--INTRODUCTION--

Searches of translated un-annotated genomic DNA sequences against protein 
databases is a useful early-stage method for discovering protein homologues 
encoded by the sequence, but generates huge amounts of output data that 
quickly becomes impregnable. BlastXtract is a web-based tool for managing
and visualizing results from large translated BLAST and FastA searches.
It combines the speed and storage benefits of Relational Database Management
Systems with an easy-to-use graphical navigation map, and greatly facilitates
the early exploration of genomic sequence.

More information can be obtained at
http://bioinfo.ucc.ie/blastXtract/

If you want to cite BlastXtract, please cite the following:

M.J. Claesson and D. van Sinderen.
BlastXtract - a new way of exploring translated searches.
Bioinformatics. 2005 Sep 15; 21(18):3667-8.

--INSTALLATION--

BlastXtract is developed using Perl 5.8.0 on the Linux RedHat 9.0 operating
system, but should work on most Linux or UNIX systems as long as the following
required Perl modules are properly installed:
	
Module		Version (or higher)
===================================
Bioperl 	1.4
CGI	 	3.05
CGI::Session 	3.95
DBI 		1.42
DBD::mysql	2.9003
or
DBD::Pg 	1.22
SVG 		2.28
GD 		2.12
GD::Text 	0.86
GD::Graph 	1.43
GD::SVG 	0.25

Also MySQL >= v3.23 or PostgreSQL >= v7.2 is needed as well as Apache web server >= v2.0.

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

blastXtract_install.pl

This script checks that all the perl modules above are installed, sets a few installation
parameters, creates the MySQL/PostgreSQL database and copies the modified program
to the appropriate webserver destination.

--IMPORTANT NOTES--

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.

The maximum query sequence length for fasta searches is 19990 bp. Longer
sequences should be divided up into smaller pieces and "stitched back" using
the BlastXtract's offset function.

Bioperl 1.4 cannot parse the word "similar", only "ungapped", in fasta34t24
outputs. It works fine with fasta34t23 output.


--COPYRIGHT--

Copyright (C) 1998,1999,2000,2001,2002  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.


--CONTACT INFORMATION--

If you have any questions, complaints, or suggestions, please email them to 

Marcus Claesson
E-mail: mclaesson@bioinfo.ucc.ie

Department of Microbiology,
National University of Ireland,
Cork, Ireland

Last Revised April 27, 2005