Iteration

The DIGS tool is designed to support exploratory, comparative analyses of genomes. These projects have a fundamentally heuristic nature, and consequently will commonly require iteration. An iterative DIGS workflow can be conceptually divided into two stages. In the first stage, paired BLAST screening is performed. In the second, information recovered via screening is examined using the screening database (i.e. using structured query language (SQL)) or external applications (e.g. phylogenetic packages, statistical analysis software). Following this characterization, new information can be incorporated into reference libraries and/or screening databases, and used to perform a more powerful or precisely-targeted screen in the next iteration.

Iterating and refining DIGS

Exploratory screening is a dynamic discovery process, and it is likely that early screening databases will be superseded by later ones that incorporate more refined probe sets and reference sequence libraries.

For example, an initial screen may lead to the creation of a more refined reference sequence library that incorporates a finer-grained classification of reference sequences, or includes novel references identified through the first round of screening.

To update the contents of the Extracted table to reflect changes in the reference library, execute the pipeline.pl script as follows.

./digs_tool.pl –m=3 –i=[path to control file]

Refreshing and deleting DIGS databases

The digs_tool.pl script can also be used to 'flush' (empty/reset) and delete databases. Execute pipeline.pl as follows to flush data a screening database.

./digs_tool.pl –m=5 –i=[path to control file]

To delete a screening database, execute pipeline.pl as follows:

./digs_tool.pl –m=6 –i=[path to control file]

This will drop (delete) the screening database specified in the control file.