This is the command norsp that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator
PROGRAM:
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
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