This article contains promotional content. (April 2018) |
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.[1]
| Founded | April 2010 |
|---|---|
| Location |
|
Members | 20,366 (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) |
| Affiliations | SEA-PHAGES (Science Education Alliance-Phage Hunters Advancing Genomics and Evolutionary Science) |
| Website | phagesdb |
Design and features
editThe creation of PhagesDB was carried out using Django, a server hosting environment.[2] 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.[3] The table below indicates the different types (by bacterial host genus) 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 |
The user can view information on groups of phages in a variety of ways.[4][5] PhagesDB has amino-acid level details about its phage genomes that are sequenced by integration with Phamerator.[6][7]
Access and rights to data
editInformation published in this database can be freely viewed by anyone, and an Application Programming Interface (API) is available.[8] PhagesDB keeps some unpublished data that is not present in any medium, including newly performed genomic sequences.[9]
See also
editReferences
edit- ^ Russell DA, Hatfull GF, [1] "PhagesDB: the actinobacteriophage database"
- ^ "The Web framework for perfectionists with deadlines | Django". www.djangoproject.com. Retrieved 2018-04-11.
- ^ 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.
- ^ "The Actinobacteriophage Database". phagesdb.org. Retrieved 2018-04-11.
- ^ "The Actinobacteriophage Database | Compare Phages". phagesdb.org. Retrieved 2018-04-11.
- ^ "Phamerator". phamerator.org. Retrieved 2018-04-18.
- ^ 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.
- ^ "Swagger UI". phagesdb.org. Retrieved 2018-04-16.
- ^ "The Actinobacteriophage Database | Terms of Use". phagesdb.org. Retrieved 2018-04-16.