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.\" ========================================================================
.\"
.IX Title "NORSP 1"
.TH NORSP 1 "2016-01-08" "1.0.6" "User Commands"
.\" For nroff, turn off justification.  Always turn off hyphenation; it makes
.\" way too many mistakes in technical documents.
.if n .ad l
.nh
.SH "NAME"
norsp \- predictor of NOn\-Regular Secondary Structure (NORS)
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
norsp [\s-1OPTIONS\s0]  \-fileSeq <seq_file> \-fileHssp <hssp_file> \-filePhd <phd_file> \-filePhdHtm <phdHtm_file> \-fileCoils <coils_file>
.SH "DESCRIPTION"
.IX Header "DESCRIPTION"
Many structurally flexible regions play important roles in biological processes. It has been shown that extended loopy regions are very abundant in nature, and that they are evolutionarily conserved. NORSp is a publicly available predictor for disordered regions in protein. Specifically, it predicts long regions with no regular secondary structure. Upon user submission of protein sequence, NORSp will analyse the protein about its secondary structure, and presence of transmembrane helices and coiled-coil. It will then return e\-mail to user about the presence and position of disordered regions.
.PP
NORSp can be useful for biologists in several ways. For example, crystallographers can check whether their proteins contain \s-1NORS\s0 regions and make the decision about whether to proceed with the experiments since \s-1NORS\s0 proteins may be difficult to crystallise, as demonstrated by the their low occurrence in \s-1PDB.\s0 Biologists interested in protein structure-function relationship may also find it interesting to verify whether the protein-protein interaction sites coincide with \s-1NORS\s0 region.
.PP
See official web site for help <https://rostlab.org/owiki/index.php/NORSp_\-_predictor_of_NOn\-Regular_Secondary_Structure>.
.SS "Output format"
.IX Subsection "Output format"
Self-annotating, see example outputs in \fI/usr/share/doc/norsp/examples\fR.
.SH "REFERENCES"
.IX Header "REFERENCES"
.IP "Liu, J. and Rost, B. (2003). NORSp: Predictions of long regions without regular secondary structure. Nucleic Acids Res, 31(13), 3833\-5." 4
.IX Item "Liu, J. and Rost, B. (2003). NORSp: Predictions of long regions without regular secondary structure. Nucleic Acids Res, 31(13), 3833-5."
.PD 0
.IP "Liu, J., H. Tan and B. Rost. Loopy proteins appear conserved in evolution. J Mol Biol, 322(1):53\-64, 2002." 4
.IX Item "Liu, J., H. Tan and B. Rost. Loopy proteins appear conserved in evolution. J Mol Biol, 322(1):53-64, 2002."
.PD
.SH "OPTIONS"
.IX Header "OPTIONS"
.IP "\-fileSeq=\fI\s-1FILE\s0\fR" 4
.IX Item "-fileSeq=FILE"
input sequence file
.IP "\-fileHssp=\fI\s-1FILE\s0\fR" 4
.IX Item "-fileHssp=FILE"
input hssp file
.IP "\-filePhd=\fI\s-1FILE\s0\fR" 4
.IX Item "-filePhd=FILE"
input secondary structure file
.IP "\-filePhdHtm=\fI\s-1FILE\s0\fR" 4
.IX Item "-filePhdHtm=FILE"
input trans-membrane helices file
.IP "\-fileCoils=\fI\s-1FILE\s0\fR" 4
.IX Item "-fileCoils=FILE"
Input coiled coils file. Note that '\fI\s-1FILE\s0\fR_raw' is also read. Generate these with \fIcoils\-wrap\fR\|(1).
.IP "\-fileSum=\fI\s-1FILE\s0\fR" 4
.IX Item "-fileSum=FILE"
output prediction summary file
.IP "\-o=\fI\s-1FILE\s0\fR" 4
.IX Item "-o=FILE"
output prediction file
.IP "\-\-win=\fI\s-1NUMBER\s0\fR" 4
.IX Item "--win=NUMBER"
window size
.IP "\-\-secCut=\fI\s-1NUMBER\s0\fR" 4
.IX Item "--secCut=NUMBER"
max structure content
.IP "\-\-accLen=\fI\s-1NUMBER\s0\fR" 4
.IX Item "--accLen=NUMBER"
minimum consecutive exposed residues
.IP "\-html" 4
.IX Item "-html"
output in \s-1HTML\s0 format
.IP "\-v, \-\-version" 4
.IX Item "-v, --version"
norsp version
.IP "\-debug" 4
.IX Item "-debug"
debugging messages
.IP "\-?, \-\-help" 4
.IX Item "-?, --help"
help screen
.SH "AUTHOR"
.IX Header "AUTHOR"
.Vb 1
\& J. Liu and B. Rost
.Ve
.SH "EXAMPLES"
.IX Header "EXAMPLES"
.Vb 1
\& norsp \-\-win=70 \-\-secCut=12 \-\-accLen=10  \-fileSeq /usr/share/doc/norsp/examples/query.fasta \-fileHssp /usr/share/doc/norsp/examples/query.hssp \-filePhd /usr/share/doc/norsp/examples/query.prof \-filePhdHtm /usr/share/doc/norsp/examples/query.phdHtm \-fileCoils /usr/share/doc/norsp/examples/query.coils \-o /tmp/query.nors \-fileSum /tmp/query.sumNors
.Ve
.SH "FILES"
.IX Header "FILES"
.IP "\fI/usr/share/doc/norsp\fR" 4
.IX Item "/usr/share/doc/norsp"
Directory with examples.