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    Command:

    prof

    
    
    

    SYNOPSIS

           prof [INPUTFILE+] [OPTIONS]
    
    
    

    DESCRIPTION

           Secondary structure is predicted by a system of neural networks rating
           at an expected average accuracy > 72% for the three states helix,
           strand and loop (Rost & Sander, PNAS, 1993 , 90, 7558-7562; Rost &
           Sander, JMB, 1993 , 232, 584-599; and Rost & Sander, Proteins, 1994 ,
           19, 55-72; evaluation of accuracy). Evaluated on the same data set,
           PROFsec is rated at ten percentage points higher three-state accuracy
           than methods using only single sequence information, and at more than
           six percentage points higher than, e.g., a method using alignment
           information based on statistics (Levin, Pascarella, Argos & Garnier,
           Prot. Engng., 6, 849-54, 1993).  PHDsec predictions have three main
           features:
    
           1. improved accuracy through evolutionary information from multiple
           sequence alignments
           2. improved beta-strand prediction through a balanced training
           procedure
           3. more accurate prediction of secondary structure segments by using a
           multi-level system
    
           Solvent accessibility is predicted by a neural network method rating at
           a correlation coefficient (correlation between experimentally observed
           and predicted relative solvent accessibility) of 0.54 cross-validated
           on a set of 238 globular proteins (Rost & Sander, Proteins, 1994, 20,
           216-226; evaluation of accuracy). The output of the neural network
           codes for 10 states of relative accessibility. Expressed in units of
           the difference between prediction by homology modelling (best method)
           and prediction at random (worst method), PROFacc is some 26 percentage
           points superior to a comparable neural network using three output
           states (buried, intermediate, exposed) and using no information from
           multiple alignments.
    
           Transmembrane helices in integral membrane proteins are predicted by a
           system of neural networks. The shortcoming of the network system is
           that often too long helices are predicted. These are cut by an
           empirical filter. The final prediction (Rost et al., Protein Science,
           1995, 4, 521-533; evaluation of accuracy) has an expected per-residue
           accuracy of about 95%. The number of false positives, i.e.,
           transmembrane helices predicted in globular proteins, is about 2%.  The
           neural network prediction of transmembrane helices (PHDhtm) is refined
           by a dynamic programming-like algorithm. This method resulted in
           correct predictions of all transmembrane helices for 89% of the 131
           proteins used in a cross-validation test; more than 98% of the
           transmembrane helices were correctly predicted. The output of this
           method is used to predict topology, i.e., the orientation of the N-term
           with respect to the membrane. The expected accuracy of the topology
           prediction is > 86%. Prediction accuracy is higher than average for
           eukaryotic proteins and lower than average for prokaryotes. PHDtopology
           is more accurate than all other methods tested on identical data sets.
           Rost, B. and Sander, C. (1994b). Conservation and prediction of solvent
           accessibility in protein families. Proteins, 20(3), 216-26.
           Rost, B., Casadio, R., Fariselli, P., and Sander, C. (1995).
           Transmembrane helices predicted at 95% accuracy. Protein Sci, 4(3),
           521-33.
    
    
    

    OPTIONS

           See each keyword for more help.  Most of these are likely to be broken.
    
           a   alternative connectivity patterns (default=3)
    
           3   predict sec + acc + htm
    
           acc predict solvent accessibility, only
    
           ali add alignment to 'human-readable' PROF output file(s)
    
           arch
               system architecture (e.g.: SGI64|SGI5|SGI32|SUNMP|ALPHA)
    
           ascii
               write 'human-readable' PROF output file(s)
    
           best
               PROF with best accuracy and longest run-time
    
           both
               predict secondary structure and solvent accessibility
    
           data
               data=<all|brief|normal|detail>  for HTML out: only those parts of
               predictions written
    
           debug
               keep most intermediate files, print debugging messages
    
           dirWork
               work directory, default: a temporary directory from
               File::Temp::tempdir. Must be fully qualified path.
    
               Known to work.
    
           doEval
               DO evaluation for list (only for known structures and lists)
    
           doFilterHssp
               filter the input HSSP file       (excluding some pairs)
    
           doHtmfil
               DO filter the membrane prediction                  (default)
    
           doHtmisit
           fast
               PROF with lowest accuracy and highest speed
    
           fileCasp
               name of PROF output in CASP format              (file.caspProf)
    
           fileDssp
               name of PROF output in DSSP format              (file.dsspProf)
    
           fileHtml
               name of PROF output in HTML format              (file.htmlProf)
    
           fileMsf
               name of PROF output in MSF format               (file.msfProf)
    
           fileNotHtm
               name of file flagging that no membrane helix was found
    
           fileOut
               name of PROF output in RDB format               (file.rdbProf)
    
               Known to work.
    
           fileProf
               name of PROF output in human readable format    (file.prof)
    
