Link to this post | posted 22 Nov, 2019 17:16
debbie	Here is what I know so far. A slippery sequence could not be found in the original EA1 and EA2 annotations. We have looked at EA1 - EA8 annotations so far. Slippery sequences have been annotated in Subclusters EA3,EA4,EA5,and EA6, not in Subclusters EA1, EA2, EA7, and EA8. So if you can find a canonical sequence for the slippage, i would recommend calling it. if you can't, then don't. 212Kb

Link to this post | posted 17 Nov, 2019 18:37

debbie

There are 2 overlapping open reading frames that can show up in your auto-annotations that are ~ the same size somewhere in the vicinity of bp 22,200. One is a HHpred hit to a helicase (difficult to differentiate further, for now). The other does not have significant hits to anything. Be careful to pick the right one. (There are incorrect calls in the database - to be correct.) An example of a good call is Wayne gp29. 11-17-19 debbie

Link to this post | posted 16 Nov, 2019 13:00
debbie	WooHoo! Thanks Chris.

Link to this post | posted 05 Nov, 2019 15:55

debbie

Hi Jordan, If I were calling this genome, I would label both of these proteins as membrane proteins. Neither are great matches to known holins, phages can have more than one holin, and while I may not know which one is a holin, I am confident that they are both membrane proteins. If you are compelled to call a holin, 32 is in a 'more canonical' place. Historically, we called the small protein after lysin A the holin. Now that we are moving away from relying on the location as the sole reason for calling a holin, I am most willing to call these proteins 'membrane proteins'. (Because I can't tell which is the holin, although they both may be holins.) The best writing about holins is from Ry Young, Texas A&M. I don't know if there is a definitive article that he has written that helps, becuase he has written a lot. I kinda liked his J Mol Microbiol, Biotechnol (2002) paper, "Bacteriophage Holins: Deadly Diversity". debbie

Link to this post | posted 01 Nov, 2019 01:06
debbie	Done!

Link to this post | posted 30 Oct, 2019 01:12
debbie	Iain, This is all up to GenBank. They have many folks working through the submissions and they get assigned in ways not know to us. I have files posted in 1 day and I have seen them posted 6 months later. debbie

Link to this post | posted 19 Oct, 2019 00:17
debbie	That would be great! debbie

Link to this post | posted 18 Oct, 2019 01:19
debbie	Hi! Yes, ArV1 is the phage of that paper. Why do you say that AR phages are siphoviridae? debbie

Link to this post | posted 03 Oct, 2019 15:57
debbie	Amy, I am the one QCing this genome and I have not gotten to it yet. Welkin, would you respond to the intron question? I think that info that may be helpful is found here https://seaphages.org/forums/topic/4926/?page=1#post-7336 Thanks, debbie Edited 03 Oct, 2019 17:06

Link to this post | posted 27 Sep, 2019 05:14

debbie

Hi all, Recently Krista Freeman, a post doc in the Hatfull lab, and Julia Kovalski, an undergrad designed primers for 60 cluster/subclusters of mycobacteriophages. These primers were designed for verification of phage lysates in the Hatfull lab (and not to prematurely assign cluster designations to unsequenced phages). Attached is an Excel sheet of the primers/phages. Krista thought having the fasta files of the phages would be helpful. I thought adding a picture of Julia and Krista would be fun! Edited 27 Sep, 2019 05:15 27Kb 2.80Mb 1.17Mb