Link to this post | posted 03 Dec, 2019 17:52
debbie	Dana, Thanks for the heads-up. This periodically happens due to the way GeneMark makes this available. It is corrected. Your auto-annotation should now include Glimmer and GeneMark calls. debbie

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