Secondary structure and solvent accessibility predictor
prof [\s-1INPUTFILE\s0+] [\s-1OPTIONS\s0]
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, \s-1PNAS\s0, 1993 , 90, 7558-7562; Rost & Sander, \s-1JMB\s0, 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:
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 \s-1RDB\s0 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.
The \s-1RDB\s0 format is self-annotating, see example outputs in /usr/share/profphd/prof/exa.
See each keyword for more help. Most of these are likely to be broken.
alternative connectivity patterns (default=3)
predict sec + acc + htm
predict solvent accessibility, only
add alignment to 'human-readable' \s-1PROF\s0 output file(s)
system architecture (e.g.: SGI64|SGI5|SGI32|SUNMP|ALPHA)
write 'human-readable' \s-1PROF\s0 output file(s)
\s-1PROF\s0 with best accuracy and longest run-time
predict secondary structure and solvent accessibility
data=<all|brief|normal|detail> for \s-1HTML\s0 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.
\s-1DO\s0 evaluation for list (only for known structures and lists)
filter the input \s-1HSSP\s0 file (excluding some pairs)
\s-1DO\s0 filter the membrane prediction (default)
\s-1DO\s0 check strength of predicted membrane helix (default)
\s-1DO\s0 refine the membrane prediction (default)
\s-1DO\s0 membrane helix topology (default)
convert \s-1PROF\s0 into \s-1DSSP\s0 format
expand insertions when converting output to \s-1MSF\s0 format
\s-1PROF\s0 with lowest accuracy and highest speed
name of \s-1PROF\s0 output in \s-1CASP\s0 format (file.caspProf)
name of \s-1PROF\s0 output in \s-1DSSP\s0 format (file.dsspProf)
name of \s-1PROF\s0 output in \s-1HTML\s0 format (file.htmlProf)
name of \s-1PROF\s0 output in \s-1MSF\s0 format (file.msfProf)
name of file flagging that no membrane helix was found
name of \s-1PROF\s0 output in \s-1RDB\s0 format (file.rdbProf) Known to work.
name of \s-1PROF\s0 output in human readable format (file.prof) Broken.
name of \s-1PROF\s0 output in \s-1RDB\s0 format (file.rdbProf) Known to work.
name of \s-1PROF\s0 output in \s-1SAF\s0 format (file.safProf)
filter the input \s-1HSSP\s0 file (excluding some pairs)
\s-1PROF\s0 with good accuracy and moderate speed
add \s-1ASCII\s0 graph to 'human-readable' \s-1PROF\s0 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 \s-1HTML\s0 format of prediction 'html' will result in that the \s-1PROF\s0 output is converted to \s-1HTML\s0 'html=body' restricts \s-1HTML\s0 file to the \s-1HTML_BODY\s0 tag part 'html=head' restricts \s-1HTML\s0 file to the \s-1HTML_HEADER\s0 tag part 'html=all' gives both \s-1HEADER\s0 and \s-1BODY\s0
keep the conversion of the input file to \s-1HSSP\s0 format
<*|doKeepFilter=1> keep the filtered \s-1HSSP\s0 file
<*|doKeepHssp=1> keep the intermediate \s-1HSSP\s0 file
<*|doKeepNetDb=1> keep the intermediate DbNet file(s)
<*|isList=1> input file is list of files
convert \s-1PROF\s0 into \s-1MSF\s0 format
give 'nice-D' to set the nice value (priority) of the job
do \s-1NOT\s0 copy file with tables into local directory
short for doSearchFile=0, i.e. no searching of \s-1DB\s0 files
surpress writing \s-1ASCII\s0 (i.e. human readable) result files
surpress writing \s-1HTML\s0 result files
job will not be niced, i.e. not run with lower priority
\s-1DO\s0 \s-1NOT\s0 check accuracy even when known structures
do \s-1NOT\s0 filter the membrane prediction
do \s-1NOT\s0 check whether or not membrane helix strong enough
do \s-1NOT\s0 refine the membrane prediction
do \s-1NOT\s0 membrane helix topology
Number of characters used for \s-1MSF\s0 file. Default: 50.
Minimal number of residues to run network, otherwise prd=symbolPrdShort. Default: 9.
Adds \s-1PHD\s0 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: `<\s-1DIRPROF\s0>/net/PROFboth_best.par'.
Parameter file for acc. Default: `<\s-1DIRPROF\s0>/net/PROFacc_best.par'.
Parameter file for sec+acc. Default: `<\s-1DIRPROF\s0>/net/PROFboth_best.par'.
Parameter file for sec. Default: `<\s-1DIRPROF\s0>/net/PROFsec_best.par'.
Minimal reliability index (\s-1RI\s0) for subset PROFacc. Default: 4.
Minimal reliability index (\s-1RI\s0) for subset PROFsec. Default: 5.
Symbol for residues predicted with \s-1RI\s0 < riSubSec/Acc. Default: `.'.
problems, manual, hints, notation, txt, known, \s-1DONE\s0, Date, date, aa, Lhssp, numaa, code
convert \s-1PROF\s0 into \s-1SAF\s0 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
B. Rost, Sander C, Fariselli P, Casadio R, Liu J, Yachdav G, Kajan L.
prof /usr/share/profphd/prof/exa/1ppt.hssp fileRdb=/tmp/1ppt.hssp.prof
prof /usr/share/profphd/prof/exa/1ppt.f fileRdb=/tmp/1ppt.f.rdbProf
/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
Override package prof package dir /usr/share/profphd.
Override location of librg-utils-perl /usr/share/librg-utils-perl.
default output file extension
default data directory
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
<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>