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>.

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.