PhagesDB
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{{Infobox organization
| name = Actinobacteriophage Database
| founded = April 2010
| location = Pittsburgh Bacteriophage Institute at the University of Pittsburgh
| 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)
| members = 20,366 (as of 3/15/2022)
| website = {{url|https://phagesdb.org}}
| affiliations = SEA-PHAGES (Science Education Alliance-Phage Hunters Advancing Genomics and Evolutionary Science)
}}File:GantcherGoblin plaques JW.jpg phage GantcherGoblin.]]
The Actinobacteriophage database, more commonly known as PhagesDB, is an interactive, comprehensive, database-backed website that collects and shares information related to the discovery, characterization and genomics of viruses that typically infect Actinobacterial hosts. It is used to compare these phages and their genomic annotations, allowing the research community to post new findings for analysis. The database provides information on more than 8,000 bacteriophages, as well as over 1,600 fully sequenced phages.Russell DA, Hatfull GF, [https://www.ncbi.nlm.nih.gov/pubmed/28365761] "PhagesDB: the actinobacteriophage database"
Design and features
The creation of PhagesDB was carried out using Django, a server hosting environment.{{Cite web|url=https://www.djangoproject.com|title=The Web framework for perfectionists with deadlines {{!}} Django|website=www.djangoproject.com|language=en|access-date=2018-04-11}} PhagesDB has individual entries for each different virus in the database, along with a separate GeneMark page, allowing a user to cross reference the position of genomes to ensure accuracy of data. 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.{{Cite journal |last1=Russell |first1=Daniel A. |last2=Hatfull |first2=Graham F. |date=2017-03-01 |title=PhagesDB: the actinobacteriophage database |journal=Bioinformatics |language=en |volume=33 |issue=5 |pages=784–786 |doi=10.1093/bioinformatics/btw711 |issn=1367-4803 |pmc=5860397 |pmid=28365761}} The table below indicates the different types (by bacterial host genus) and numbers of phages sequenced:
| class="wikitable"
!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 |
Users can view information on groups of phages in a variety of ways.{{Cite web|url=http://phagesdb.org/filter/|title=The Actinobacteriophage Database|website=phagesdb.org|access-date=2018-04-11}}{{Cite web|url=http://phagesdb.org/compare/|title=The Actinobacteriophage Database {{!}} Compare Phages|website=phagesdb.org|access-date=2018-04-11}} PhagesDB has amino-acid level details about its phage genomes that are sequenced by integration with Phamerator.{{Cite web|url=http://phamerator.org|title=Phamerator|website=phamerator.org|access-date=2018-04-18}}{{Cite journal|last=Cresawn|first=S.G.|date=2011|title=Phamerator: a bioinformatic tool for comparative bacteriophage genomics|journal=BMC Bioinform|volume=12|pages=395|doi=10.1186/1471-2105-12-395|pmid=21991981|pmc=3233612 |doi-access=free }}
Access and rights to data
Information published in this database can be freely viewed by anyone, and an Application Programming Interface (API) is available.{{Cite web|url=http://phagesdb.org/api/schema/|title=Swagger UI|website=phagesdb.org|access-date=2018-04-16}} PhagesDB keeps some unpublished data that is not present in any medium, including newly performed genomic sequences.{{Cite web|url=http://phagesdb.org/terms/|title=The Actinobacteriophage Database {{!}} Terms of Use|website=phagesdb.org|access-date=2018-04-16}}
See also
References
{{reflist}}
External links
- [http://phagesdb.org/ Homepage]