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garnier |
Function
Predicts protein secondary structureDescription
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 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 Sequence database USA
[-outfile] report Output report file name
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.
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
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 deaths
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| Standard (Mandatory) qualifiers | Allowed values | Default | |
|---|---|---|---|
| [-sequence] (Parameter 1) |
Sequence database USA | Readable sequence(s) | Required |
| [-outfile] (Parameter 2) |
Output report file name | Report output file | |
| Additional (Optional) qualifiers | Allowed values | Default | |
| (none) | |||
| Advanced (Unprompted) qualifiers | Allowed values | Default | |
| -idc | 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 |
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 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 STANDARD; PRT; 384 AA.
AC P27017;
DT 01-AUG-1992 (Rel. 23, Created)
DT 01-DEC-1992 (Rel. 24, Last sequence update)
DT 15-DEC-1998 (Rel. 37, Last annotation update)
DE ALIPHATIC AMIDASE EXPRESSION-REGULATING PROTEIN.
GN AMIC.
OS Pseudomonas aeruginosa.
OC Bacteria; Proteobacteria; gamma subdivision; Pseudomonas group;
OC Pseudomonas.
RN [1]
RP SEQUENCE FROM N.A., AND SEQUENCE OF 1-18.
RC STRAIN=PAC;
RX MEDLINE; 91317707.
RA WILSON S.A., DREW R.E.;
RT "Cloning and DNA sequence of amiC, a new gene regulating expression
RT of the Pseudomonas aeruginosa aliphatic amidase, and purification of
RT the amiC product.";
RL J. Bacteriol. 173:4914-4921(1991).
RN [2]
RP X-RAY CRYSTALLOGRAPHY.
RX MEDLINE; 92106343.
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 [3]
RP X-RAY CRYSTALLOGRAPHY (2.1 ANGSTROMS).
RX MEDLINE; 95112789.
RA PEARL L.H., O'HARA B., 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).
CC -!- FUNCTION: NEGATIVELY REGULATES THE EXPRESSION OF THE ALIPHATIC
CC AMIDASE OPERON. AMIC FUNCTIONS BY INHIBITING THE ACTION OF AMIR
CC AT THE PROTEIN LEVEL. IT BINDS TO AMIR. IT EXHIBITS PROTEIN KINASE
CC ACTIVITY.
CC -!- SUBUNIT: HOMODIMER.
CC -!- DOMAIN: CONSISTS OF TWO BETA-ALPHA-BETA DOMAINS WITH A CENTRAL
CC CLEFT IN WHICH THE AMIDE BINDS.
CC --------------------------------------------------------------------------
CC This SWISS-PROT entry is copyright. It is produced through a collaboration
CC between the Swiss Institute of Bioinformatics and the EMBL outstation -
CC the European Bioinformatics Institute. There are no restrictions on its
CC use by non-profit institutions as long as its content is in no way
CC modified and this statement is not removed. Usage by and for commercial
CC entities requires a license agreement (See http://www.isb-sib.ch/announce/
CC or send an email to license@isb-sib.ch).
CC --------------------------------------------------------------------------
DR EMBL; X13776; CAA32024.1; -.
DR PIR; A40359; A40359.
DR PDB; 1PEA; 03-APR-96.
KW Transferase; Kinase; Repressor; 3D-structure.
FT INIT_MET 0 0
SQ SEQUENCE 384 AA; 42704 MW; 68FF861F CRC32;
GSHQERPLIG LLFSETGVTA DIERSHAYGA LLAVEQLNRE GGVGGRPIET LSQDPGGDPD
RYRLCAEDFI RNRGVRFLVG CYMSHTRKAV MPVVERADAL LCYPTPYEGF EYSPNIVYGG
PAPNQNSAPL AAYLIRHYGE RVVFIGSDYI YPRESNHVMR HLYRQHGGTV LEEIYIPLYP
SDDDLQRAVE RIYQARADVV FSTVVGTGTA ELYRAIARRY GDGRRPPIAS LTTSEAEVAK
MESDVAEGQV VVAPYFSSID TPASRAFVQA CHGFFPENAT ITAWAEAAYW QTLLLGRAAQ
AAGNWRVEDV QRHLYDIDID APQGPVRVER QNNHSRLSSR IAEIDARGVF QVRWQSPEPI
RPDPYVVVHN LDDWSASMGG GPLP
//
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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: Fri Jul 15 2005 12:00:00
# Report_format: tagseq
# Report_file: amic_pseae.garnier
########################################
#=======================================
#
# Sequence: AMIC_PSEAE from: 1 to: 384
# HitCount: 111
#
# DCH = 0, DCS = 0
#
# Please cite:
# Garnier, Osguthorpe and Robson (1978) J. Mol. Biol. 120:97-120
#
#
#=======================================
. 10 . 20 . 30 . 40 . 50
GSHQERPLIGLLFSETGVTADIERSHAYGALLAVEQLNREGGVGGRPIET
helix HHHHHHHHHHHHHHHHHHH
sheet EE EEEEE EEEE
turns T TTTT
coil CCCCC CCCCC 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
YPRESNHVMRHLYRQHGGTVLEEIYIPLYPSDDDLQRAVERIYQARADVV
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
VVAPYFSSIDTPASRAFVQACHGFFPENATITAWAEAAYWQTLLLGRAAQ
helix HHHH HHHHHHHHHHHHH HHHH
sheet EEEE E EE E
turns TTT T T TTT TT
coil CCC C CCC C CCC
. 310 . 320 . 330 . 340 . 350
AAGNWRVEDVQRHLYDIDIDAPQGPVRVERQNNHSRLSSRIAEIDARGVF
helix HHHHHHH HHH
sheet E EEEE EEEEE EEE EE
turns TT T TT T TTT
coil CCCCCC C CCC CCC CCC
. 360 . 370 . 380
QVRWQSPEPIRPDPYVVVHNLDDWSASMGGGPLP
helix
sheet EE EEEEEEE E
turns TT TT TTT TTT
coil CCCC CCC C C CCCCC
#---------------------------------------
#
# Residue totals: H:111 E: 98 T: 81 C: 94
# percent: H: 30.2 E: 26.6 T: 22.0 C: 25.5
#
#---------------------------------------
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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 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