SEA-PHAGES | All posts created by DrCatalase

Link to this post \| posted 18 May, 2022 13:16
DrCatalase	Hello all, I cannot access phamerator I was able to the day on Monday but not yesterday or today. I have tried with wifi and ethernet on my computer and wifi and data on my phone. I get this message… phamerator.org took too long to respond. Try: Checking the connection Checking the proxy and the firewall Running Windows Network Diagnostics ERR_CONNECTION_TIMED_OUT Someone, please help I am trying to finish up an already late annotation (lol, sorry) Thank you, Sean Edited 18 May, 2022 13:19

Link to this post | posted 18 May, 2022 13:16

Hello all,
I cannot access phamerator I was able to the day on Monday but not yesterday or today. I have tried with wifi and ethernet on my computer and wifi and data on my phone. I get this message…

phamerator.org took too long to respond.
Try:

Checking the connection
Checking the proxy and the firewall
Running Windows Network Diagnostics
ERR_CONNECTION_TIMED_OUT

Someone, please help I am trying to finish up an already late annotation (lol, sorry)
Thank you,
Sean

Edited 18 May, 2022 13:19

Posted in: Phamerator → Phamerator down?

Link to this post \| posted 17 Dec, 2020 15:12
DrCatalase	debbie Dr. Catalase, Yes. Please use the validation function in DNA Master to do this when you renumber the genes. It is always best to let DNA Master auto-fill any field that you can debbie Thank you.

Posted in: Notes and Final Files → Filling in the Product field

Link to this post \| posted 16 Dec, 2020 22:02
DrCatalase	Is it okay to have "hypothetical protein" in the function field of your your complete notes file? Thank you.

Posted in: Notes and Final Files → Filling in the Product field

Link to this post \| posted 15 Dec, 2020 22:01
DrCatalase	cdshaffer ok release of starterator reports for database version 387 are now available and are tagged as the current version. Links from pecaan and phagesdb should now be working (at least until the next database update). Please report if any links fail at this point. Thank you, Chris!

Posted in: Starterator → Read First: Common Starterator Troubleshooting

Link to this post \| posted 15 Dec, 2020 17:06
DrCatalase	cdshaffer These are typically due to database at phagesdb being out of sync with the current database for the starterator reports but this should not be happening "for weeks". Are you using pecaan or phagesdb for your links? Could you post the pham numbers you are looking for? Used the links from both to doublecheck. Peel 30 pham 45194 Peel 33 pham 45744 Peel 32 pham 45569

Posted in: Starterator → Read First: Common Starterator Troubleshooting

Link to this post \| posted 15 Dec, 2020 16:25
DrCatalase	PEEL K1 cluster phage has several genes (28, 30, and 31) with functions (30 and 31) that have been giving us the… Page/Report not found Error 404 The requested Pham report could not be found. Possible reasons for a missing pham report beyond a simply typo in the URL: 1. Your protein is an orpham (reports are not generated for phams with only one member as there is nothing to compare it to.) Check phagesdb.org for the size of the pham. 2. The phamerator database has been updated and the pham number has changed. You can double check for the correct pham number at phagesdb.org. If neither of the above apply and you believe a report is missing in error it is important that you please post to the seaphages starterator forum. Error for weeks. This is through Pecaan and Phagesdb. Thank you. Sean

Link to this post | posted 15 Dec, 2020 16:25

DrCatalase

PEEL K1 cluster phage has several genes (28, 30, and 31) with functions (30 and 31) that have been giving us the…

Page/Report not found Error 404
The requested Pham report could not be found.

Possible reasons for a missing pham report beyond a simply typo in the URL:

1. Your protein is an orpham (reports are not generated for phams with only one member as there is nothing to compare it to.) Check phagesdb.org for the size of the pham.
2. The phamerator database has been updated and the pham number has changed. You can double check for the correct pham number at phagesdb.org.
If neither of the above apply and you believe a report is missing in error it is important that you please post to the seaphages starterator forum.

Error for weeks. This is through Pecaan and Phagesdb. Thank you.
Sean

Posted in: Starterator → Read First: Common Starterator Troubleshooting

Link to this post \| posted 14 Nov, 2019 15:17
DrCatalase	Thank you all. I will try cleaning the DNA and digesting for longer. BTW I did the PEG protocol 9.2a from the instructor's guide. Edited 14 Nov, 2019 15:27

Posted in: Phage Discovery/Isolation → DNA Isolation from M. foliorum - any updates?

Link to this post \| posted 13 Nov, 2019 22:10
DrCatalase	Help, We got decent yields of DNA that and we tried to digest with NspI. the lanes are from two different phage lysates. Lanes: 1. DNA1 water 2. DNA1 water Buffer NspI (NEB 37 degrees 15 minutes) 3. DNA1 water Buffer 4. Ladder 5. DNA2 water 6. DNA2 water Buffer NspI (NEB 37 degrees 15 minutes) 7. DNA2 water Buffer We got no digestion except smearing in lane 6… we want to try again anyone have any suggestions? Thanks, Sean 90Kb

Link to this post | posted 13 Nov, 2019 22:10

DrCatalase

Help,
We got decent yields of DNA that and we tried to digest with NspI. the lanes are from two different phage lysates.
Lanes:
1. DNA1 water
2. DNA1 water Buffer NspI (NEB 37 degrees 15 minutes)
3. DNA1 water Buffer
4. Ladder
5. DNA2 water
6. DNA2 water Buffer NspI (NEB 37 degrees 15 minutes)
7. DNA2 water Buffer

We got no digestion except smearing in lane 6… we want to try again anyone have any suggestions?
Thanks,
Sean

Posted in: Phage Discovery/Isolation → DNA Isolation from M. foliorum - any updates?

Link to this post \| posted 30 Apr, 2019 13:51
DrCatalase	After uranyl acetate staining how long is the sample on the grid usable for EM? Thanks Sean

Posted in: Phage Discovery/Isolation → EM Sample Stability

Link to this post \| posted 08 Dec, 2018 03:48
DrCatalase	Thanks I will try tomorrow.

Posted in: Using WINE to run DNA Master on a Mac → Help with WINE

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