EMBOSS: garnier

| ## EMBOSS: garnier

# Program 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
    Input sequence: sw:amic_pseae
    Output file [amic_pseae.garnier]:

## Command line arguments

       Mandatory qualifiers:
      [-sequencea]         seqall     Sequence database USA
      [-outfile]           report     (no help text) report value

       Optional qualifiers: (none)
       Advanced qualifiers:
       -idc                integer    idc param

       General qualifiers:
      -help                bool       report command line options. More
                                      information on associated and general
                                      qualifiers can be found with -help -verbose

Mandatory qualifiers | Allowed values | Default
--- | --- | ---
[-sequencea] (Parameter 1) | Sequence database USA | Readable sequence(s) | Required
[-outfile] (Parameter 2) | (no help text) report value | Report file |
Optional qualifiers | Allowed values | Default
(none)
Advanced qualifiers | Allowed values | Default
-idc | idc param | 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

Any protein sequence.

## 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://www.uk.embnet.org/Software/EMBOSS/Themes/ReportFormats.html for further information on report formats.

By default garnier writes a 'tagseq' report file.

Here is the output from the example run.

    ########################################
    # Program: garnier
    # Rundate: Mon Feb 11 13:42:25 2002
    # Report_file: amic_pseae.garnier
    ########################################

    #=======================================
    #
    # Sequence: AMIC_PSEAE     from: 1   to: 384
    # HitCount: 113
    #
    # DCH = 0, DCS = 0
    #
    #  Please cite:
    #  Garnier, Osguthorpe and Robson (1978) J. Mol. Biol. 120:97-120
    #
    #
    #
    #=======================================

              .   10    .   20    .   30    .   40    .   50
          GSHQERPLIGLLFSETGVTADIERSQRYGALLAVEQLNREGGVGGRPIET
    helix                    HHHHH        HHHHH
    sheet      EE EEEEE                 EE              EEEE
    turns        T                TTTT          TTTT
     coil CCCCC        CCCCCC         CC       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
          YPRESNHVMRHLYRQHGGTVLEEIYIPLYPSDDDVQRAVERIYQARADVV
    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
          VVAPYFSSIDTAASRAFVQACHGFFPENATITAWAEAAYWQTLLLGRAAQ
    helix            HHHHHHH           HHHHHHHHHHHHH    HHHH
    sheet EEEE  EEE         EE                      E
    turns     TT              TTT   TT
     coil          CC            CCC  C              CCC

              .  310    .  320    .  330    .  340    .  350
          AAGSWRVEDVQRHLYDICIDAPQGPVRVERQNNHSRLSSRIAEIDARGVF
    helix H     HHHH                                HHH
    sheet                 EEEE     EEEEE         EEE      EE
    turns           TTTTTT     T        TT   T         TTT
     coil  CCCCC              C CCC       CCC CCC

              .  360    .  370    .  380
          QVRWQSPEPIRPDPYVVVHNLDDWSASMGGGALP
    helix
    sheet EE           EEEEEEE     E       E
    turns   TT    TT           TTT   TTT

## 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

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 exist 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

None.

## Target users

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

## Comments