SEA-PHAGES | Pham not found in Starterator

Link to this post \| posted 21 Jun, 2021 17:31
kbutela	If the phams in question aren't orphams, I think the best choice would be to wait a few days and try again to access the reports. Another option would be to have the students clear their browser cache and cookies regularly just in case their browsers are going to outdated links and are showing the error message instead of the regular Starterator report. Here is a link to my video on an intro to Starterator and how to access reports both from PECAAN and from PhagesDB. Hope it helps! Start Site Evaluation Tools: Starterator

Link to this post | posted 21 Jun, 2021 17:31

If the phams in question aren't orphams, I think the best choice would be to wait a few days and try again to access the reports. Another option would be to have the students clear their browser cache and cookies regularly just in case their browsers are going to outdated links and are showing the error message instead of the regular Starterator report.

Here is a link to my video on an intro to Starterator and how to access reports both from PECAAN and from PhagesDB. Hope it helps!

Start Site Evaluation Tools: Starterator

Link to this post \| posted 21 Jun, 2021 22:01
cdshaffer	Thanks for being patient, I have been away visiting my sister There have been some issues with phagesdb pham assignments lately. So phamerator.org, Starterator and PECAAN all agree with each other but phagesdb has those same genes in a different pham, thus the link from phagesdb to starterator will not work. I just checked a few genes in Tarkin and could not find any broken links, so the most recent update to version 414 may have fixed things. If not, the best thing to do is double check the pham number on phamerator.org that should give you the correct pham number for the starterator report. I do appreciate the desire to delay some curriculum until students are somewhat comfortable with the the basics, I do the same with my class. So if you have not introduced phamerator.org or PECAAN you can use the "whole phage" starterator report. When I use these reports I just use the search feature in my PDF viewer to search for the stop coordinate, this will usually only appear in the top table and the last page of the report for the gene. I then scroll up to find all the other bits. The "whole phage" Starterator report for phage Tarkin is available here: https://wustl.box.com/s/7xsd2c9zvh44iob96avgdqa3urh3uwzy P.S. For anyone else, feel free to post a request here for a whole phage report or send a request by email. They take about 3 minutes of my time to start the process and about 2 minutes to post once the analysis is done, so happy to post reports for any requests.

Link to this post | posted 21 Jun, 2021 22:01

cdshaffer

Thanks for being patient, I have been away visiting my sister

There have been some issues with phagesdb pham assignments lately. So phamerator.org, Starterator and PECAAN all agree with each other but phagesdb has those same genes in a different pham, thus the link from phagesdb to starterator will not work. I just checked a few genes in Tarkin and could not find any broken links, so the most recent update to version 414 may have fixed things.

If not, the best thing to do is double check the pham number on phamerator.org that should give you the correct pham number for the starterator report. I do appreciate the desire to delay some curriculum until students are somewhat comfortable with the the basics, I do the same with my class. So if you have not introduced phamerator.org or PECAAN you can use the "whole phage" starterator report. When I use these reports I just use the search feature in my PDF viewer to search for the stop coordinate, this will usually only appear in the top table and the last page of the report for the gene. I then scroll up to find all the other bits. The "whole phage" Starterator report for phage Tarkin is available here:

https://wustl.box.com/s/7xsd2c9zvh44iob96avgdqa3urh3uwzy

P.S. For anyone else, feel free to post a request here for a whole phage report or send a request by email. They take about 3 minutes of my time to start the process and about 2 minutes to post once the analysis is done, so happy to post reports for any requests.

Link to this post \| posted 21 Jun, 2021 22:33
kcornely	Chris, I hope that you had a nice visit with your sister. Thanks for the "whole page" Starterator report–I just downloaded it! I also had my student watch Kristin's video. Best wishes to you both, Kathleen

Link to this post \| posted 22 Jun, 2021 13:17
DanRussell	Hi all, This is partly my fault! Since we switched to a new web-hosting company back during the winter break, I haven't managed to successfully update all of my updating scripts, and hence I've needed to update to each new Phamerator database manually and often been behind. But I just tried to update the Phamerator script on PhagesDB and make sure it's correct going forward, so hopefully there won't be major issues anymore. –Dan

Link to this post | posted 22 Jun, 2021 13:17

DanRussell

Hi all,

This is partly my fault! Since we switched to a new web-hosting company back during the winter break, I haven't managed to successfully update all of my updating scripts, and hence I've needed to update to each new Phamerator database manually and often been behind.

But I just tried to update the Phamerator script on PhagesDB and make sure it's correct going forward, so hopefully there won't be major issues anymore.

