Link to this post | posted 10 Jan, 2019 15:58
debbie	Hi all. I just reviewed the genes between the capsid and tapemeasure and propose this revision (to gene 8 of phage Blair). gene 8 (5293-5649) head-to-tail adaptor gene 9 NKF gene 10 major tail protein gene 11 minor tail protein (see forum post https://seaphages.org/forums/topic/4836/?page=1#post-6932 ) gene 12 NKF gene 13 tapemeasure Edited 10 Jan, 2019 15:58

Link to this post | posted 09 Jan, 2019 22:18

debbie

Nikki, Hi. I went back and looked at the genes around capsid, major tail, and tape measure because of your question. I am going to ask Welkin what she thinks about this gene because I still want to call it a minor tail protein. However, I want to make some changes/confirmations in the nearby genes. Using PECAAN (and phamerator's gene numbering) I would call the following functions in that area: gene 8 (5293 - 5649) is a head-to-tail adaptor gene 9 is NKF gene 10 is the major tail gene 11 is the one I want to keep as a minor tail. Mostly because of the pfam hit to P2's Phage tail S gene. It also matches HK97 gp 10 (Pfam) which we are not calling as a function, but know it is a structural gene but also know we (I mean the folks who study HK97) don't know what it does. gene 12 is the tape measure. Not helpful yet, but getting there. debbie

Link to this post | posted 06 Jan, 2019 23:17
debbie	Mary Ann, We believe that both of genes are real. Not exactly sure how they are working together, but call that BIG overlap; its OK! debbie

Link to this post | posted 14 Dec, 2018 13:55
debbie	Rick, Yes. it is down. We (including Steve) are at the 2018 Bioinformatic Workshop. We are wrapping things up and heading home today. Steve cannot connect to his server here, he will re-boot the server upon his return to campus. Edited 14 Dec, 2018 13:57

Link to this post | posted 08 Dec, 2018 00:45
debbie	Hi. Do you only get one feature? There is only 1 sequence for each fasta. I can't tell what you mean. Could you post or send me the file? djs@pitt.edu

Link to this post | posted 29 Nov, 2018 17:04
debbie	Remember to look for the tmRNA in these genomes. Just about all, but not all, of them have 1!

Link to this post | posted 29 Nov, 2018 17:03

debbie

I have been clearing the Cluster C1 genomes on the Genome Exchange. Here's my tRNA tips! I made a decision to follow the tRNA calls of an RNA guy here at Pitt (Dr. Craig Peebles). Some of these tRNAs may not make the infernal score cut-offs, but have passed his inspection. Please follow these tRNA calls in your cluster C1 genomes. I am getting all Cluster C1 genomes from the genome Exchange processed. So far, you can look for these specific gene calls in Bonray, TinyTim, Khaleesi, McWolfish, Morizzled23, Jessibeth14. The original genomes that were looked at by Dr. Peebles include: Bxz1, Catera, ET08, LRRHood, Myrna, Rizal, ScottMcG, Spud. Any of these should have reviewed tRNA calls. Edited 30 Nov, 2018 18:09

Link to this post | posted 29 Nov, 2018 17:02

debbie

While there is never going to be one perfect genome, my students and I are using comparative analyses to arrive at some of our best gene calling. We have recently submitted a set of genomes that are close. As we do more, I will add them. Here are the current ones. Bonray, TinyTim, Khaleesi, McWolfish, Morizzled23, Jessibeth14 Note: I made a decision to follow the tRNA calls of an RNA guy here at Pitt (Dr. Craig Peebles). Some of these tRNAs may not make the infernal score cut-offs, but have passed his inspection. Please follow these tRNA calls in your Cluster C1 genomes.

Link to this post | posted 27 Nov, 2018 17:39
debbie	Steve, I just called a different genome with the same configuration. I think it is appropriate to call this gene the holin.

Link to this post | posted 23 Nov, 2018 18:54
debbie	Steve, you mean the table at the end of the case study, right? That is because that gene only hits F and not E. I am not sure how to avoid the confusion. E is in the Functional Assignment list appropriately. If you have a better suggestion let me know.