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Database-integrated genome screening (DIGS): exploring genomes heuristically using sequence similarity search tools and a relational database

Henan Zhu, Tristan Dennis, Joseph Hughes, Robert J. Gifford
doi: https://doi.org/10.1101/246835
Henan Zhu
1MRC-University of Glasgow Centre for Virus Research, Glasgow, Scotland, UK
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Tristan Dennis
1MRC-University of Glasgow Centre for Virus Research, Glasgow, Scotland, UK
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Joseph Hughes
1MRC-University of Glasgow Centre for Virus Research, Glasgow, Scotland, UK
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Robert J. Gifford
1MRC-University of Glasgow Centre for Virus Research, Glasgow, Scotland, UK
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ABSTRACT

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.uk

Supplementary information Supplementary data are available at Bioinformatics online.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted April 25, 2018.
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Database-integrated genome screening (DIGS): exploring genomes heuristically using sequence similarity search tools and a relational database
Henan Zhu, Tristan Dennis, Joseph Hughes, Robert J. Gifford
bioRxiv 246835; doi: https://doi.org/10.1101/246835
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Database-integrated genome screening (DIGS): exploring genomes heuristically using sequence similarity search tools and a relational database
Henan Zhu, Tristan Dennis, Joseph Hughes, Robert J. Gifford
bioRxiv 246835; doi: https://doi.org/10.1101/246835

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