–Dan

Link to this post \| posted 19 Aug, 2021 17:54
ncastro	Hello, I am working on phage Ganymede_Draft and looking at Gene 1. There doesn't appear to be a Starterator report for Gene 1 start site. I noticed there was a discrepancy in the gene family number. On phamerator, I can see that this gene has a different family number, 73206, than it does on phagesdb.org (74409). Anybody know how I can get the starterator report for this gene? Nancy

Link to this post \| posted 20 Aug, 2021 00:55
cdshaffer	Nancy, These discrepancies typically happen due to the database updates coming out at different times for the different sites. things can often slow down a bit in the summer with vacations and the like as well. You can use these links if you want to see which version of the database is being used at each site: phagesdb see: http://databases.hatfull.org/Actino_Draft/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 Currently Starterator and Phamerator are behind on 424 and phagesdb is on 425, so you want to use the phamerator number to get to the starterator report. The instructions on the various ways to get to the starterator report if the one from phagesdb is not working can be found here: https://seaphagesbioinformatics.helpdocsonline.com/article-37 In this particular case, since you know you want pham 73206 you can just type the address out manually (or copy/paste this address ). http://phages.wustl.edu/starterator/Pham73206Report.pdf That page has the report on Ganymede_Draft gene 1.

Link to this post | posted 20 Aug, 2021 00:55

cdshaffer

Nancy,
These discrepancies typically happen due to the database updates coming out at different times for the different sites. things can often slow down a bit in the summer with vacations and the like as well. You can use these links if you want to see which version of the database is being used at each site:
phagesdb see: http://databases.hatfull.org/Actino_Draft/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

Currently Starterator and Phamerator are behind on 424 and phagesdb is on 425, so you want to use the phamerator number to get to the starterator report.

The instructions on the various ways to get to the starterator report if the one from phagesdb is not working can be found here:

https://seaphagesbioinformatics.helpdocsonline.com/article-37

In this particular case, since you know you want pham 73206 you can just type the address out manually (or copy/paste this address ).

http://phages.wustl.edu/starterator/Pham73206Report.pdf

That page has the report on Ganymede_Draft gene 1.

Link to this post \| posted 09 Nov, 2021 10:44
mary.preuss	I'm annotating DustyDino (ED2) and pham 56633 is not coming up in Starterator. Not an orpham and don't see that the pham number has been updated? Version numbers are the same….. Thanks!

Link to this post \| posted 09 Nov, 2021 17:53
cdshaffer	Wow thanks for this, you are correct that pham is missing. You have actually located a bug in Starterator, which crashes when you try to analyze that pham. This is excellent, as we find and fix these bugs the program works better and better. I did a quick check and I found the general location of the problematic pham in the analysis but will need time to dig deeper into why it is happening. I will post more info once I get this bug squashed. Thanks for posting.

Link to this post | posted 09 Nov, 2021 17:53

cdshaffer

Wow thanks for this, you are correct that pham is missing. You have actually located a bug in Starterator, which crashes when you try to analyze that pham. This is excellent, as we find and fix these bugs the program works better and better. I did a quick check and I found the general location of the problematic pham in the analysis but will need time to dig deeper into why it is happening. I will post more info once I get this bug squashed. Thanks for posting.

Link to this post \| posted 09 Nov, 2021 21:24
cdshaffer	OK preliminary analysis suggests this is some kind of error in start codon annotations in phage ISF9 gene 29. This is a non-SEA phage from genbank that was added to the Actino_Draft database. The annotated start for this gene in the Actino_Draft is not a valid start codon once it is analyzed by Starterator. So it could be a bug in Starterator or a data entry error in Actino_Draft database. Determining that will take time, but in the mean time I just hand edited my local copy of the database to remove the problematic gene from pham 56633. I then ran the starterator analysis with all members of the pham except ISF9_29. The report should now be available but you will want to download the file for later use as it is likely to disappear again with the next database update, as I am not sure how long it will take to track down the exact issue. For documentation purposes this link should work for the next 3-4 months: http://phages.wustl.edu/438/Pham56633Report.pdf

Link to this post | posted 09 Nov, 2021 21:24

cdshaffer

OK preliminary analysis suggests this is some kind of error in start codon annotations in phage ISF9 gene 29. This is a non-SEA phage from genbank that was added to the Actino_Draft database. The annotated start for this gene in the Actino_Draft is not a valid start codon once it is analyzed by Starterator. So it could be a bug in Starterator or a data entry error in Actino_Draft database. Determining that will take time, but in the mean time I just hand edited my local copy of the database to remove the problematic gene from pham 56633. I then ran the starterator analysis with all members of the pham except ISF9_29. The report should now be available but you will want to download the file for later use as it is likely to disappear again with the next database update, as I am not sure how long it will take to track down the exact issue.

For documentation purposes this link should work for the next 3-4 months:
http://phages.wustl.edu/438/Pham56633Report.pdf

Link to this post \| posted 10 Nov, 2021 07:21
mary.preuss	Awesome, thanks Chris for looking at this so quickly!

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Pham not found in Starterator