Using PhamDB
PhamDB is a web application which provides a GUI for creating and managing Phamerator databases. Use PhamDB to create genome databases, and then connect to them with Phamerator for further analysis.
- Creating your first database
- Connecting to your database with Phamerator
- Setting a Password on PhamDB
- Editing a database
- Importing a database
In the PhamDB toolbar, click "Create Database". Give your database a name, and optionally a description.
Checking "Search Conserved Domain Database" will search for each gene in NCBI's conserved domain database. You can then use Phamerator to view conserved domains. Searching for conserved domains takes a very long time, so leave it unchecked for now.
Now, it's time to upload your genbank files. Upload a file for each organism you would like to analyze. For now, just upload two or three phages to try it out.
PhamDB will show a list of the files you have uploaded, along with the name and number of genes in each organism.
If a file is invalid, PhamDB will show error messages detailing which lines in the file are problematic.
If you change your mind about a file you uploaded, you can uncheck it to exclude it from the database.
At the bottom of the page is a summary which includes the number of organisms to add. When you're ready, click "Create Database". This will queue the job for processing by PhamDB.
After clicking 'Create Database', PhamDB will show you a status page. Here you can see how long your job has been running and how much progress it has made.
If you only added a few phages, the job should only take a few seconds. However, creating and modifying Phamerator databases is computationally intensive and can take minutes, hours, or sometimes even days depending on how many genes are involved. To alleviate the logistical problems of long wait times, PhamDB provides a job queuing system so that you can run several jobs over night. You can even close your web browser while jobs are running.
When multiple jobs are queued, they will run one at a time.
When the job is done, PhamDB will show a page with information about your database. Here you can download a backup of the database as well as genbank files for each phage.
More importantly, this page provides information on connecting to your database with Phamerator.
This guide assumes that you already have Phamerator installed on your computer. If not, you can download it here.
In the menu at the top of Phamerator, click "Edit", then "Preferences". Add a new server and database using the information listed on your database's PhamDB page. Then, click "close".
Phamerator will connect to PhamDB and download your database. You can now use your database with Phamerator!
If you want to restrict access to PhamDB, you can set a password. This will prevent people without the password from using PhamDB.
To set a password, click on "Settings" on the upper right. Here you can set a password.
Note that anyone with access will be able to change or remove the password.
The edit database page is nearly identical to the 'create database' page.
Remove phages from a database by unchecking them.
Upload new phages from genbank files.
Import phages from other databases by clicking the database, then the phage.
A summary is shown at the bottom.
Click "Submit" to queue the job.
You can import databases from SQL backups. This feature is provided for the convenience of advanced users, and is less robust than the "Create Database" page. Database imports are not queued as jobs. Rather, you must keep the browser open until the import is finished. Depending on the database size, this could take several minutes.
Database backups created by PhamDB are fully supported. You can safely import databases which were previously downloaded from PhamDB. This can be used to, for example, create a copy of an existing database without having to re-compute phams.
Databases created by Phamerator have only limited support. You can import them, but you may encounter errors when editing them. This is because the database import tool does not do any phage validation, so it is possible to import databases with phages which PhamDB considers to be invalid.