BCov

Command-line tool for predicting protein beta-sheets from sequence.

Introduction

BCov is a software package designed for predicting protein beta-sheet topology from amino acid sequence.

BCov is based on the PSICOV residue contact predictor[1], dynamic-programming algorithm for beta-strand alignments and integer programming for beta-sheet topology prediction[2].

Download

BCov is a free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 3 of the License, or (at your option) any later version.

Source code: bcov-1.0.tar.gz

Requirements

BCov is entirely written in the C programming language and designed to run on Unix/Linux systems. BCov requires the GNU Linear Programming Kit available at http://www.gnu.org/software/glpk/ and also installable through the apt system under Ubuntu/Debian Linux distributions.:

To install these packages under Linux Ubuntu/Debian (you need to be a superuser):

$> sudo apt-get install glpk libglpk-dev

Installation

Download the BCov tarball and unconpress it. To compile and install BCov, from the package root run:

./configure
make
make install

By default the program will be installed under /usr/local/bin . If you want to install BCov into a different location you need to set the --exec-prefix argument of the configure script. For instance, to install BCov into /home/cas/bin run:

./configure --exec-prefix=/home/cas
make
make install

Basic usage

References

[1] Jones DT, Buchan DW, Cozzetto D, Pontil M. PSICOV: precise structural contact prediction using sparse inverse covariance estimation on large multiple sequence alignments. Bioinformatics. 2012 Jan 15;28(2):184-90.

[2] Castrense Savojardo, Piero Fariselli, Pier Luigi Martelli, and Rita Casadio, BCov: a method for predicting β-sheet topology using sparse inverse covariance estimation and integer programming. Bioinformatics first published online September 23, 2013.