Molecular sequence data are highly information rich, and are now being generated much faster than they can be analysed. Consequently, the immense quantities of genome, transcriptome, and metagenome data accumulating in public databases contain multitudes of gene, pseudogene, transposon, virus, and non-coding element sequences that have not been yet been identified, or are only poorly described.
Database-integrated genome screening (DIGS) is an approach for exploring genomes and transcriptomes using sequence similarity search tools.
In DIGS, the output of sequence similarity-based searches is captured in a relational database. This allows for the interrogation and manipulation of output data using structured query language (SQL). In addition, it provides all the benefits of a relational database management system (RDBMS) with respect to features such as data recoverability, multi-user support and network access.
The DIGS tool is a PERL program for implementing DIGS. It is designed for use with assembled sequence data (i.e. not short read data). It uses the Basic Local Alignment Search Tool (BLAST) to perform sequence similarity searches, and the MySQL to capture their output.
The DIGS tool can be used to systematically search for sequences of interest, and to support investigations of their distribution, diversity and evolution.
DIGS requires PERL (with DBD::MySQL package), BLAST and MySQL.
If you want to install the DIGS tool on a mac, you will need to find a way to get the DBD::mysql package to install and work. The problems with this perl library on macintosh are well known and have been an issue for years . There are many online articles offering solutions (e.g. see here, here, and here) but none of these worked for me. Last time I attempted a mac install I gave up, so my suggestion is to stick with unix/linux when using this tool.
To install DIGS:
- Install Perl DBI and DBD::MySQL packages (if they are not already installed)
- Set $DIGS_HOME and $DIGS_GENOMES environment variables
- $DIGS_HOME = path to this repository
- $DIGS_GENOMES = path to the top level of the target genomes directory
- Create a MySQL user for DIGS
- Set $DIGS_MYSQL_USER and $DIGS_MYSQL_PASSWORD environment variables
To see options for screening:
./digs_tool.pl -h
Detailed instructions for installing and running the DIGS tool can be found on these pages
Lead Developer:
Robert J. Gifford (robert.gifford@glasgow.ac.uk).
DISCLAIMER
We do not accept responsibility for any problems that arise from use of this software.