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 structureInput protein sequence(s): tsw:amic_pseaeOutput report [amic_pseae.garnier]:    Go to the input files for this example   Go to the output files for this exampleCommand 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 messagesInput 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_pseaeID   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 expressionRT   of the Pseudomonas aeruginosa aliphatic amidase, and purification ofRT   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 negativeRT   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 transcriptionRT   antitermination in the amidase operon of Pseudomonas aeruginosa.";RL   EMBO J. 13:5810-5817(1994).CC   -!- FUNCTION: NEGATIVELY REGULATES THE EXPRESSION OF THE ALIPHATICCC       AMIDASE OPERON. AMIC FUNCTIONS BY INHIBITING THE ACTION OF AMIRCC       AT THE PROTEIN LEVEL. IT BINDS TO AMIR. IT EXHIBITS PROTEIN KINASECC       ACTIVITY.CC   -!- SUBUNIT: HOMODIMER.CC   -!- DOMAIN: CONSISTS OF TWO BETA-ALPHA-BETA DOMAINS WITH A CENTRALCC       CLEFT IN WHICH THE AMIDE BINDS.CC   --------------------------------------------------------------------------CC   This SWISS-PROT entry is copyright. It is produced through a collaborationCC   between  the Swiss Institute of Bioinformatics  and the  EMBL outstation -CC   the European Bioinformatics Institute.  There are no  restrictions on  itsCC   use  by  non-profit  institutions as long  as its content  is  in  no  wayCC   modified and this statement is not removed.  Usage  by  and for commercialCC   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      0SQ   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//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: Sat 15 Jul 2006 12:00:00# Commandline: garnier#    -sequence tsw:amic_pseae# 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      GSHQERPLIGLLFSETGVTADIERSHAYGALLAVEQLNREGGVGGRPIEThelix                   HHHHHHHHHHHHHHHHHHHsheet      EE EEEEE                                 EEEEturns        T                              TTTT coil CCCCC        CCCCC                   C    CCCC          .   60    .   70    .   80    .   90    .  100      LSQDPGGDPDRYRLCAEDFIRNRGVRFLVGCYMSHTRKAVMPVVERADALhelix               HHHHHH            HHHH H     HHHHHHsheet E         EEEE           EEEE          EEEE      Eturns  TT TT   T          TTTTT    TTT    T T coil    C  CCC          .  110    .  120    .  130    .  140    .  150      LCYPTPYEGFEYSPNIVYGGPAPNQNSAPLAAYLIRHYGERVVFIGSDYIhelix                              HHHsheet EEE    E       EE           E   EEEE    EEEEEturns       T TTT  TT  T     TT           TT T     TTTT coil    CCC     CC     CCCCC  CCC          C          C          .  160    .  170    .  180    .  190    .  200      YPRESNHVMRHLYRQHGGTVLEEIYIPLYPSDDDLQRAVERIYQARADVVhelix       HHHH                       HHHHHHHHHHHHHsheet           EEE       EEEEEEE                   EEEEturns   TTT        TTT             TTTT coil CC   C          CCCC       CC          .  210    .  220    .  230    .  240    .  250      FSTVVGTGTAELYRAIARRYGDGRRPPIASLTTSEAEVAKMESDVAEGQVhelix          HHHHHHH                HHHHHHHHHHHHHHHHHsheet EEEE            EE         EEE                   Eturns                   TTTTTT coil     CCCCC               CCC   CC          .  260    .  270    .  280    .  290    .  300      VVAPYFSSIDTPASRAFVQACHGFFPENATITAWAEAAYWQTLLLGRAAQhelix               HHHH           HHHHHHHHHHHHH    HHHHsheet EEEE   E          EE                      Eturns     TTT T   T       TTT   TT coil          CCC C         CCC  C              CCC          .  310    .  320    .  330    .  340    .  350      AAGNWRVEDVQRHLYDIDIDAPQGPVRVERQNNHSRLSSRIAEIDARGVFhelix       HHHHHHH                             HHHsheet              E  EEEE     EEEEE         EEE      EEturns               TT     T        TT   T         TTT coil CCCCCC              C CCC       CCC CCC          .  360    .  370    .  380      QVRWQSPEPIRPDPYVVVHNLDDWSASMGGGPLPhelixsheet EE           EEEEEEE     Eturns   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##---------------------------------------#---------------------------------------# Total_sequences: 1# Total_hitcount: 111#---------------------------------------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 sheetReferences    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):97-120Warnings   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 regionsAuthor(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