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.

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?