Welcome to the forums at seaphages.org. Please feel free to ask any questions related to the SEA-PHAGES program. Any logged-in user may post new topics and reply to existing topics. If you'd like to see a new forum created, please contact us using our form or email us at info@seaphages.org.
Recent Activity
All posts created by debbie
| Link to this post | posted 18 Mar, 2021 00:17 | |
|---|---|
|
Chris, To back up in the sequence, we run into stop codons and I don't see how to slip over them. I went back in the literature and found another paper with a list of published slippages. There is a supplemental table with lots of examples, providing a bit more confidence in the CCCAAAT sequence. (attached) I think we should call it. It is compelling that if the BK sequences slip, the BE sequences must also. Even the GeneMark shows a pattern that suggests it also overlaps/slips. I don't think I can call, it but even without HHPred data for the "T" gene, i would still suggest it is the tail assembly chaperone. Well - all of you that are looking at these phages, what do you think? debbie |
112KbPosted in: Frameshifts and Introns → No frameshift in cluster BK1?
| Link to this post | posted 17 Mar, 2021 21:25 | |
|---|---|
|
|
Hi all, I just looked at a couple of these. In the paper referenced in the manual, the sequence XXXYYYZ is described as the canonical sequence. Right? In the 2-3 sequences that I looked at there is such a sequence CCCAAATctt (Position 22920 in Emma1919). Lee does your genomes have that sequence? Is CCCAAAT conical enough (not really found on the list)? Does HHPRED have hits for either G or T to the TAC? What other evidence is needed? I think that together we can come up with a really good answer to this (and then make changes to the other files). Let me know what you think! Lee - thanks for checking in on this one. debbie |
Posted in: Frameshifts and Introns → No frameshift in cluster BK1?
| Link to this post | posted 16 Mar, 2021 15:16 | |
|---|---|
|
|
Hi Sara and students, I believe we took the function "capsid morphogenesis protein" on purpose. As I review the HHPred for this gene I am inclined to call it "capsid maturation protease and MuF-like fusion protein". What do you think? debbie |
| Link to this post | posted 12 Mar, 2021 15:36 | |
|---|---|
|
|
Here is how I would call GiKK's frameshift. |
Posted in: PECAAN → Choice of join in frameshift
| Link to this post | posted 12 Mar, 2021 15:21 | |
|---|---|
|
|
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 |
Posted in: PECAAN → Choice of join in frameshift
| Link to this post | posted 11 Mar, 2021 02:22 | |
|---|---|
|
|
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/ |
Posted in: Cluster B Annotation Tips → PreQ^o Pathway
| Link to this post | posted 11 Mar, 2021 02:17 | |
|---|---|
|
|
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 | |
|---|---|
|
|
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 |
Posted in: Shared SEA-PHAGES Phages → Shared SEA-PHAGES Phages
| Link to this post | posted 06 Mar, 2021 23:11 | |
|---|---|
|
|
Hi all, When is an exonucleaase a Cas4 family exonuclease? debbie |
Posted in: Functional Annotation → Phage gene annotation has matching phage genes have 4 different proteins - which one is a match?
| Link to this post | posted 03 Mar, 2021 17:25 | |
|---|---|
|
|
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 |
Posted in: Annotation → ORPHAMs