SEA-PHAGES | Wrap around HNH endonuclease

Link to this post \| posted 11 Apr, 2019 22:55
washj	There is an HNH endonuclease which wraps around in the DT phage Ewald 41027-41524;1-49. How should I handle it? The phage has defined ends with 3' overhang. Thanks!

Link to this post \| posted 13 Apr, 2019 01:26
debbie	Jackie, It is annotated as a gene with 2 regions (just like a programmed frameshift). GenBank will squawk about it, phamerator won't like it, but that is how you will submit the file. Biologically, the phage doesn't care, it exists in the host as a circle.

Link to this post \| posted 10 Jun, 2019 18:00
asprenkle	Hi All, I'm posting this end piece to my 'introns' post just to prove that I'm looking for relevant topics, but not necessarily finding them…and I wanted to contact directly with Jackie as well after the symposium. I hope that's OK, and that the Faculty meeting is going well. If there is anything I can do to improve Hannaconda that is awaiting QC, please let me know. With regard to the HNH endonucleases, there are many of them in Hannaconda (though none of them wrap around!), and my understanding of their function is as tenuous as my understanding of introns and splicing, although I think I understand that they can function together, but do not always have to be associated in the genome. To that point, we found one called with some orphams by the autoannotation in the middle of Hannaconda-Draft (genes 113-116), but there was GeneMark support for a longer ORF that had similarity to a DNA Methylase (113), so I deleted gp 114-116 for our submission. At our 2019 poster, we learned that Yeet-draft (J)had a similar issue with gp 199-123. Tom d'Elia is working on that one. I will post this last bit in an endonuclease forum as well for any feedback.

Link to this post | posted 10 Jun, 2019 18:00

asprenkle

Hi All,
I'm posting this end piece to my 'introns' post just to prove that I'm looking for relevant topics, but not necessarily finding them…and I wanted to contact directly with Jackie as well after the symposium. I hope that's OK, and that the Faculty meeting is going well.
If there is anything I can do to improve Hannaconda that is awaiting QC, please let me know.

With regard to the HNH endonucleases, there are many of them in Hannaconda (though none of them wrap around!), and my understanding of their function is as tenuous as my understanding of introns and splicing, although I think I understand that they can function together, but do not always have to be associated in the genome. To that point, we found one called with some orphams by the autoannotation in the middle of Hannaconda-Draft (genes 113-116), but there was GeneMark support for a longer ORF that had similarity to a DNA Methylase (113), so I deleted gp 114-116 for our submission. At our 2019 poster, we learned that Yeet-draft (J)had a similar issue with gp 199-123. Tom d'Elia is working on that one. I will post this last bit in an endonuclease forum as well for any feedback.

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Wrap around HNH endonuclease