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 Predicts 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 Predicts 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 Predicts protein secondary structure using GOR method Version: EMBOSS:6.4.0.0 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 -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 -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 18-MAY-2010, entry version 73. DE RecName: Full=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 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: Fri 15 Jul 2011 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 Predicts 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