disulfinder1

Usage

Overview

'disulfinder' is for predicting the disulfide bonding state of cysteines and their disulfide connectivity starting from sequence alone. Disulfide bridges play a major role in the stabilization of the folding process for several proteins. Prediction of disulfide bridges from sequence alone is therefore useful for the study of structural and functional properties of specific proteins. In addition, knowledge about the disulfide bonding state of cysteines may help the experimental structure determination process and may be useful in other genomic annotation tasks. 'disulfinder' predicts disulfide patterns in two computational stages: (1) the disulfide bonding state of each cysteine is predicted by a BRNN-SVM binary classifier; (2) cysteines that are known to participate in the formation of bridges are paired by a Recursive Neural Network to obtain a connectivity pattern.

References

A. Ceroni, A. Passerini, A. Vullo and P. Frasconi. DISULFIND: a Disulfide Bonding State and Cysteine Connectivity Prediction Server, Nucleic Acids Research, 34(Web Server issue):W177-W181, 2006.

For the disulphide connectivity predictor see:

A. Vullo and P. Frasconi. Disulfide Connectivity Prediction using Recursive Neural Networks and Evolutionary Information, Bioinformatics, 20, 653-659, 2004.

For the cystein bonding state predictor see:

P. Frasconi, A. Passerini, and A. Vullo. A Two-Stage SVM Architecture for Predicting the Disulfide Bonding State of Cysteines, Proc. IEEE Workshop on Neural Networks for Signal Processing, pp.25-34, 2002.

A.Ceroni, P.Frasconi, A.Passerini and A.Vullo. Predicting the Disulfide Bonding State of Cysteines with Combinations of Kernel Machines, Journal of VLSI Signal Processing, 35, 287-295, 2003.

Options

-a, --alternatives=NUMBER

alternative connectivity patterns (default=3)

-o, --output=DIR

output dir where predictions will be saved (default=$PWD)

-p, --psi2=FILE|DIR

input in psi2 format (PSI-BLAST Matrix in ASCII), either a single file or a directory(?). Generate this with "blastpgp -j <N> -Q FILE" where N >= 2.

-r, --rootdir=DIR

work directory (default=~/disulfinder)

-k, --pkgdatadir=DIR

package data directory containing Models (default=/usr/share/disulfinder)

-F, --format={html|ascii}

output format type (default=ascii)

-d --blastdb=DIR

blastpgp -d option (default=/data/sp+trembl)

-c, --cleanpred

cleanup intermediate prediction files (default=false)

-P, --usepssm

use pssm instead of counts for profiles (default=false)

-C, --knownbondingstate

assume bonding state is known (one file for each chain in directory <rootdir>/Predictions/Bondstate/Viterbi) (default=false)

-v, --version

disulfinder version

-?, --help

help screen

Examples

"disulfinder -a 1 -p /usr/share/doc/disulfinder/examples/res_id_41483.blastPsiMatTmb -o ./disulfinder_results_dir"

Files

/usr/share/disulfinder

default package data directory

~/disulfinder

default work directory

Restrictions

The work directory is not cleaned up automatically.

Copyright and license

GPL