| garnier

## Wiki

The master copies of EMBOSS documentation are available at http://emboss.open-bio.org/wiki/Appdocs on the EMBOSS Wiki.

Please help by correcting and extending the Wiki pages.

## Function

Predict protein secondary structure using GOR method

## Description

garnier is an implementation of the original Garnier Osguthorpe Robson algorithm (GOR I) for predicting protein secondary structure. It reads an input protein sequence and writes a standard EMBOSS report file with the predicted secondary structure. The Garnier method is not regarded as the most accurate prediction, but is simple to calculate on most workstations.

## Algorithm

The '-idc' option sets offsets to the weights applied to the helix and sheet terms used in the GOR algorithm to assign a residue to a secondary structure state. The option has a value from 0 - 6. This gives 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.

## Usage

Here is a sample session with garnier

    % garnier
    Predict protein secondary structure using GOR method
    Input protein 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

    Predict protein secondary structure using GOR method
    Version: EMBOSS:6.6.0.0

       Standard (Mandatory) qualifiers:
      [-sequence]          seqall     Protein sequence(s) filename and optional
                                      format, or reference (input USA)
      [-outfile]           report     [*.garnier] Output report file name (default
                                      -rformat tagseq)

       Additional (Optional) qualifiers: (none)
       Advanced (Unprompted) qualifiers:
       -idc                integer    [0] 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)

       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
       -scircular1         boolean    Sequence is circular
       -squick1            boolean    Read id and sequence only
       -sformat1           string     Input sequence format
       -iquery1            string     Input query fields or ID list
       -ioffset1           integer    Input start position offset
       -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
       -rstrandshow2       boolean    Show the nucleotide strand in the report
       -rusashow2          boolean    Show the full USA in the report
       -rmaxall2           integer    Maximum total hits to report
       -rmaxseq2           integer    Maximum hits to report for one sequence

       General qualifiers:
       -auto               boolean    Turn off prompts
       -stdout             boolean    Write first file to standard output
       -filter             boolean    Read first file from standard input, write
                                      first file to 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 and exit. 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 dying program messages
       -version            boolean    Report version number and exit

Qualifier | Type | Description | Allowed values | Default
--- | --- | --- | --- | ---
Standard (Mandatory) qualifiers
[-sequence] (Parameter 1) | seqall | Protein sequence(s) filename and optional format, or reference (input USA) | Readable sequence(s) | Required
[-outfile] (Parameter 2) | report | Output report file name | (default -rformat tagseq) | <*>.garnier
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. | Integer from 0 to 6 | 0
Associated qualifiers
"-sequence" associated seqall qualifiers
-sbegin1 -sbegin_sequence | integer | Start of each sequence to be used | Any integer value | 0
-send1 -send_sequence | integer | End of each sequence to be used | Any integer value | 0
-sreverse1 -sreverse_sequence | boolean | Reverse (if DNA) | Boolean value Yes/No | N
-sask1 -sask_sequence | boolean | Ask for begin/end/reverse | Boolean value Yes/No | N
-snucleotide1 -snucleotide_sequence | boolean | Sequence is nucleotide | Boolean value Yes/No | N
-sprotein1 -sprotein_sequence | boolean | Sequence is protein | Boolean value Yes/No | N
-slower1 -slower_sequence | boolean | Make lower case | Boolean value Yes/No | N
-supper1 -supper_sequence | boolean | Make upper case | Boolean value Yes/No | N
-scircular1 -scircular_sequence | boolean | Sequence is circular | Boolean value Yes/No | N
-squick1 -squick_sequence | boolean | Read id and sequence only | Boolean value Yes/No | N
-sformat1 -sformat_sequence | string | Input sequence format | Any string |
-iquery1 -iquery_sequence | string | Input query fields or ID list | Any string |
-ioffset1 -ioffset_sequence | integer | Input start position offset | Any integer value | 0
-sdbname1 -sdbname_sequence | string | Database name | Any string |
-sid1 -sid_sequence | string | Entryname | Any string |
-ufo1 -ufo_sequence | string | UFO features | Any string |
-fformat1 -fformat_sequence | string | Features format | Any string |
-fopenfile1 -fopenfile_sequence | string | Features file name | Any string |
"-outfile" associated report qualifiers
-rformat2 -rformat_outfile | string | Report format | Any string | tagseq
-rname2 -rname_outfile | string | Base file name | Any string |
-rextension2 -rextension_outfile | string | File name extension | Any string |
-rdirectory2 -rdirectory_outfile | string | Output directory | Any string |
-raccshow2 -raccshow_outfile | boolean | Show accession number in the report | Boolean value Yes/No | N
-rdesshow2 -rdesshow_outfile | boolean | Show description in the report | Boolean value Yes/No | N
-rscoreshow2 -rscoreshow_outfile | boolean | Show the score in the report | Boolean value Yes/No | Y
-rstrandshow2 -rstrandshow_outfile | boolean | Show the nucleotide strand in the report | Boolean value Yes/No | Y
-rusashow2 -rusashow_outfile | boolean | Show the full USA in the report | Boolean value Yes/No | N
-rmaxall2 -rmaxall_outfile | integer | Maximum total hits to report | Any integer value | 0
-rmaxseq2 -rmaxseq_outfile | integer | Maximum hits to report for one sequence | Any integer value | 0
General qualifiers
-auto | boolean | Turn off prompts | Boolean value Yes/No | N
-stdout | boolean | Write first file to standard output | Boolean value Yes/No | N
-filter | boolean | Read first file from standard input, write first file to standard output | Boolean value Yes/No | N
-options | boolean | Prompt for standard and additional values | Boolean value Yes/No | N
-debug | boolean | Write debug output to program.dbg | Boolean value Yes/No | N
-verbose | boolean | Report some/full command line options | Boolean value Yes/No | Y
-help | boolean | Report command line options and exit. More information on associated and general qualifiers can be found with -help -verbose | Boolean value Yes/No | N
-warning | boolean | Report warnings | Boolean value Yes/No | Y
-error | boolean | Report errors | Boolean value Yes/No | Y
-fatal | boolean | Report fatal errors | Boolean value Yes/No | Y
-die | boolean | Report dying program messages | Boolean value Yes/No | Y
-version | boolean | Report version number and exit | Boolean value Yes/No | N

