Link to this post | posted 20 Feb, 2019 17:05

debbie

Hi all, I can weigh in on this. In the papers that we wrote about Cluster O, J, and M, we did some mass spec. The data showed that where there were 2 starts in a row, no methionine was present in that mass spec data. The interpretation of that is likely that post-translational chopping of the initiation methionine occurred. (So there could only be one present to chop.) I just scanned the papers to see if we wrote that in one of them but couldn't find it. So by all means take a look to see if it is there. But that is why we suggest that the second start codon (1 base overlap) be called. It is hard to do, when you are progammed (like me) to look for the 4-base pair overlap and all other data - usually the SD score - points to the first start codon as the better call. But you can do it! It also was not done on lots of files and it is difficult to pinpoint to fix.

Link to this post | posted 11 Feb, 2019 22:12
debbie	I believe that GeneMark is now working! Back in business! debbie

Link to this post | posted 11 Feb, 2019 11:20
debbie	Dana, Hi. I believe that the issue is a licensing issue that we need to do on our end. It should be fixed later today. debbie

Link to this post | posted 05 Feb, 2019 20:00
debbie	Rick, You are right, because Emporer and the prophage in G. westfalica are identical sequences, the Emporer hit is buried. Check out the alignment, you will see +2 more titles. You will find Emporer there.

Link to this post | posted 05 Feb, 2019 17:53
debbie	Rick, I believe the simple explanation is that the BLASTp database(s) have not incorporated the Emperor submission yet. Which, I agree seems odd.

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