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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 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
Standard (Mandatory) qualifiers:
[-sequence] seqall Protein sequence(s) filename and optional
format, or reference (input USA)
[-outfile] report [*.garnier] Output report file name
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
-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
-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 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 dying program messages
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 Reviewed; 385 AA.
AC P27017;
DT 01-AUG-1992, integrated into UniProtKB/Swiss-Prot.
DT 23-JAN-2007, sequence version 5.
DT 20-MAR-2007, entry version 50.
DE Aliphatic amidase expression-regulating protein.
GN Name=amiC; OrderedLocusNames=PA3364;
OS Pseudomonas aeruginosa.
OC Bacteria; Proteobacteria; Gammaproteobacteria; Pseudomonadales;
OC Pseudomonadaceae; Pseudomonas.
OX NCBI_TaxID=287;
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.
RC STRAIN=PAC1;
[Part of this file has been deleted for brevity]
FT /FTId=PRO_0000064581.
FT VARIANT 106 106 T -> N (in strain: PAC181; butyramide
FT inducible phenotype).
FT CONFLICT 27 28 QR -> HA (in Ref. 1).
FT CONFLICT 186 186 V -> L (in Ref. 1).
FT CONFLICT 263 263 A -> P (in Ref. 1).
FT CONFLICT 305 305 S -> N (in Ref. 1).
FT CONFLICT 319 319 C -> D (in Ref. 1).
FT CONFLICT 383 383 A -> P (in Ref. 1).
FT STRAND 8 12
FT STRAND 15 17
FT HELIX 20 38
FT TURN 39 42
FT STRAND 49 53
FT HELIX 59 71
FT STRAND 77 80
FT HELIX 84 96
FT STRAND 100 103
FT STRAND 116 118
FT HELIX 123 125
FT HELIX 127 135
FT TURN 136 138
FT STRAND 140 149
FT HELIX 150 165
FT STRAND 169 176
FT HELIX 182 195
FT STRAND 198 203
FT HELIX 208 220
FT STRAND 228 232
FT HELIX 235 238
FT HELIX 243 246
FT STRAND 250 254
FT HELIX 262 272
FT HELIX 283 302
FT HELIX 307 314
FT STRAND 319 321
FT STRAND 324 328
FT TURN 330 332
FT STRAND 335 337
FT STRAND 340 344
FT STRAND 350 355
FT HELIX 368 370
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, 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: Sun 15 Jul 2007 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_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 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
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