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 reads one or more protein sequences.

The input is a standard EMBOSS sequence query (also known as a 'USA').

Major sequence database sources defined as standard in EMBOSS installations include srs:embl, srs:uniprot and ensembl

Data can also be read from sequence output in any supported format written by an EMBOSS or third-party application.

The input format can be specified by using the command-line qualifier `-sformat xxx`, where 'xxx' is replaced by the name of the required format. The available format names are: gff (gff3), gff2, embl (em), genbank (gb, refseq), ddbj, refseqp, pir (nbrf), swissprot (swiss, sw), dasgff and debug.

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

### 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              Reviewed;         385 AA.
    AC   P27017;
    DT   01-AUG-1992, integrated into UniProtKB/Swiss-Prot.
    DT   23-JAN-2007, sequence version 5.
    DT   16-MAY-2012, entry version 83.
    DE   RecName: Full=Aliphatic amidase expression-regulating protein;
    GN   Name=amiC; OrderedLocusNames=PA3364;
    OS   Pseudomonas aeruginosa (strain ATCC 15692 / PAO1 / 1C / PRS 101 / LMG
    OS   12228).
    OC   Bacteria; Proteobacteria; Gammaproteobacteria; Pseudomonadales;
    OC   Pseudomonadaceae; Pseudomonas.
    OX   NCBI_TaxID=208964;
    RN   [1]
    RP   NUCLEOTIDE SEQUENCE [GENOMIC DNA], AND PROTEIN SEQUENCE OF 2-19.
    RC   STRAIN=PAC;
    RX   MEDLINE=91317707; PubMed=1907262;
    RA   Wilson S.A., Drew R.E.;
    RT   "Cloning and DNA sequence of amiC, a new gene regulating expression of
    RT   the Pseudomonas aeruginosa aliphatic amidase, and purification of the
    RT   amiC product.";
    RL   J. Bacteriol. 173:4914-4921(1991).
    RN   [2]
    RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    RC   STRAIN=ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228;
    RX   MEDLINE=20437337; PubMed=10984043; DOI=10.1038/35023079;
    RA   Stover C.K., Pham X.-Q.T., Erwin A.L., Mizoguchi S.D., Warrener P.,
    RA   Hickey M.J., Brinkman F.S.L., Hufnagle W.O., Kowalik D.J., Lagrou M.,
    RA   Garber R.L., Goltry L., Tolentino E., Westbrock-Wadman S., Yuan Y.,
    RA   Brody L.L., Coulter S.N., Folger K.R., Kas A., Larbig K., Lim R.M.,
    RA   Smith K.A., Spencer D.H., Wong G.K.-S., Wu Z., Paulsen I.T.,
    RA   Reizer J., Saier M.H. Jr., Hancock R.E.W., Lory S., Olson M.V.;
    RT   "Complete genome sequence of Pseudomonas aeruginosa PAO1, an
    RT   opportunistic pathogen.";
    RL   Nature 406:959-964(2000).
    RN   [3]
    RP   CRYSTALLIZATION.
    RX   MEDLINE=92106343; PubMed=1762155; DOI=10.1016/0022-2836(91)90579-U;
    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   [4]
    RP   X-RAY CRYSTALLOGRAPHY (2.1 ANGSTROMS), AND SEQUENCE REVISION TO 27-28.
    RX   MEDLINE=95112789; PubMed=7813419;
    RA   Pearl L.H., O'Hara B.P., 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).
    RN   [5]
    RP   X-RAY CRYSTALLOGRAPHY (2.25 ANGSTROMS) OF COMPLEX WITH AMIR.

