pdm_utils: a SEA-PHAGES MySQL phage database management toolkit

Travis N Mavrich; Christian Gauthier; Lawrence Abad; Charles A Bowman; Steven G Cresawn; Graham F Hatfull

doi:10.1093/bioinformatics/btaa983

pdm_utils: a SEA-PHAGES MySQL phage database management toolkit

Bioinformatics. 2021 Aug 25;37(16):2464-2466. doi: 10.1093/bioinformatics/btaa983.

Authors

Travis N Mavrich¹, Christian Gauthier¹, Lawrence Abad¹, Charles A Bowman², Steven G Cresawn³, Graham F Hatfull¹

Affiliations

¹ Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA.
² Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.
³ Department of Biology, James Madison University, Harrisonburg, VA 22807, USA.

Abstract

Summary: Bacteriophages (phages) are incredibly abundant and genetically diverse. The volume of phage genomics data is rapidly increasing, driven in part by the SEA-PHAGES program, which isolates, sequences and manually annotates hundreds of phage genomes each year. With an ever-expanding genomics dataset, there are many opportunities for generating new biological insights through comparative genomic and bioinformatic analyses. As a result, there is a growing need to be able to store, update, explore and analyze phage genomics data. The package pdm_utils provides a collection of tools for MySQL phage database management designed to meet specific needs in the SEA-PHAGES program and phage genomics generally.

Availability and implementation: https://pypi.org/project/pdm-utils/.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Bacteriophages* / genetics
Computational Biology
Genome, Viral
Genomics
Phylogeny

Abstract

Publication types

MeSH terms

Grants and funding