SEA-PHAGES | HNH vs methylase in Cluster J phages.

Link to this post \| posted 10 Jun, 2019 17:52
asprenkle	We from cohort 11 adopted a Cluster J phage in the spring of 2019 to make sure we really got trained in all of the bioinformatics tools available. Hannaconda did not disappoint. I relied heavily on the Pope J Cluster paper for guidance, and worked on the TAC frameshift successfully from the excellent bioinformatics guide and help from Welkin. We used PECAAN and had two tRNAs called, and I learned at the symposium that the web-based aragorn would call introns as well. I failed to throughly explore this tool before submitting the genome, so I will continue to work on that. I message in this string because when searching for J cluster and introns, this is what pops up. It is not at all clear to me how one uses phamerator to see the introns, because they are not described in phamerator the way they are in the paper. Also, some of the J phage from the paper have an intron and others do not. Those that do are not consistent with regard to their association with HNH endonucleases. Any help with better calling of an intron would be appreciated. With regard to the HNH endonucleases, there are many of them in Hannaconda, 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 17:52

We from cohort 11 adopted a Cluster J phage in the spring of 2019 to make sure we really got trained in all of the bioinformatics tools available. Hannaconda did not disappoint. I relied heavily on the Pope J Cluster paper for guidance, and worked on the TAC frameshift successfully from the excellent bioinformatics guide and help from Welkin. We used PECAAN and had two tRNAs called, and I learned at the symposium that the web-based aragorn would call introns as well. I failed to throughly explore this tool before submitting the genome, so I will continue to work on that. I message in this string because when searching for J cluster and introns, this is what pops up. It is not at all clear to me how one uses phamerator to see the introns, because they are not described in phamerator the way they are in the paper. Also, some of the J phage from the paper have an intron and others do not. Those that do are not consistent with regard to their association with HNH endonucleases.
Any help with better calling of an intron would be appreciated.

With regard to the HNH endonucleases, there are many of them in Hannaconda, 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 26 Jun, 2019 16:56
welkin	copied over from Cluster J annotation tips. Intron question has been moved to "Frameshifts and Introns" Edited 26 Jun, 2019 18:53

Link to this post \| posted 26 Jun, 2019 18:55
welkin	REgarding the HNH and DNA methylase overlap– we have some wet bench evidence that out-of-frame HNHs are made when found within the context of overlapping a DNA methylase or DNA polymerase gene. So in these instances, it is OK to call both genes, even with the large overlap– as long as you are confident that both are intact and functional.

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HNH vs methylase in Cluster J phages.