Provided by: norsp_1.0.6-3_all 
NAME
norsp - predictor of NOn-Regular Secondary Structure (NORS)
SYNOPSIS
norsp [OPTIONS] -fileSeq <seq_file> -fileHssp <hssp_file> -filePhd <phd_file> -filePhdHtm <phdHtm_file>
-fileCoils <coils_file>
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.
NORSp can be useful for biologists in several ways. For example, crystallographers can check whether
their proteins contain NORS regions and make the decision about whether to proceed with the experiments
since NORS proteins may be difficult to crystallise, as demonstrated by the their low occurrence in PDB.
Biologists interested in protein structure-function relationship may also find it interesting to verify
whether the protein-protein interaction sites coincide with NORS region.
See official web site for help
<https://rostlab.org/owiki/index.php/NORSp_-_predictor_of_NOn-Regular_Secondary_Structure>.
Output format
Self-annotating, see example outputs in /usr/share/doc/norsp/examples.
REFERENCES
Liu, J. and Rost, B. (2003). NORSp: Predictions of long regions without regular secondary structure.
Nucleic Acids Res, 31(13), 3833-5.
Liu, J., H. Tan and B. Rost. Loopy proteins appear conserved in evolution. J Mol Biol, 322(1):53-64,
2002.
OPTIONS
-fileSeq=FILE
input sequence file
-fileHssp=FILE
input hssp file
-filePhd=FILE
input secondary structure file
-filePhdHtm=FILE
input trans-membrane helices file
-fileCoils=FILE
Input coiled coils file. Note that 'FILE_raw' is also read. Generate these with coils-wrap(1).
-fileSum=FILE
output prediction summary file
-o=FILE
output prediction file
--win=NUMBER
window size
--secCut=NUMBER
max structure content
--accLen=NUMBER
minimum consecutive exposed residues
-html
output in HTML format
-v, --version
norsp version
-debug
debugging messages
-?, --help
help screen
AUTHOR
J. Liu and B. Rost
EXAMPLES
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
FILES
/usr/share/doc/norsp
Directory with examples.