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.

Link to this post | posted 23 Nov, 2018 18:30
debbie	Steve, 5A21_E is listed along with 5A21_F as a head-to-tail stopper. debbie

Link to this post | posted 21 Nov, 2018 12:15

debbie

Steve, I am usually reluctant to call that hit to the Pfam data. There is no primary evidence provided. I see that no transmembrane domains are found by TmHmm; Sosui calls 1 transmembrane helix. Can you explain that HHPred (at HHPred) reports a probability of 89.9% but is 34.6% in PECAAN? It is in a believable position in the genome (next to the lysins). Are there any other membrane proteins in the genome?

Link to this post | posted 13 Nov, 2018 17:50
debbie	Done!

Link to this post | posted 31 Oct, 2018 21:11
debbie	Kayla, I have been looking closely at the Cluster B1 phages. I concur with the genes being polynucleotide kinase and terminase. There is no evidence that a small terminase is present in the genome……yet. debbie

Link to this post | posted 31 Oct, 2018 14:17
debbie	Jordan, Hi. I would recommend that you not cite it independently, but rather consider it included in a citation for using the SEA-PHAGES Bioinformatics Guide and procedures. debbie

Link to this post | posted 28 Oct, 2018 14:40

debbie

Rick, Hi. You can find out which clusters of actinobacteriophages are predicted to be temperate by checking the cluster list. http://phagesdb.org/clusters/ There can always be exceptions, but the clues will be present in the genomes. My student researchers have been looking for lysogens by microbacterium phages for a while now. To date, we have one. It appears Zeta1847 forms lysogens. It is a M. paraoxydans phage. debbie Edited 28 Oct, 2018 14:41

Link to this post | posted 24 Oct, 2018 19:10

debbie

Hi all! Sometimes you may be looking for a reference genome and this might help. As of Sept., 2018 I am trying to clear the backlog of genomes and am attacking them cluster by cluster. Cluster B1s are on my list. As of today, October 24, 2018, I have QC'd 9 Cluster B1 phages to the best of my ability. I have cross-checked starts, respected Start-Associated-Sequences and addressed functions as well as I could. I will continue to bust through the list of whatever else is out there, but please use the following genomes as well scrutinized guides for your current/future Cluster B1 annotations: Altwerkus, Cannibal, Dione, Jillium, Keitherie, LuckyMarjie, Riggan, Spartan300, and Zelda. As I do more, I will add them to the list.