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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
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 (c) 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
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