SEA-PHAGES Logo

The official website of the HHMI Science Education Alliance-Phage Hunters Advancing Genomics and Evolutionary Science program.

Phamerator Database Updates

***UPDATE***

As of late 2015, all phages of Actinobacteria will be consolidated into a single Phamerator database. The server/datbase information is (case-sensitive):

Server: http://phamerator.webfactional.com/databases_Hatfull

Database: Actino_Draft

To update your copy of Phamerator to point to this new database, open Phamerator then go to Edit-->Preferences and enter the database and server above, taking care to type them exactly as shown. Click "Force Database Update", then when Phamerator tells you it's ready to restart, do so. If you're prompted for a password, it is "phage".

The Pham-building information below is still correct, but the non-Bacillus databases are no longer maintained.

Phamerator Database Updates

With recent changes to the way we define phamilies, pham building has become a much faster process.  As a result, we are able to add your recently finished genomes to our databases at a record pace.  Phamerator database updates are performed weekly for all hosts, minimizing time between sequencing and availability in Phamerator.

Phamerator Databases

In order to accommodate the growing populations of Arthrobacter and Rhodococcus phages, we have prepared alternative databases where faculty and students working with these hosts can access data for their phages. (No longer true, see UPDATE above.)

Accessing alternative Phamerator databases requires some quick changes to your Phamerator settings.  In the Phamerator preferences menu ("Edit" -> "Preferences"), you can add the following case sensitive server/database setting pairs:

http://phamerator.csm.jmu.edu/sea
Bacillus_Draft
Mycobacteriophage_Draft

http://phamerator.webfactional.com/databases_Hatfull
Arthrobacter_Draft
Propionibacterium_Draft
Rhodococcus_Draft
Streptomyces_Draft

After you change databases and close the preferences dialog, Phamerator will either switch to that database or set up the database if it is your first time using it.  During this process, you will be asked for a "Database Setup Password".  If you are using the SEA Virtual Machine, this is "phage", otherwise it is your MySQL root password.  If you are setting up the database for the first time, it is important to refrain from using the program until after it has restarted.

Please contact us if you are having issues switching your databases, and happy Phamerating!

Next entry:

Previous entry:

comments powered by Disqus

Current Events

Phage Discovery Workshop 17A

June 22, 2024 to June 28, 2024

2024 Phage Discovery Workshop 17A

June 22, 2024 to June 28, 2024

Upcoming Events

Phage Discovery Workshop 17B

July 13, 2024 to July 19, 2024

2024 Phage Discovery Workshop 17B

July 13, 2024 to July 19, 2024

2024 Phage Genomics Workshop

December 9, 2024 to December 13, 2024

Recent Events

Annual SEA Faculty Meeting

June 7, 2024 to June 10, 2024

2024 SEA Faculty Meeting

June 7, 2024 to June 10, 2024

Forum Activity

afreise posted in Jumbo phage annotation

Debbie Jacobs-Sera posted in Jumbo phage annotation

afreise posted in Jumbo phage annotation

FORUMS HOME PAGE