               Broken.
    
           fileRdb
               name of PROF output in RDB format               (file.rdbProf)
    
               Known to work.
    
           fileSaf
               name of PROF output in SAF format               (file.safProf)
    
           filter
               filter the input HSSP file       (excluding some pairs)
    
           good
               PROF with good accuracy and moderate speed
    
           graph
               add ASCII graph to 'human-readable' PROF output file(s)
    
           htm use: 'htm=<N|0.N>' gives minimal transmembrane helix detected
               default is 'htm=8' (resp. htm=0.8)  smaller numbers more false
               positives and fewer false negatives!
    
           html   argument
               'hmtl' or 'html=<all|body|head>' write HTML format of prediction
               'html' will result in that the PROF output is converted to HTML
               <*|doKeepNetDb=1>       keep the intermediate DbNet file(s)
    
           list argument
               <*|isList=1>      input file is list of files
    
           msf convert PROF into MSF format
    
           nice
               give 'nice-D' to set the nice value (priority) of the job
    
           noProfHead
               do NOT copy file with tables into local directory
    
           noSearch
               short for doSearchFile=0, i.e. no searching of DB files
    
           noascii
               surpress writing ASCII (i.e. human readable) result files
    
           nohtml
               surpress writing HTML result files
    
           nonice
               job will not be niced, i.e. not run with lower priority
    
           notEval
               DO NOT check accuracy even when known structures
    
           notHtmfil
               do NOT filter the membrane prediction
    
           notHtmisit
               do NOT check whether or not membrane helix strong enough
    
           notHtmref
               do NOT refine the membrane prediction
    
           notHtmtop
               do NOT membrane helix topology
    
           nresPerLineAli
               Number of characters used for MSF file. Default: 50.
    
           numresMin
               Minimal number of residues to run network, otherwise
               prd=symbolPrdShort. Default: 9.
    
           optJury
               Adds PHD to jury. Default: 'normal,usePHD'.
    
               Many other parameters change the default for this one as a side-
               effect, the list is not comprehensive:
    
           paraSec
               Parameter file for sec. Default: '<DIRPROF>/net/PROFsec_best.par'.
    
           riSubAcc
               Minimal reliability index (RI) for subset PROFacc. Default: 4.
    
           riSubSec
               Minimal reliability index (RI) for subset PROFsec. Default: 5.
    
           riSubSym
               Symbol for residues predicted with RI < riSubSec/Acc. Default: '.'.
    
           s_k_i_p
               problems, manual, hints, notation, txt, known, DONE, Date, date,
               aa, Lhssp, numaa, code
    
           saf convert PROF into SAF format
    
           scrAddHelp
           scrGoal
               neural network switching
    
           scrHelpTxt
               Input file formats accepted:
               hssp,dssp,msf,saf,fastamul,pirmul,fasta,pir,gcg,swiss
    
           scrIn
               list_of_files (or single file) parameter_file
    
           scrName
               prof
    
           scrNarg
               2
    
           sec predict secondary structure,   only
    
           silent
               no information written to screen - this is the default
    
           skipMissing
               do not abort if input file missing!
    
           sourceFile
               prof
    
           test
               is just a test (faster)
    
           translate-jobid-in-param-values
               String 'jobid' gets substituted with $par{jobid}
                prof /usr/share/profphd/prof/exa/1ppt.hssp fileRdb=/tmp/1ppt.hssp.prof
    
           Prediction from a single sequence
                prof /usr/share/profphd/prof/exa/1ppt.f fileRdb=/tmp/1ppt.f.rdbProf
    
           phd.pl invocation
                /usr/share/profphd/prof/embl/phd.pl /usr/share/profphd/prof/exa/1ppt.hssp htm fileOutPhd=/tmp/query.phdPred  fileOutRdb=/tmp/query.phdRdb  fileNotHtm=/tmp/query.phdNotHtm
    
    
    

    ENVIRONMENT

           PROFPHDDIR
               Override package prof package dir /usr/share/profphd.
    
           RGUTILSDIR
               Override location of librg-utils-perl /usr/share/librg-utils-perl.
    
    
    

    FILES

           *.rdbProf
               default output file extension
    
           /usr/share/profphd/prof
               default data directory
    
    
    

    BUGS

           Please report bugs at
           <https://rostlab.org/bugzilla3/enter_bug.cgi?product=profphd>.
    
    
    

    SEE ALSO

           Main website
               <http://www.predictprotein.org/>
    
           Documentation
               <http://www.predictprotein.org/docs.php>
    
           Community website
               <http://groups.google.com/group/PredictProtein>
    
           FTP <ftp://rostlab.org/pub/cubic/downloads/prof>
    
           Newsgroups
               <http://groups.google.com/group/PredictProtein>
    
    
    

    1.0.38 2011-10-27 PROF(1)

    
    
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