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Pham not found in Starterator

| posted 08 Mar, 2017 23:26
We are annotating Pham 24884 in Kalah2, and we can't find a report for it in Starterator. We looked in the Index of /starterator as well as searching for the Pham directly in Starterator (in the VM). Is there a reason why it's not there, or are we doing something wrong?
Thanks in advance for any help!
| posted 09 Mar, 2017 16:17
There are two main reasons (other than the simple typo) that would cause a missing starterator report.

The first is that the pham number has changed with a recent database update and all the support databases have not caught up and are still on the old number; the second is that your gene is an orpham and there is no Starterator report since there is nothing to compare.

I cannot see pham 24884 assigned to any gene in Kalah2 for the most recent database update so your issue is the former. To get the current up to date pham assignment for any gene check phagesdb (all the other web pages lag behind phagesdb by some amount of time). On phagesdb there an info page for each gene which includes the current pham number. The easiest way to get to a gene page is to go the gene list pull down menu on the kalah2 phage page.
| posted 10 Mar, 2017 00:01
Ok I ran phamerator again on Kalah2 and the Pham number for that gene was different. When did this database update occur? I guess I missed it! And how often does it get updated? Thanks so much Chris!
| posted 10 Mar, 2017 17:43
During Feb and March when there are lots of new phage sequences coming out the database gets updated once or twice a week. The only way to know there has been a new update is to manually check this page and see if the version number has changed. For the most part pham numbers remain the same from one database version to another so following database versions is probably a waste of time for most users.

This is a good teaching moment for your students, they should understand that pretty much all online biological databases are being updated and when they find inconsistencies its always a good idea to consider if it is due to recent changes to the underlying database. This is especially true when comparing info from one website to another since the two websites are likely to be on different update cycles.
| posted 06 May, 2018 16:03
I'm working on Ali17, gp63, and can't locate a Starterator report for pham 45669. It's not an orpham and I've checked Phagesdb to make sure the pham hasn't been renumbered.
| posted 06 May, 2018 20:55
The updated phamerator database has now been fully run though starterator and the results have been posted. You will now find your report available:
Edited 07 May, 2018 03:12
| posted 07 May, 2018 12:52
Got it. Thanks.
| posted 22 Jan, 2019 22:22
Got a Page/Report not found error for Pham 60238. 34 members and number seems current.
| posted 24 Jan, 2019 01:19
The most recent version of the database, which includes pham 60238 is now posted so you should be good to go.
| posted 17 May, 2019 16:46
Annotating J cluster this pham is not found in starterator, but is in phages.db and is not an orpham. I see that CDShaffer is away, but just thought I'd post as per the instructions on the file not found page.
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