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PROF(1) User Commands 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 /share/profphd/prof/exa.

REFERENCES

OPTIONS

See each keyword for more help. Most of these are likely to be broken.

alternative connectivity patterns (default=3)
3
predict sec + acc + htm
predict solvent accessibility, only
add alignment to 'human-readable' PROF output file(s)
system architecture (e.g.: SGI64|SGI5|SGI32|SUNMP|ALPHA)
write 'human-readable' PROF output file(s)
PROF with best accuracy and longest run-time
predict secondary structure and solvent accessibility
data=<all|brief|normal|detail> for HTML out: only those parts of predictions written
keep most intermediate files, print debugging messages
work directory, default: a temporary directory from File::Temp::tempdir. Must be fully qualified path.

Known to work.

DO evaluation for list (only for known structures and lists)
filter the input HSSP file (excluding some pairs)
DO filter the membrane prediction (default)
DO check strength of predicted membrane helix (default)
DO refine the membrane prediction (default)
DO membrane helix topology (default)
convert PROF into DSSP format
expand insertions when converting output to MSF format
PROF with lowest accuracy and highest speed
name of PROF output in CASP format (file.caspProf)
name of PROF output in DSSP format (file.dsspProf)
name of PROF output in HTML format (file.htmlProf)
name of PROF output in MSF format (file.msfProf)
name of file flagging that no membrane helix was found
name of PROF output in RDB format (file.rdbProf)

Known to work.

name of PROF output in human readable format (file.prof)

Broken.

name of PROF output in RDB format (file.rdbProf)

Known to work.

name of PROF output in SAF format (file.safProf)
filter the input HSSP file (excluding some pairs)
PROF with good accuracy and moderate speed
add ASCII graph to 'human-readable' PROF output file(s)
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!
'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
keep the conversion of the input file to HSSP format
<*|doKeepFilter=1> keep the filtered HSSP file
<*|doKeepHssp=1> keep the intermediate HSSP file
<*|doKeepNetDb=1> keep the intermediate DbNet file(s)
<*|isList=1> input file is list of files
convert PROF into MSF format
give 'nice-D' to set the nice value (priority) of the job
do NOT copy file with tables into local directory
short for doSearchFile=0, i.e. no searching of DB files
surpress writing ASCII (i.e. human readable) result files
surpress writing HTML result files
job will not be niced, i.e. not run with lower priority
DO NOT check accuracy even when known structures
do NOT filter the membrane prediction
do NOT check whether or not membrane helix strong enough
do NOT refine the membrane prediction
do NOT membrane helix topology
Number of characters used for MSF file. Default: 50.
Minimal number of residues to run network, otherwise prd=symbolPrdShort. Default: 9.
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

Parameter file for sec+acc+htm. Default: `<DIRPROF>/net/PROFboth_best.par'.
Parameter file for acc. Default: `<DIRPROF>/net/PROFacc_best.par'.
Parameter file for sec+acc. Default: `<DIRPROF>/net/PROFboth_best.par'.
Parameter file for sec. Default: `<DIRPROF>/net/PROFsec_best.par'.
Minimal reliability index (RI) for subset PROFacc. Default: 4.
Minimal reliability index (RI) for subset PROFsec. Default: 5.
Symbol for residues predicted with RI < riSubSec/Acc. Default: `.'.
problems, manual, hints, notation, txt, known, DONE, Date, date, aa, Lhssp, numaa, code
convert PROF into SAF format
neural network switching
Input file formats accepted: hssp,dssp,msf,saf,fastamul,pirmul,fasta,pir,gcg,swiss
list_of_files (or single file) parameter_file
prof
2
predict secondary structure, only
no information written to screen - this is the default
do not abort if input file missing!
prof
is just a test (faster)
String 'jobid' gets substituted with $par{jobid}
quick run through program, low accuracy
user name
Print version

AUTHOR

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

EXAMPLES

 prof /share/profphd/prof/exa/1ppt.hssp fileRdb=/tmp/1ppt.hssp.prof
    
 prof /share/profphd/prof/exa/1ppt.f fileRdb=/tmp/1ppt.f.rdbProf
    
 /share/profphd/prof/embl/phd.pl /share/profphd/prof/exa/1ppt.hssp htm fileOutPhd=/tmp/query.phdPred  fileOutRdb=/tmp/query.phdRdb  fileNotHtm=/tmp/query.phdNotHtm

ENVIRONMENT

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

FILES

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

BUGS

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

Use 'optJury=normal' and 'both' like this: 

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

SEE ALSO

<http://www.predictprotein.org/>
<http://www.predictprotein.org/docs.php>
<http://groups.google.com/group/PredictProtein>
<ftp://rostlab.org/pub/cubic/downloads/prof>
<http://groups.google.com/group/PredictProtein>
2018-07-13 1.0.42