      [Part of this file has been deleted for brevity]

    FT   VARIANT     106    106       T -> N (in strain: PAC181; butyramide
    FT                                inducible phenotype).
    FT   CONFLICT     27     28       QR -> HA (in Ref. 1; CAA32024).
    FT   CONFLICT    186    186       V -> L (in Ref. 1; CAA32024).
    FT   CONFLICT    263    263       A -> P (in Ref. 1; CAA32024).
    FT   CONFLICT    305    305       S -> N (in Ref. 1; CAA32024).
    FT   CONFLICT    319    319       C -> D (in Ref. 1; CAA32024).
    FT   CONFLICT    383    383       A -> P (in Ref. 1; CAA32024).
    FT   STRAND        9     13
    FT   STRAND       16     18
    FT   HELIX        21     39
    FT   TURN         40     43
    FT   STRAND       50     54
    FT   HELIX        60     72
    FT   STRAND       78     81
    FT   HELIX        85     97
    FT   STRAND      101    104
    FT   STRAND      117    119
    FT   HELIX       124    126
    FT   HELIX       128    136
    FT   TURN        137    139
    FT   STRAND      141    150
    FT   HELIX       151    166
    FT   STRAND      170    177
    FT   HELIX       183    196
    FT   STRAND      199    204
    FT   HELIX       209    221
    FT   STRAND      229    233
    FT   HELIX       236    239
    FT   HELIX       244    247
    FT   STRAND      251    255
    FT   HELIX       263    273
    FT   HELIX       284    303
    FT   HELIX       308    315
    FT   STRAND      320    322
    FT   STRAND      325    329
    FT   TURN        331    333
    FT   STRAND      336    338
    FT   STRAND      341    345
    FT   STRAND      351    356
    FT   HELIX       369    371
    FT   HELIX       376    378
    SQ   SEQUENCE   385 AA;  42807 MW;  33924B6C36017B79 CRC64;
         MGSHQERPLI GLLFSETGVT ADIERSQRYG ALLAVEQLNR EGGVGGRPIE TLSQDPGGDP
         DRYRLCAEDF IRNRGVRFLV GCYMSHTRKA VMPVVERADA LLCYPTPYEG FEYSPNIVYG
         GPAPNQNSAP LAAYLIRHYG ERVVFIGSDY IYPRESNHVM RHLYRQHGGT VLEEIYIPLY
         PSDDDVQRAV ERIYQARADV VFSTVVGTGT AELYRAIARR YGDGRRPPIA SLTTSEAEVA
         KMESDVAEGQ VVVAPYFSSI DTAASRAFVQ ACHGFFPENA TITAWAEAAY WQTLLLGRAA
         QAAGSWRVED VQRHLYDICI DAPQGPVRVE RQNNHSRLSS RIAEIDARGV FQVRWQSPEP
         IRPDPYVVVH NLDDWSASMG GGALP
    //

## 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, dasgff, debug, listfile, dbmotif, diffseq, draw, restrict, excel, feattable, motif, nametable, 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: Mon 15 Jul 2013 12:00:00
    # Commandline: garnier
    #    -sequence tsw:amic_pseae
    # Report_format: tagseq
    # Report_file: amic_pseae.garnier
    ########################################

