TY - JOUR T1 - Database-integrated genome screening (DIGS): exploring genomes heuristically using sequence similarity search tools and a relational database JF - bioRxiv DO - 10.1101/246835 SP - 246835 AU - Henan Zhu AU - Tristan Dennis AU - Joseph Hughes AU - Robert J. Gifford Y1 - 2018/01/01 UR - http://biorxiv.org/content/early/2018/04/25/246835.abstract N2 - A significant fraction of most genomes is comprised of DNA sequences that have been incompletely investigated. This genomic ‘dark matter’ contains a wealth of useful biological information that can be recovered by systematically screening genomes in silico using sequence similarity search tools. Specialized computational tools are required to implement these screens efficiently. Here, we describe the database-integrated genome-screening (DIGS) tool: a computational framework for performing these investigations. To demonstrate, we screen mammalian genomes for endogenous viral elements (EVEs) derived from the Filoviridae, Parvoviridae, Circoviridae and Bornaviridae families, identifying numerous novel elements in addition to those that have been described previously. The DIGS tool provides a simple, robust framework for implementing a broad range of heuristic, sequence analysis-based explorations of genomic diversity.Availability http://giffordlabcvr.github.io/DIGS-tool/Contact robert.gifford{at}glasgow.ac.ukSupplementary information Supplementary data are available at Bioinformatics online. ER -