BlastXtract2 facilitates early exploration of un-annotated genomic and metagenomic sequences. Various formats of translated searches of multiple sequences against multiple protein databases can be uploaded to a MySQL server accessed by a locally installed BlastXtract2 web-server. There, an intuitive GUI allows straightforward data-mining and enables quick detection of potential frameshifts and poorly sequenced/assembled regions.
Before installing feel free to test a demo version at http://bioinfo.ucc.ie/cgi-bin/blastXtract2/blastXtract2.pl
BlastXtract2 is developed using Perl 5.8.0 on the Linux Ubuntu 12.0 operating system. To install BlastXtract, make sure you have permission to write to the cgi-enabled directory to create databases in MySQL/PostgreSQL, which should be up and running. Then run the installation program blastXtract2_install.pl This script checks that all the perl modules are installed, sets a few installation parameters, creates the MySQL/PostgreSQL database and copies the modified program to the appropriate webserver destination.
In the Apache configuration file, set TimeOut to at least 600, since large output files can take long time to upload. If installing the DBD::mysql module make sure to also have mysql-server, mysql-devel, zlib and zlib-devel installed. Also do 'unset LANG' or 'LANG="c"' before compiling the module.
--MODIFICATION OF COG DATABASE--
The original COG database at ftp://ftp.ncbi.nih.gov/pub/COG/COG can be modified so that COG categories are visible in BLASTx output results and can be colour-coded and summarised in BlastXtract2. To do this, follow instructions in 'how_COGdb_was_created'.
Copyright (C) 2015 Genome Research Limited
This program is 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 2 of the License, or (at your option) any later version. This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with this program; if not, write to the Free Software Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
If you have any questions, complaints, or suggestions, please email them to Marcus Claesson E-mail: email@example.com School of Microbiology, University College Cork, Cork, Ireland Last Revised February 16, 2015