Link to this post | posted 26 May, 2019 19:47
lhughes	Steven Caruso These are big phages. S. Yep! At least the large terminal repeats actually bring the total down a little bit (since both ends should be identical, you only have to annotate one end and then just match the other one), but still large. And the massive number of tRNA's increases the workload too. Lee

Link to this post | posted 24 May, 2019 21:03
lhughes	Steve, I would just note that any tRNA calls for most of the BE1 phages already in GenBank were called using the rules AS THEY EXISTED AT THE TIME of their annotation. That could be part of the discrepancy. Keep in mind that some rules also overrule other rules, so that could also be part of the difference. Lee

Link to this post | posted 10 Apr, 2019 13:54

lhughes

My best guess is that the field isn't actually empty, but has something in it (a space perhaps, or a hard return), which is why it isn't being labeled. You probably need to make sure those fields are actually empty in order to get them to write. If you are copying and pasting into the Function field at some point in the process, you might have an extra hard return in the data (this can happen when copying from other programs) that is still in the field and causing the problem. Lee

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