RT Journal Article
SR Electronic
T1 Database-integrated genome screening (DIGS): exploring genomes heuristically using sequence similarity search tools and a relational database
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 246835
DO 10.1101/246835
A1 Henan Zhu
A1 Tristan Dennis
A1 Joseph Hughes
A1 Robert J. Gifford
YR 2018
UL http://biorxiv.org/content/early/2018/04/25/246835.abstract
AB 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.