Link to this post | posted 05 May, 2025 14:46

c.sunnen

Hi! Annotating B1 phage AngelCake. Phamerator gene 33 (stop=33956) has a very good HHPred hit to a newly published protein complex: https://www.rcsb.org/structure/8JOU. The hit has 99.9% probability, 97% coverage (the hit protein doesn't extend beyond the query C or N terminals), e-29. The second hit is to another phage protein that appears to be in the "neck" complex, but the article isn't published, and the specific chain doesn't have a distinct function attached: https://www.rcsb.org/structure/9C39 This is also newly published. Other B1 phages we annotated last year (Hartsy, LasagnaCat, CampRoach) did NOT hit to either of these proteins, but they both appear to have been added to the database recently. The gene in question is immediately downstream of the minor tail proteins and has 614 members of the pham, but the protein(s) it's hitting to seem to be tail fibers and/or adaptors from a podophage, as well as neck proteins in a Shigella phage. Any guidance on what to call this? For now I assume NKF, but clearly this is a structural something… Picture of HHPred alignments attached. Nikki 141Kb

Link to this post | posted 20 Feb, 2025 18:52
c.sunnen	I tried opening and closing DNA Master, but that didn't fix it. Haven't tried a reboot of the actual computer. I'll give that try a bit later, and if still no luck, I'll shoot the file to you. Thanks, Debbie!

Link to this post | posted 20 Feb, 2025 16:58
c.sunnen	Hi! I am trying to make a genome profile of M. smeg, and I am also getting this "Floating point division by zero" error message. I've tried unchecking the "Load into Excel" box and a variety of other check/uncheck options, but I keep getting the error. My students want to see all of the tRNAs, and this seemed easier than having them pour through the entry on GenBank… Thanks for your help! Nikki

Link to this post | posted 04 May, 2024 13:29
c.sunnen	Thanks, Debbie. Will check back in later, before we send it in.

Link to this post | posted 03 May, 2024 17:55

c.sunnen

The paper you linked has a nice RNAseq map of Fruitloop in Figure 4, in addition to the mass spec data in Table 1. Yes, that's very helpful! Fruitloop does have 95% sequence similarity in this region to PhesterPhotato, and Fruitloop doesn't call either of these genes (46 and 47 in PhesterPhotato). When I look at GM-S coding potential from Fruitloop in this area, there is a little CP in the forward direction in the gap between 43 and 44 (between 45 and 48 in PhesterPhotato), but it's only atypical, and not as strong as it is in PhesterPhotato. The RNA seq from Fruitloop makes it look like MAYBE there's a reverse gene in there that gets expressed during lysogeny, but it's hard to see, and definitely there's not a forward gene expressed. The mass spec doesn't show these genes being made (nor the flanking reverse genes, either though, including the immunity repressor), but I guess that's still evidence that neither of these is real. I'll delete both 46 and 47 from PhesterPhotato, so that it matches with Fruitloop. Thank-you!

Link to this post | posted 03 May, 2024 17:55

c.sunnen

The paper you linked has a nice RNAseq map of Fruitloop in Figure 4, in addition to the mass spec data in Table 1. Yes, that's very helpful! Fruitloop does have 95% sequence similarity in this region to PhesterPhotato, and Fruitloop doesn't call either of these genes (46 and 47 in PhesterPhotato). When I look at GM-S coding potential from Fruitloop in this area, there is a little CP in the forward direction in the gap between 43 and 44 (between 45 and 48 in PhesterPhotato), but it's only atypical, and not as strong as it is in PhesterPhotato. The RNA seq from Fruitloop makes it look like MAYBE there's a reverse gene in there that gets expressed during lysogeny, but it's hard to see, and definitely there's not a forward gene expressed. The mass spec doesn't show these genes being made (nor the flanking reverse genes, either though, including the immunity repressor), but I guess that's still evidence that neither of these is real. I'll delete both 46 and 47 from PhesterPhotato, so that it matches with Fruitloop. Thank-you!

Link to this post | posted 02 May, 2024 21:23

c.sunnen

Hi! We are annotating PhesterPhotato, an F1 cluster phage, and it's got some extra weirdness, even for an F1! Please see the attached Phamerator + Genemark output picture. There's a forward gene (47) in the middle of a small group of reverse genes. It overlaps. But there may be a reverse gene instead (46). There's evidence for both, though better CP for the forward (47) than the reverse. Some other F1s call the forward (12 total members in pham), some call the reverse gene (again, 12 total members). If I call the reverse, in order to capture the CP, I'd have to create an overlap with gene #48, which no one does, so I'm feeling like this tiny reverse gene isn't real. But why would there be a forward in the middle of these reverse? Creating an overlap? Most other phages don't call either, and just leave a big (300bp) gap. Please help. It's in PECAAN if you want to look at it there. No evidence for function for either 46 or 47, but 48 is likely the immunity repressor. Thanks! Nikki & the SJU team 1.89Mb

Link to this post | posted 12 Jan, 2024 20:59
c.sunnen	Thank-you, David, for all that you have given to us, to the program, and to the students. Congratulations on your much-earned retirement! You will be missed, but your legacy will live on. Congratulations! Nikki Sunnen Associate Prof of Practice Saint Joseph's University (and formerly University of the Sciences) csunnen@sju.edu

Link to this post | posted 17 Mar, 2023 12:49
c.sunnen	Thanks for that, Debbie! I often wonder what exactly makes the sequence "slippery" other than the obvious repeat of bases, but it's nice to know that as long as the amino acid sequence comes out right, we don't have to worry too much about which coordinate/base we annotate as being repeated.

Link to this post | posted 16 Mar, 2023 18:27

c.sunnen

I am QC-ing the frameshift in DY cluster phage Tarzan. It is a GN to GK, -1 frameshift with a slippery sequence of GGG.GGA.AAC, where it appears that the first A gets counted twice. This is most similar to the GN to GK slip seen as #15 in the table within the Bioinformatics guide (GGGAAAT). However, 2 of the 3 annotated phages (Jojo24 and Reyja) annotate the slip at the third G instead, making the slip actually a GG to GG. I lean towards the GN to GK, since it's more similar to others where it slips at the first A, but perhaps there's something I don't know? Which one is it? Screenshot from Tarzan attached. 1.22Mb