DR   PIR; A40359; A40359.
DR   PDB; 1PEA; 03-APR-96.
KW   Transferase; Kinase; Repressor; 3D-structure.
FT   INIT_MET      0      0
SQ   SEQUENCE   384 AA;  42704 MW;  68FF861F CRC32;
     GSHQERPLIG LLFSETGVTA DIERSHAYGA LLAVEQLNRE GGVGGRPIET LSQDPGGDPD
     RYRLCAEDFI RNRGVRFLVG CYMSHTRKAV MPVVERADAL LCYPTPYEGF EYSPNIVYGG
     PAPNQNSAPL AAYLIRHYGE RVVFIGSDYI YPRESNHVMR HLYRQHGGTV LEEIYIPLYP
     SDDDLQRAVE RIYQARADVV FSTVVGTGTA ELYRAIARRY GDGRRPPIAS LTTSEAEVAK
     MESDVAEGQV VVAPYFSSID TPASRAFVQA CHGFFPENAT ITAWAEAAYW QTLLLGRAAQ
     AAGNWRVEDV QRHLYDIDID APQGPVRVER QNNHSRLSSR IAEIDARGVF QVRWQSPEPI
     RPDPYVVVHN LDDWSASMGG GPLP
//

Output file format

   The output is a standard EMBOSS report file.

   The results can be output in one of several styles by using the
   command-line qualifier -rformat xxx, where 'xxx' is replaced by the
   name of the required format. The available format names are: embl,
   genbank, gff, pir, swiss, trace, listfile, dbmotif, diffseq, excel,
   feattable, motif, regions, seqtable, simple, srs, table, tagseq

   See: http://emboss.sf.net/docs/themes/ReportFormats.html for further
   information on report formats.

   By default garnier writes a 'tagseq' report file.

  Output files for usage example

  File: amic_pseae.garnier

########################################
# Program: garnier
# Rundate: Thu Jul 15 2004 12:00:00
# Report_format: tagseq
# Report_file: amic_pseae.garnier
########################################

#=======================================
#
# Sequence: AMIC_PSEAE     from: 1   to: 384
# HitCount: 111
#
# DCH = 0, DCS = 0
#
#  Please cite:
#  Garnier, Osguthorpe and Robson (1978) J. Mol. Biol. 120:97-120
#
#
#=======================================

          .   10    .   20    .   30    .   40    .   50
      GSHQERPLIGLLFSETGVTADIERSHAYGALLAVEQLNREGGVGGRPIET
helix                   HHHHHHHHHHHHHHHHHHH
sheet      EE EEEEE                                 EEEE
turns        T                              TTTT
 coil CCCCC        CCCCC                   C    CCCC
          .   60    .   70    .   80    .   90    .  100
      LSQDPGGDPDRYRLCAEDFIRNRGVRFLVGCYMSHTRKAVMPVVERADAL
helix               HHHHHH            HHHH H     HHHHHH
sheet E         EEEE           EEEE          EEEE      E
turns  TT TT   T          TTTTT    TTT    T T
 coil    C  CCC
          .  110    .  120    .  130    .  140    .  150
      LCYPTPYEGFEYSPNIVYGGPAPNQNSAPLAAYLIRHYGERVVFIGSDYI
helix                              HHH
sheet EEE    E       EE           E   EEEE    EEEEE
turns       T TTT  TT  T     TT           TT T     TTTT
 coil    CCC     CC     CCCCC  CCC          C          C
          .  160    .  170    .  180    .  190    .  200
      YPRESNHVMRHLYRQHGGTVLEEIYIPLYPSDDDLQRAVERIYQARADVV
helix       HHHH                       HHHHHHHHHHHHH
sheet           EEE       EEEEEEE                   EEEE
turns   TTT        TTT             TTTT
 coil CC   C          CCCC       CC
          .  210    .  220    .  230    .  240    .  250
      FSTVVGTGTAELYRAIARRYGDGRRPPIASLTTSEAEVAKMESDVAEGQV
helix          HHHHHHH                HHHHHHHHHHHHHHHHH
sheet EEEE            EE         EEE                   E
turns                   TTTTTT
 coil     CCCCC               CCC   CC
          .  260    .  270    .  280    .  290    .  300
      VVAPYFSSIDTPASRAFVQACHGFFPENATITAWAEAAYWQTLLLGRAAQ
helix               HHHH           HHHHHHHHHHHHH    HHHH
sheet EEEE   E          EE                      E
turns     TTT T   T       TTT   TT
 coil          CCC C         CCC  C              CCC
          .  310    .  320    .  330    .  340    .  350
      AAGNWRVEDVQRHLYDIDIDAPQGPVRVERQNNHSRLSSRIAEIDARGVF
helix       HHHHHHH                             HHH
sheet              E  EEEE     EEEEE         EEE      EE
turns               TT     T        TT   T         TTT
 coil CCCCCC              C CCC       CCC CCC
          .  360    .  370    .  380
      QVRWQSPEPIRPDPYVVVHNLDDWSASMGGGPLP
helix
sheet EE           EEEEEEE     E
turns   TT    TT           TTT  TTT
 coil     CCCC  CCC       C   C    CCCCC

