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.

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