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.