PROF(1)

NAME
prof - secondary structure and solvent accessibility predictor

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.

If no output file option (such as --fileRdb or --fileOut) is given the RDB formatted output is written into ./INPUTFILENAME.prof where 'prof' replaces the extension of the input file. In lack of extension '.prof' is appended to the input file name.

  Output format
The RDB format is self-annotating, see example outputs in /usr/share/profphd/prof/exa.

REFERENCES

Rost, B. and Sander, C. (1994a). Combining evolutionary information and neural networks to predict protein secondary structure. Proteins, 19(1), 55-72.
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
    DO check strength of predicted membrane helix (default)

doHtmref
    DO refine the membrane prediction (default)

doHtmtop
    DO membrane helix topology (default)

dssp
    convert PROF into DSSP format

expand
    expand insertions when converting output to MSF format

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 'html=body' restricts HTML file to the HTML_BODY tag part 'html=head' restricts HTML file to the HTML_HEADER tag part 'html=all' gives both HEADER and BODY

keepConv
    keep the conversion of the input file to HSSP format

keepFilter argument
    <*|doKeepFilter=1> keep the filtered HSSP file

keepHssp  argument
    <*|doKeepHssp=1> keep the intermediate HSSP file

keepNetDb argument
    <*|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:

    phd, nophd, /^para(3|Both|Sec|Acc|Htm|CapH|CapE|CapHE)/, /^para?/, jct

para3
    Parameter file for sec+acc+htm. Default: `<DIRPROF>/net/PROFboth_best.par'.

paraAcc
    Parameter file for acc. Default: `<DIRPROF>/net/PROFacc_best.par'.

paraBoth
    Parameter file for sec+acc. Default: `<DIRPROF>/net/PROFboth_best.par'.

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}

tst quick run through program, low accuracy

user
    user name

--version
    Print version

AUTHOR
B. Rost, Sander C, Fariselli P, Casadio R, Liu J, Yachdav G, Kajan L.

EXAMPLES

Prediction from alignment in HSSP file for best results
     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>.

Prediction from HSSP file fails when residue lines with exclamation marks `!' are present:
    Use 'optJury=normal' and 'both' like this:

     prof /tmp/1a3q.hssp fileRdb=/tmp/1a3q.hssp.profRdb optJury=normal both

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>