| 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