Link to this post | posted 30 May, 2018 16:09
ksaville	Hi I tried submitting our annotation on phagesdb and received a 502 gateway error. I tried a second time and received an 'internal server' error. Please advise

Link to this post | posted 24 May, 2018 19:42
ksaville	HI The instructions for the authors file for the annotation submission say to include last name, first name, and middle initial in three columns but the example has last name, first initial, middle initial should we include first name or first initial?

Link to this post | posted 22 May, 2018 01:10
ksaville	Awesome. Thanks chris

Link to this post | posted 21 May, 2018 20:13
ksaville	We think we have a translational frameshift of the tail assembly protein. We found the slippery sequence GGGAAA and annotated the two regions. When validating, we get a message saying the two genes share a 5' coordinate. Are we supposed to delete the first gene after editing the second gene to have 2 regions? this gets rid of the error, but I don't see that in the instructions.

Link to this post | posted 15 May, 2018 14:59
ksaville	We have that too. I think it's OK. The 3 bp overlap between the end of the wrap around gene and gene 1 is pretty common. 15-18 The end of the wrap around is ATGA. The TGA is a stop here 15-18 The beginning of gene 1 is ATGA the ATG is a start here. I guess this is a 4 bp overlap - again, pretty common

Link to this post | posted 15 May, 2018 13:21
ksaville	Related to this. We also have a wrap around gene in a C1 phage. The online documentation explains how to annotate this situation, but in the online example the wrap around gene is listed as the first gene in the list, even tho it's gene 252. Ours is gene 258 and is listed as gene 258, is this OK?

Link to this post | posted 26 Jan, 2018 15:57
ksaville	I have been unable to get web phamerator to work. When I click white space next to a phage, nothing happens and then eventually I get a phamerator not responding message. Is this a wide spread issue or something on my end?

Link to this post | posted 23 Jan, 2018 21:12
ksaville	Thanks Lee

Link to this post | posted 23 Jan, 2018 18:24
ksaville	When I get to the web phamerator page, there are check boxes for various clusters. It seems to take a long time to draw all the maps of the clusters. How do I pick just a few phage at a time? Or, better yet Is there an instruction guide specific for the web version? Sorry if I've missed something obvious Ken

Link to this post | posted 17 Nov, 2016 22:06

ksaville

Thank you Stephanie - that's an awesome protocol. I will defintitely give it a try next time around. We ended up designing primers that would distinguish just the two phages we were working on. I had students compare their phage to others on phamerator to find a region that was somewhat specific to their phage. Then design primers based on that sequence. We then ordered them and did PCR on the two different phages we were working on in the lab. it worked well with each primer set amplifying the expected phage but not the other one. These phages were in different clusters and we knew ahead of time that the regions were different, but it was still nice to see it work. for the PCR we simply used a pipet tip to take a plug of a plaque, heated that up, spun it down and used the supernatatant as the template. i'd have to dig deeper for any more details than that. Ken