Link to this post | posted 11 Sep, 2019 14:02
welkin	Hi Christine, I moved your thread to "gene or not a gene" because it is not really a question about using PECAAN but more about how to use GeneMark data to determine the gene content of your annotation. In order to give you the best answer, we need some more information— which phage is it? Could you please provide the GeneMark output you are looking at here? Thanks so much! Welkin

Link to this post | posted 12 Aug, 2019 18:19
welkin	Hi Steve, I think 121 is located too far away from the other called terminase gene to be a viable candidate— unless we demonstrate it at the bench. so not for now.

Link to this post | posted 16 Jul, 2019 16:50
welkin	I think if the small term or a pham with equivalent phyre predictions is present in every cluster K, it makes sense to designate both as small and large. Are there any that are missing the "small"?

Link to this post | posted 16 Jul, 2019 13:56
welkin	Hi All, Debbie and I spoke about this one, and decided to go with "antirestriction protein, OCR-like" for consistency. I do like the "DNA mimic" label– it is far more descriptive of what the protein actually does. Maybe we need to start writing some of function glossary to capture what these do. Welkin

Link to this post | posted 15 Jul, 2019 14:53
welkin	Hi Steve, We think "tellurium resistance protein D family" is the way to go. "Ter" is also the TLA for the terminase genes (which we also don't use) and we may sow confusion if we don't spell things out. Thanks!

Link to this post | posted 12 Jul, 2019 16:47
welkin	Hi! I think the first should stay as "minor tail protein" and the the second as "NKF". Tail fibers can be all sorts of sizes; they are best identified by wet bench work. Bioinformatically, they have long extended trimeric regions like triple-coiled coils or "collagen" domains.

Link to this post | posted 01 Jul, 2019 13:21
welkin	Hi All, Aragorn is back up and working. Best, Welkin

Link to this post | posted 28 Jun, 2019 15:51
welkin	I've heard back from Bjorn CAnback— he is aware that the server is down and is working to bring it back online.

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.

Link to this post | posted 26 Jun, 2019 18:52

welkin

From Amy Sprenkle: "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."