PhagesDB

The Actinobacteriophage database, more commonly known as PhagesDB, is a website and database that gathers and shares information related to the discovery, characterization and genomics of viruses that prefer to infect Actinobacterial hosts. It is used to compare phages and their genomic annotations. The database provides information on more than 8,000 bacteriophages, including over 1,600 with already sequenced genomes.[1]

Actinobacteriophage Database
FoundedApril 2010
Location
  • Pittsburgh Bacteriophage Institute at the University of Pittsburgh
Members
20366 (as of 3/15/2022)
Key people
Dr. Graham Hatfull (HHMI Professor), Dan Russell (Webmaster), Debbie Jacobs-Sera (Phagehunting Program Coordinator), Dr. Welkin H. Pope (Research Assistant Professor), and Dr. Viknesh Sivanathan (HHMI Program Officer)
AffiliationsSEA-PHAGES (Science Education Alliance-Phage Hunters Advancing Genomics and Evolutionary Science)
Websitephagesdb.org
Plaque exhibiting bacterial lawn with clearings made by Artharobacter phage GantcherGoblin.

Background

PhagesDB provides the Actinobacteriophage research community with a database to post findings for analysis and further research.[2][3][4][5][6][7][8][9]

Design and features

The creation of PhagesDB was carried out using Django[10] and was hosted on a WebFaction server. The database website opens up with a mostly green and black lobby page and on the top left, a search bar is present. Phage names can be, sequenced and/or draft, typed in the search bar and results immediately pop up.[2]

PhagesDB has individual pages for every phage in the database. Along with all these, there is a separate GeneMark page for each phage which allows one to cross reference the position of genomes within the draft phages to ensure that there is indeed a genome present at a certain spot. PhagesDB can be used on its own but is found to be more accurate when used in collaboration with another bio-informatics website like NCBI Blast.[2] The figure below[11] indicates the different types and numbers of phages sequenced:

Phage Types Sequenced Number Sequenced
Actinoplanes 1
Arthrobacter 240
Brevibacterium 2
Corynebacterium 12
Gordonia 296
Kocuria 4
Microbacterium 98
Mycobacterium 1590
Propionibacterium 55
Rhodococcus 53
Rothia 1
Streptomyces 167
Tetrasphaera 1
Tsukamurella 2

There are many different ways in PhagesDB where the user is able to view and contact with groups of phages.[12][13] PhagesDB has amino-acid level details about its phage genomes that are sequenced by integration with Phamerator[14][15]

Access and rights to data

PhagesDB data can be freely viewed by anyone.

Additionally, the site gives multiple ways of bringing back the fundamental data.[16]

An Application Programming Interface (API) is available.[17] PhagesDB keeps some unpublished data that is not present in any medium, including genome sequences that have been done recently.[18]

See also

References
  1. Russell DA, Hatfull GF, "PhagesDB: the actinobacteriophage database"
  2. Russell, Daniel A.; Hatfull, Graham F. (2017-03-01). "PhagesDB: the actinobacteriophage database". Bioinformatics. 33 (5): 784–786. doi:10.1093/bioinformatics/btw711. ISSN 1367-4803. PMC 5860397. PMID 28365761.
  3. Hatfull, Graham "Genomic Databases:DNA Annotation"
  4. Hatfull G.F., Sarkis G.J. (1993). "DNA sequence, structure and gene expression of mycobacteriophage L5: a phage system for mycobacterial genetics". Mol. Microbiol. 7 (3): 395–405. doi:10.1111/j.1365-2958.1993.tb01131.x. PMID 8459766. S2CID 10188307.
  5. Pedulla, M.L. (2003). "Origins of highly mosaic mycobacteriophage genomes". Cell. 113 (2): 171–182. doi:10.1016/S0092-8674(03)00233-2. PMID 12705866. S2CID 14055875.
  6. Hanauer, D.I. (2006). "Inquiry learning. Teaching scientific inquiry". Science. 314 (5807): 1880–1881. doi:10.1126/science.1136796. PMID 17185586. S2CID 142760427.
  7. Hatfull, G.F. (2006). "Exploring the mycobacteriophage metaproteome: phage genomics as an educational platform". PLOS Genet. 2 (6): e92. doi:10.1371/journal.pgen.0020092. PMC 1475703. PMID 16789831.
  8. Hatfull, G.F. (2015). "Innovations in undergraduate science education: going viral". J. Virol. 89 (16): 8111–8113. doi:10.1128/JVI.03003-14. PMC 4524241. PMID 26018168.
  9. Jordan, T.C. (2014). "A broadly implementable research course in phage discovery and genomics for first-year undergraduate students". mBio. 5 (1): e01051–e01013. doi:10.1128/mbio.01051-13. PMC 3950523. PMID 24496795.
  10. "The Web framework for perfectionists with deadlines | Django". www.djangoproject.com. Retrieved 2018-04-11.
  11. "The Actinobacteriophage Database | Home". phagesdb.org. Retrieved 2018-04-18.
  12. "The Actinobacteriophage Database". phagesdb.org. Retrieved 2018-04-11.
  13. "The Actinobacteriophage Database | Compare Phages". phagesdb.org. Retrieved 2018-04-11.
  14. "Phamerator". phamerator.org. Retrieved 2018-04-18.
  15. Cresawn, S.G. (2011). "Phamerator: a bioinformatic tool for comparative bacteriophage genomics". BMC Bioinform. 12: 395. doi:10.1186/1471-2105-12-395. PMC 3233612. PMID 21991981.
  16. "The Actinobacteriophage Database | Home". phagesdb.org. Retrieved 2018-04-16.
  17. "Swagger UI". phagesdb.org. Retrieved 2018-04-16.
  18. "The Actinobacteriophage Database | Terms of Use". phagesdb.org. Retrieved 2018-04-16.
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