Link to this post | posted 04 Oct, 2019 17:28

asprenkle

Thank you so much, Debbie and Welkin! I know you have so much to do. I was noticing on the phagesdb page for Hannaconda, it is not in the archives, which might lower any enthusiasm to get it out of the genome exchange and publish the sequence anyway. It was such a good exercise for us as newbies with no genome of our own though, and I'm glad we tried to tackle it. I will keep focused on meeting the goal this second semester to get enough phage of our own to archive and sequence!

Link to this post | posted 01 Oct, 2019 20:57
asprenkle	I noticed this request for help in calling introns had received no reply, and Hannaconda is still awaiting QC, whereas our other phage from the Genome exchange has received an accession number. Is there anything I should be doing to address this?

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 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 17 May, 2019 16:46
asprenkle	http://phages.wustl.edu/starterator/Pham52558Report.pdf Annotating J cluster this pham is not found in starterator, but is in phages.db and is not an orpham. I see that CDShaffer is away, but just thought I'd post as per the instructions on the file not found page.

Link to this post | posted 07 Apr, 2019 20:10
asprenkle	Yes, it's working now. And I got the pleasant surprise of logging on and seeing that students had actually been working on our phage outside of class. Little victories…

Link to this post | posted 05 Apr, 2019 14:21
asprenkle	Friday AM 4/5/2019 This site can’t be reached discover.kbrinsgd.org refused to connect. Try: Checking the connection Checking the proxy and the firewall ERR_CONNECTION_REFUSED

Link to this post | posted 06 Jul, 2018 23:05
asprenkle	Cohort 11, going to the 11B workshop tomorrow! Downloaded the app from Google Play to my android phone. Tried to create account using .edu email and nothing happens. Preparatory info for the workshop suggests that I should get a link confirming the account from my email? Tried restarting my phone, no effect. Any ideas?