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Pham not found in Starterator

| posted 22 May, 2019 16:45
We are working with phage Fulbright and cannot access Starterator reports for the following genes. None of them are orphams.

Starterator report 55791 report not found for Gene 43 Fulbright
https://phagesdb.org/phams/55791/
Starterator report 55563 report not found for Gene 51 Fulbright
https://phagesdb.org/phams/55563/
Starterator report 55854 report not found for Gene 59 Fulbright
https://phagesdb.org/phams/55854/
Starterator report 55837 report not found for Gene 65 Fulbright
https://phagesdb.org/phams/55837/
Starterator report 55152 report not found for Gene 72 Fulbright
https://phagesdb.org/phams/55152/
| posted 23 May, 2019 10:46
Also checking annotations for Bunnies and seeing missing starterator reports unavailable in Pecaan and on phagesdb for phams that are not orphams!
| posted 23 May, 2019 10:48
As an example - Bunnies gene 32 (immunity repressor) pham 56415 (pham number from phagesdb) report is missing
| posted 28 May, 2019 20:12
I have just returned from vacation and have updated the the starterator pages to the most recent version of the phamerator database which was posted this morning. I checked bunnies gene 32, it is now in pham 39047 and appears to be in sync across pecaan, starterator, phagesdb.org and phamerator.org. Checking phage Fulbright shows some discrepancies across the various platforms but that could be syncronization issues since the last update was posted so recently. I would give it a day and if reports are still missing please repost and I can look into it.
| posted 06 Feb, 2020 15:32
Annotating Rie18_gp40. Starterator report for pham 109510 not found. Not an orpham and number appears to still be good.
Roy
| posted 06 Feb, 2020 17:48
Hi Roy,

I think you've caught things between versions of the Phamerator database. If you go to phamerator.org and click on the little dropdown database menu in the top left, it'll show you what version of the database you're currently viewing. As of now, I see Actino_Draft version 338.

Meanwhile, Chris has recently made a link where you can check the version of the database Starterator is using.
http://phages.wustl.edu/starterator/database.version

Earlier today, it showed 337, but I just checked again and now it's showing 338, so hopefully things are back in sync now.

–Dan
| posted 07 Feb, 2020 18:38
Was Starterator just updated? I cannot find any Starterator data for genes that are not orphams. Should I just wait a day to have it updated? All was fine until about 30 minutes ago. I'm not sure how to check my gene list to see if it is up to date as suggested in these other posts. Thanks!
| posted 08 Feb, 2020 00:29
Yes there was a new version of the database posted this morning. Since each site updates as it can things can get out of sync.
Not sure how you generated what you are calling your "gene list" but pecaan and phagesdb were updated earlier today so the links out of pecaan and out of phagesdb were pointing to pages that did not exist until starterator was also updated to the new version 339. This is how you can get the info on which version each site is on (links will only work between two sites if they are on the same version):
phagesdb see: http://phamerator.webfactional.com/databases_Hatfull/Actino_Draft.version
starterator see: http://phages.wustl.edu/starterator/database.version
pecaan: look on any "pham maps" page just above the map
phamerator.org: open the pull down menu in the top left
Edited 08 Feb, 2020 00:30
 
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