Link to this post | posted 05 Mar, 2019 20:43
lhughes	Most of the members of that phamily are called that way now. Steve, I don't know if your original BLAST analysis included the more recent BB1 and BB2 phages since most of those just went live within the last month, but they are updated in Phamerator now. (PECAAN doesn't update automatically unless you ask it to rerun the analysis). Lee

Link to this post | posted 01 Mar, 2019 17:55

lhughes

Have you also looked at some of the other BI1 phages on Phamerator. Several were just added to GenBank and might not have come up during your initial review. These would include IceWarrior, Popy, and Namo. Those all have a holin identified that was not labeled in older genomes like OlympicHelado and Spectropatronm. There is an endolysin gene identified in all the BI1 genomes mentioned above. That is gp5 in all of those. Lee

Link to this post | posted 29 Jan, 2019 04:53

lhughes

Kathleen Cornely Thanks for your suggestion about the profile, Chris! And I did see that all of the starterator genes were on line. But I wanted a full report so that I could upload it to PECAAN. And once I looked up how to upload the database, Starterator worked fine. Thanks again! You don't have to upload the Starterator report in PECAAN. Once you upload the FASTA and the GeneMark file, the data for the Starterator reports will link automatically for each gene. Lee

Link to this post | posted 06 Aug, 2018 19:14

lhughes

I would definitely be on-board with the idea of making the longer call for the second gene (even with the overlap) much like we do with the two overlapping DNA primase genes in many other phage clusters. In this case as in that one, we believe there is a frameshift that we just can't identify, so the longer call would capture more of the information. I think we would be better off not calling the function at this time until there is more evidence to support the call. Debbie/Welkin - if we want to make a change across the board for the genomes already in GenBank/Phamerated, what is your recommended process? Lee

Link to this post | posted 05 Aug, 2018 00:47

lhughes

Hi Ivan, I guess I have a couple of questions on this, as I've tended to err on the side of not calling things unless I felt there was plenty of evidence to make the call. Synteny would say that these are in the correct location to be the tail assembly chaperone proteins. However, the first ORF has no hits at all to any other TAC proteins on either BLAST or HHPRED. To me, the other evidence you provide becomes less certain without this (though quite possibly correct). The inability to find the potential slippery sequence complicates this further. Another question I have relates to the potential DnaJ homology you discuss. Are DnaJ chaperones anything like the chaperone function of TAC proteins (ie. is this an actual relationship of function or not)? I guess part of my conundrum is whether it is "better" to call the long overlap or to call it shorter, given that both are probably wrong. I also don't know if we have enough evidence to make the function call at this point in time (but that is my tendency to call more conservatively). Lee

Link to this post | posted 28 Jun, 2018 17:43
lhughes	Phages in Cluster BE have very large terminal repeats (>10,000 bp). Gene position calls and functional calls for the repeated regions should be identical.

Link to this post | posted 27 Jun, 2018 19:46
lhughes	I just found that the anticodons were incorrect (which doesn't sound like what the error message said) but maybe that is throwing things off. I'm correcting that and trying to submit them again to see if they work now. Lee

Link to this post | posted 25 Jun, 2018 17:35

lhughes

I get the following error from the final Phamerator file check after submission: "SparkleGoddess failed to be imported into Phamerator for the following reason(s): -tRNA at 77662 doesn't appear to have the correct terminal nucleotide" The tRNA is called by Aragorn, but not by tRNA-ScanSE. The acceptor stem does seem to be odd (one mismatch but seven matches) and of course the error above about terminal nucleotide (you can find this genome in PECAAN, but screenshot of the Aragorn output in PECAAN attached). Should this call be deleted? A similar genome, Comrade, has the same error (tRNA at 77362 in that genome). Let me know your thoughts and then I will make corrections to resubmit the genomes to PhagesDB. Lee 79Kb

Link to this post | posted 22 Jun, 2018 18:04
lhughes	Ok - thanks. I'm glad it wasn't just me. I'll make the updates manually in the files that I am submitting. Lee

Link to this post | posted 22 Jun, 2018 03:57

lhughes

I am working on 4 Cluster BK1 genomes which all have lots of tRNAs. When I reached my final review of the genomes and comparisons of their labeled functions, including tRNA, I was surprised to find that the tRNA notes were not matching the tRNA output from Aragorn/tRNAScan. Basically, what I think is happening is that the exported notes are showing the Codon sequence, not the Anticodon sequence. For example, in Annadreamy, the first tRNA (4218-4145 Reverse) shows the anticodon as GGT when you look at the Aragorn/tRNA scan information, but the output from PECAAN gives it as ACC. The reason I noticed it originally was because I had downloaded another BK1, Blueeyedbeauty, sometime last year and it had GGT in the output (but if I re-download now it gives me ACC). Please help me figure this out. These genomes each have over 35 tRNAs in them so I need to make sure I'm getting them in the correct format (and hopefully this is not an issue for others who've done tRNA's recently). Thanks, Lee