EnglishFrenchSpanish

OnWorks favicon

norsp - Online in the Cloud

Run norsp in OnWorks free hosting provider over Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator

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

Use norsp online using onworks.net services


Free Servers & Workstations

Download Windows & Linux apps

  • 1
    strace
    strace
    The strace project has been moved to
    https://strace.io. strace is a
    diagnostic, debugging and instructional
    userspace tracer for Linux. It is used
    to monitor a...
    Download strace
  • 2
    gMKVExtractGUI
    gMKVExtractGUI
    A GUI for mkvextract utility (part of
    MKVToolNix) which incorporates most (if
    not all) functionality of mkvextract and
    mkvinfo utilities. Written in C#NET 4.0,...
    Download gMKVExtractGUI
  • 3
    JasperReports Library
    JasperReports Library
    JasperReports Library is the
    world's most popular open source
    business intelligence and reporting
    engine. It is entirely written in Java
    and it is able to ...
    Download JasperReports Library
  • 4
    Frappe Books
    Frappe Books
    Frappe Books is a free and open source
    desktop book-keeping software that's
    simple and well-designed to be used by
    small businesses and freelancers. It'...
    Download Frappe Books
  • 5
    Numerical Python
    Numerical Python
    NEWS: NumPy 1.11.2 is the last release
    that will be made on sourceforge. Wheels
    for Windows, Mac, and Linux as well as
    archived source distributions can be fou...
    Download Numerical Python
  • 6
    CMU Sphinx
    CMU Sphinx
    CMUSphinx is a speaker-independent large
    vocabulary continuous speech recognizer
    released under BSD style license. It is
    also a collection of open source tools ...
    Download CMU Sphinx
  • More »

Linux commands

crm
crm
Use crm online using onworks.net
services. ...
Run crm
  • 4
    crmgr
    crmgr
    crmgr - administration utility for QDBM
    Curia ...
    Run crmgr
  • 5
    gappletviewer
    gappletviewer
    gappletviewer - Load and runs an applet
    ...
    Run gappletviewer
  • 6
    gaps
    gaps
    mummer - package for sequence alignment
    of multiple genomes ...
    Run gaps
  • s-processed="true">
    g15stats
    g15stats - A CPU/Memory/Swap usage
    meter for G15Daemon DESCRIPTION: The
    packages provides the following usage
    meter for LCD on some Logitech
    keyboards, usind g...
    Run g15stats
  • More »
  • Ad