SEA-PHAGES | Pham not found in Starterator

Link to this post \| posted 16 May, 2023 14:32
plconnerly	Hello, We are annotating Vordorf and have found two features so far, 5 (stop at 4282) and 21 (stop at 18380), that are each in phams with many members (so not orphams), but are each not found in Starterator. When I checked versions, both Phamerator and Starterator are on version 512, but the pham numbers for these features are different in phamerator and starterator (feature 5 is in pham 80704 in phamerator, but 78088 in starterator; feature 21 is in pham 80706 in phamerator, but 78092 in starterator). Is this a situation where we just need to wait for starterator to catch up, or is there perhaps something else going on? The fact that the version numbers match is throwing me off. Thanks! Pam

Link to this post | posted 16 May, 2023 14:32

Hello,
We are annotating Vordorf and have found two features so far, 5 (stop at 4282) and 21 (stop at 18380), that are each in phams with many members (so not orphams), but are each not found in Starterator. When I checked versions, both Phamerator and Starterator are on version 512, but the pham numbers for these features are different in phamerator and starterator (feature 5 is in pham 80704 in phamerator, but 78088 in starterator; feature 21 is in pham 80706 in phamerator, but 78092 in starterator). Is this a situation where we just need to wait for starterator to catch up, or is there perhaps something else going on? The fact that the version numbers match is throwing me off.
Thanks!
Pam

Link to this post \| posted 16 May, 2023 15:47
cdshaffer	I am looking on the server and everything looks good here. I see vordorf gene 5 in this starterator report for 80704 as described in Phamerator http://phages.wustl.edu/starterator/Pham80704Report.pdf. and gene 21 here: http://phages.wustl.edu/starterator/Pham80706Report.pdf Your pham numbers you quote for starterator are out of sync. Those numbers 78088 and 78092 are from version 510 of the database. You can actually get older starterator reports using the version number in the URL, so here are the same genes in the older starterator reports for version 510 and the pham numbers you mentioned: http://phages.wustl.edu/510/Pham78088Report.pdf http://phages.wustl.edu/510/Pham78092Report.pdf

Link to this post | posted 16 May, 2023 15:47

cdshaffer

I am looking on the server and everything looks good here. I see vordorf gene 5 in this starterator report for 80704 as described in Phamerator http://phages.wustl.edu/starterator/Pham80704Report.pdf. and gene 21 here: http://phages.wustl.edu/starterator/Pham80706Report.pdf

Your pham numbers you quote for starterator are out of sync. Those numbers 78088 and 78092 are from version 510 of the database. You can actually get older starterator reports using the version number in the URL, so here are the same genes in the older starterator reports for version 510 and the pham numbers you mentioned:

http://phages.wustl.edu/510/Pham78088Report.pdf
http://phages.wustl.edu/510/Pham78092Report.pdf

Link to this post \| posted 16 May, 2023 16:44
plconnerly	Thank you so much, Chris! That's really helpful. We got those starterator pham numbers from PhagesDB. It looks like phamerator and starterator are both on the updated 512 version, but that the starterator links in PhagesDB are directing to the 510 version starterator pham numbers. From what you've described we can workaround by adjusting the URLs. Thanks again!

Link to this post \| posted 27 Apr, 2024 01:25
ClaireRinehart	I verified that the Starterator and Database are both version 561 but pham 161446 at URL: http://phages.wustl.edu/starterator/Pham161446Report.pdf gives me a 404 error, page not found. I checked many of the other Starterator phams and they seem to be working now that you have updated. Thanks for your help.

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Pham not found in Starterator