Database-integrated genome screening (DIGS)

Molecular sequence data are highly information rich, and are now being generated much faster than they can be analysed. Consequently, published genome sequences contain many features (e.g. genes, pseudogenes, transposons) that have not been yet been formally described, or are unreliably annotated.

In DIGS, the output of sequence similarity search-based screens is captured in a relational database This allows for the interrogation and manipulation of output data using structured query language (SQL).

The DIGS tool

The DIGS tool is a PERL program for implementing DIGS with assembled sequence data (not short read data). It uses the Basic Local Alignment Search Tool (BLAST) to perform sequence similarity searches, and the MySQL RDBMS to capture their output.

Instructions for installing and running the DIGS tool can be found on the DIGS tool wiki

Author

Robert J. Gifford (robert.gifford@glasgow.ac.uk)