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garnier |
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.
% garnier Input sequence: sw:amic_pseae Output file [amic_pseae.garnier]:
Mandatory qualifiers: [-sequencea] seqall Sequence database USA [-outfile] report Output report file name Optional qualifiers: (none) Advanced qualifiers: -idc integer idc param General qualifiers: -help boolean Report command line options. More information on associated and general qualifiers can be found with -help -verbose |
Mandatory qualifiers | Allowed values | Default | |
---|---|---|---|
[-sequencea] (Parameter 1) |
Sequence database USA | Readable sequence(s) | Required |
[-outfile] (Parameter 2) |
Output report file name | Report file | |
Optional qualifiers | Allowed values | Default | |
(none) | |||
Advanced qualifiers | Allowed values | Default | |
-idc | idc param | 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."
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://www.uk.embnet.org/Software/EMBOSS/Themes/ReportFormats.html for further information on report formats.
By default garnier writes a 'tagseq' report file.
Here is the output from the example run.
######################################## # Program: garnier # Rundate: Mon Feb 11 13:42:25 2002 # Report_file: amic_pseae.garnier ######################################## #======================================= # # Sequence: AMIC_PSEAE from: 1 to: 384 # HitCount: 113 # # DCH = 0, DCS = 0 # # Please cite: # Garnier, Osguthorpe and Robson (1978) J. Mol. Biol. 120:97-120 # # # #======================================= . 10 . 20 . 30 . 40 . 50 GSHQERPLIGLLFSETGVTADIERSQRYGALLAVEQLNREGGVGGRPIET helix HHHHH HHHHH sheet EE EEEEE EE EEEE turns T TTTT TTTT coil CCCCC CCCCCC CC 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 YPRESNHVMRHLYRQHGGTVLEEIYIPLYPSDDDVQRAVERIYQARADVV 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 VVAPYFSSIDTAASRAFVQACHGFFPENATITAWAEAAYWQTLLLGRAAQ helix HHHHHHH HHHHHHHHHHHHH HHHH sheet EEEE EEE EE E turns TT TTT TT coil CC CCC C CCC . 310 . 320 . 330 . 340 . 350 AAGSWRVEDVQRHLYDICIDAPQGPVRVERQNNHSRLSSRIAEIDARGVF helix H HHHH HHH sheet EEEE EEEEE EEE EE turns TTTTTT T TT T TTT coil CCCCC C CCC CCC CCC . 360 . 370 . 380 QVRWQSPEPIRPDPYVVVHNLDDWSASMGGGALP helix sheet EE EEEEEEE E E turns TT TT TTT TTT
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
You are advised to use several of the latest Web-based prediction sites and combine them to make a consensus prediction.
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 |
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.