Link to this post | posted 12 Mar, 2021 15:36
debbie	Here is how I would call GiKK's frameshift. 420Kb

Link to this post | posted 12 Mar, 2021 15:21
debbie	Here is how I would call Juicer's frameshift. I use the six-frame translation in DNA Master to find the slippery sequence. I'll look at GiKK next. debbie 327Kb

Link to this post | posted 11 Mar, 2021 02:22
debbie	Follow the case study in the Bioinformatics Guide for calling the function of the genes involved in 7-Deazaguanine modifications. These are genes 1-5 in Rosebush and gene 20 in Orion. https://seaphagesbioinformatics.helpdocsonline.com/article-1596481355 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6884629/

Link to this post | posted 11 Mar, 2021 02:17
debbie	Joe, I think we have some revision work to do. I would follow the case study in the Bioinformatics Guide. Gene 2 should be named "dpdA-like tRNA-guanine transglycosylase". This in accordance with the biochemical analyses from this paper. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6884629/ debbie

Link to this post | posted 06 Mar, 2021 23:43

debbie

Dear SEA-PHAGES faculty, As you know, all of the SEA-PHAGES phage isolates are archived here at the University of Pittsburgh, and these represent a unique and powerful resource. We frequently get requests for these from researchers both within and beyond the SEA-PHAGES program. When sharing phages we try to communicate back to those schools and faculty that we have distributed a phage their students isolated, but to simplify the process we are posting a link on seaphages.org on a forum page that lists requests made (and honored) from SEA-PHAGES faculty for other SEA-PHAGES phages. In this way, it will be fully transparent which of your phages are being shared. In general, this should help to advance the community aspect of the SEA program, if there is some reason you would do not want a phage listed there that you have requested, we will certainly consider it. For requests coming from faculty beyond the SEA-PHAGES program, we will try to communicate to the schools and faculty directly. And of course, all transfers are accompanied by an MTA and abides by the terms of the MTA for SEA-PHAGES phage archiving. Thanks again for all of your contributions to a high impact scientific and education program. debbie and the SEA-PHAGES Team 96Kb

Link to this post | posted 06 Mar, 2021 23:11
debbie	Hi all, When is an exonucleaase a Cas4 family exonuclease? debbie

Link to this post | posted 03 Mar, 2021 17:25
debbie	Hi! Orphams are annotated just like any other gene. If you have evidence for a function, it is added. If there is no data for a function, it is a Hypothetical Protein. Technically, an orpham is a temporal state. Hope that helps! debbie

Link to this post | posted 02 Mar, 2021 22:19
debbie	Hi Susanne, Yes. That is a classic presentation of a programmed frameshift found in tail assembly chaperone genes. There is some introductory info in the Bioinformatic Guide: https://seaphagesbioinformatics.helpdocsonline.com/article-54 https://seaphagesbioinformatics.helpdocsonline.com/article-6 Lots have been written about them in the literature. debbie

Link to this post | posted 02 Mar, 2021 18:41
debbie	The rIIA-like protein and rIIB-like protein assignments are now on the SEA-PHAGES Functional Assignments List. The significant hits are seen when using the UniProt-SwissProt-viral database at HHPred. debbie Also, this links to an excellent read on the proteins. Edited 02 Mar, 2021 18:43

Link to this post | posted 01 Mar, 2021 00:52
debbie	The pfam hits to holin are not great but also not shabby. The typical order of genes is not present in the B1s, so that is also not helpful. However, it is interesting that this gene has 4 transmembrane domains, and the 2 subsequent genes each have 2 transmembrane domains. So I would be inclined to call all three "membrane proteins". Edited 01 Mar, 2021 00:52