#---------------------------------------
#
#  Residue totals: H:111   E: 98   T: 81   C: 94
#         percent: H: 30.2 E: 26.6 T: 22.0 C: 25.5
#
#---------------------------------------

Data files

   None.

Notes

   The Garnier method is not regarded as the most accurate prediction,
   but is simple to calculate on most workstations.

   The Web servers for PHD, DSC, and others are generally preferred.

   Do not rely on this (or any other) program alone to make your
   predictions with. Use several programs and take a consensus of the
   results.

   The 3D structure for the example sequence is known, although the 2D
   structure elements were not in the SwissProt feature table for release
   38 when the test data was extracted.

   DSSP shows:
 From     To   Structure
    9     13   E beta sheet
   21     39   H alpha helix
   50     54   E beta sheet
   60     72   H alpha helix
   78     81   E beta sheet
   85     97   H alpha helix
  101    104   E beta sheet
  117    119   E beta sheet
  128    136   H alpha helix
  142    148   E beta sheet
  151    166   H alpha helix
  170    177   E beta sheet
  183    196   H alpha helix
  200    204   E beta sheet
  208    221   H alpha helix
  229    231   E beta sheet
  236    239   H alpha helix
  244    247   H alpha helix
  251    254   E beta sheet
  263    273   H alpha helix
  284    303   H alpha helix
  308    315   H alpha helix
  320    322   E beta sheet
  325    329   E beta sheet
  336    337   E beta sheet
  341    345   E beta sheet
  351    356   E beta sheet

References

    1. Garnier J, Osguthorpe DJ, Robson B Analysis of the accuracy and
       implications of simple methods for predicting the secondary
       structure of globular proteins. J Mol Biol 1978 Mar
       25;120(1):97-120

Warnings

   The accuracy of any secondary structure prediction program is not much
   better than 70% to 80% at best. This is an early algorithm and will
   probably not predict with much better than about 65% accuracy.

   You are advised to use several of the latest Web-based prediction
   sites and combine them to make a consensus prediction.

Diagnostic Error Messages

   None.

Exit status

   It always exits with a status of 0.

Known bugs

   None.

See also

    Program name             Description
   helixturnhelix Report nucleic acid binding motifs
   hmoment        Hydrophobic moment calculation
   pepcoil        Predicts coiled coil regions
   pepnet         Displays proteins as a helical net
   pepwheel       Shows protein sequences as helices
   tmap           Displays membrane spanning regions

Author(s)

   This program ('GARNIER') was originally written by William Pearson
   (wrp@virginia.edu) and released as part of his FASTA package.

   This application was modified for inclusion in EMBOSS by Rodrigo Lopez
   (rls © ebi.ac.uk)
   European Bioinformatics Institute, Wellcome Trust Genome Campus,
   Hinxton, Cambridge CB10 1SD, UK

History

Target users

   This program is intended to be used by everyone and everything, from
   naive users to embedded scripts.

Comments

   None
