garnier

 

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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