Link to this post | posted 01 Feb, 2019 03:50
debbie	Hi Denise, If you find one transmembrane domain with TMHMM, you can only call it a membrane protein if you can validate it with a different transmembrane finder (such as SOSUI). (If two different algorithms detect a trans membrane domain, you can hopefully rule out false positives.) Does that clarify it? debbie

Link to this post | posted 22 Jan, 2019 01:54
debbie	The infernal score for the tRNAs called is lower than what is described in the guide. Use an infernal score of 20 for the tRNA calls in Cluster C annotations.

Link to this post | posted 22 Jan, 2019 01:52
debbie	In the past few months, my students and I have annotated ~60 Cluster C genomes. While not perfect, they are as good as I get get for now. Remember to follow the guide call the tRNAs EXCEPT using a lower infernal score. We used scores as low as 20.

Link to this post | posted 22 Jan, 2019 01:47
debbie	Sometimes there is an HNH in the nucleotidyl transferase. Call the nucleotidyl transferase.

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!