    #=======================================
    #
    # Sequence: AMIC_PSEAE     from: 1   to: 385
    # HitCount: 113
    #
    # DCH = 0, DCS = 0
    #
    #  Please cite:
    #  Garnier, Osguthorpe and Robson (1978) J. Mol. Biol. 120:97-120
    #
    #
    #=======================================

              .   10    .   20    .   30    .   40    .   50
          MGSHQERPLIGLLFSETGVTADIERSQRYGALLAVEQLNREGGVGGRPIE
    helix                     HHHHH        HHHHH
    sheet       EE EEEEE                 EE              EEE
    turns         T                TTTT          TTTT
     coil CCCCCC        CCCCCC         CC       C    CCCC
              .   60    .   70    .   80    .   90    .  100
          TLSQDPGGDPDRYRLCAEDFIRNRGVRFLVGCYMSHTRKAVMPVVERADA
    helix                HHHHHH            HHHH H     HHHHHH
    sheet EE         EEEE           EEEE          EEEE
    turns   TT TT   T          TTTTT    TTT    T T
     coil     C  CCC
              .  110    .  120    .  130    .  140    .  150
          LLCYPTPYEGFEYSPNIVYGGPAPNQNSAPLAAYLIRHYGERVVFIGSDY
    helix                               HHH
    sheet EEEE    E       EE           E   EEEE    EEEEE
    turns        T TTT  TT  T     TT           TT T     TTTT
     coil     CCC     CC     CCCCC  CCC          C
              .  160    .  170    .  180    .  190    .  200
          IYPRESNHVMRHLYRQHGGTVLEEIYIPLYPSDDDVQRAVERIYQARADV
    helix        HHHH                       HHHHHHHHHHHHH
    sheet            EEE       EEEEEEE                   EEE
    turns    TTT        TTT             TTTT
     coil CCC   C          CCCC       CC
              .  210    .  220    .  230    .  240    .  250
          VFSTVVGTGTAELYRAIARRYGDGRRPPIASLTTSEAEVAKMESDVAEGQ
    helix           HHHHHHH                HHHHHHHHHHHHHHHHH
    sheet EEEEE            EE         EEE
    turns                    TTTTTT
     coil      CCCCC               CCC   CC
              .  260    .  270    .  280    .  290    .  300
          VVVAPYFSSIDTAASRAFVQACHGFFPENATITAWAEAAYWQTLLLGRAA
    helix             HHHHHHH           HHHHHHHHHHHHH    HHH
    sheet EEEEE  EEE         EE                      E
    turns      TT              TTT   TT
     coil           CC            CCC  C              CCC
              .  310    .  320    .  330    .  340    .  350
          QAAGSWRVEDVQRHLYDICIDAPQGPVRVERQNNHSRLSSRIAEIDARGV
    helix HH     HHHH                                HHH
    sheet                  EEEE     EEEEE         EEE      E
    turns            TTTTTT     T        TT   T         TTT
     coil   CCCCC              C CCC       CCC CCC
              .  360    .  370    .  380
          FQVRWQSPEPIRPDPYVVVHNLDDWSASMGGGALP
    helix
    sheet EEE           EEEEEEE     E       E
    turns    TT    TT           TTT   TTT
     coil      CCCC  CCC       C   C C   CCC

    #---------------------------------------
    #
    #  Residue totals: H:103   E:102   T: 86   C: 94
    #         percent: H: 27.9 E: 27.6 T: 23.3 C: 25.5
    #
    #---------------------------------------

    #---------------------------------------
    # Total_sequences: 1
    # Total_length: 385
    # Reported_sequences: 1
    # Reported_hitcount: 113
    #---------------------------------------

## 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 most stand-alone secondary structure prediction programs is not much better than 70% to 80% at best. The GOR I alogorithm is one of the first semi-successful methods, and will probably not predict with much better than about 65% accuracy. 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 Web servers for PHD, DSC, and others are generally preferred.

## Diagnostic Error Messages

None.

## Exit status

It always exits with a status of 0.

## Known bugs

None.

## See also

Program name | Description
--- | ---
helixturnhelix | Identify nucleic acid-binding motifs in protein sequences
pepcoil | Predict coiled coil regions in protein sequences
pepnet | Draw a helical net for a protein sequence
pepwheel | Draw a helical wheel diagram for a protein sequence

## 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
European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK

Please report all bugs to the EMBOSS bug team (emboss-bug © emboss.open-bio.org) not to the original author.

## History

## Target users

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

## Comments

None