Link to this post | posted 01 May, 2020 20:00
debbie	Hi Jamie, I would continue to call this a tail terminator for 2 reasons. One, the minor tail protein of lambda that it hits is a tail terminator along with the SPP1 hits. Secondly, it is in the right place for it. I agree, we fall under the threshold of 90% probability, and I usually don't consider anything under 90%, but in this case I think it is a good prediction.

Link to this post | posted 30 Apr, 2020 09:31
debbie	Fred, I too would be inclined to delete this gene. debbie

Link to this post | posted 30 Apr, 2020 09:22

debbie

Hi Fred, My recommendation is to not take any one piece of data when making this decision. I believe the best start can most easily be derived from the Starterator report. Take a look. comparative data is always useful. Let me know if you have additional questions. debbie PS There is a lot of biology in the answer to your general question. The ribosome loves to treat the sequence like one big operon, but that isn't what happens. Starts and stops along the way have to do with regulation, most of which falls into the 'I don't know why' category.

Link to this post | posted 26 Apr, 2020 14:47

debbie

Hi Fred, Thanks. First of all, Heath is a cluster B4 phage. Have you noticed the orange lines that crisscross the B4 genomes in phamerator. Do you know what that is indicating? They are likely some sort of repeats. There are 2 resources to point you to: 1. A paper: Cluster K mycobacteriophages: insights into the evolutionary origins of mycobacteriophage TM4 2. Check out Section 4.2.3.in this doc "Exploring bacteriophage biology". It would be great to look for them! What you don't want to do is include the repeats in your protein calls. In both cases, I would call the genes much shorter than you, mostly to respect the coding potential. For gene 79, I think most of the data fits a start at 63861. For gene 74, I think that most of the data fits a start at 62311. Let me know what you think or if you have additional questions. Please add the forum post (just a link) to your cover letter when you submit this genome. So that the reviewer knows the energy that you invested in the calls. debbie

Link to this post | posted 25 Apr, 2020 13:03
debbie	Hi Fred, I would need additional info to help evaluate. What is the phage? Would you attach your DNA Master file? Have you looked at Starterator data? debbie

Link to this post | posted 24 Apr, 2020 14:37
debbie	Hi. I was able to get on a minute ago. Wanna try again? debbie

Link to this post | posted 08 Apr, 2020 22:13
debbie	Susanne, Yes! The correct way to document your tRNA is found here: https://seaphagesbioinformatics.helpdocsonline.com/documenting-trnas-in-dna-master Good Luck, debbie Edited 08 Apr, 2020 22:18

Link to this post | posted 31 Mar, 2020 13:25

debbie

Hi Deb, I knew that the data obtained in PECAAN was static, meaning if you ran the programs on March 2019 and then reviewed on March 2020, the results would be different because the PECAAN data was out-of-date. What I didn't know, or rather didn't quite put together, is that the HHPred databases are downloaded periodically at WKU, allowing all of the programs to run faster. So, Claire Rinehart and colleague, Dex Wood, are actually looking for results such as what you just got to know that the data is discrepant enough to check on database dates. Today Dex found 2 databases out of date and will upload them tonight. When you re-run your HHPred data, the results will change a bit. Good catch! debbie

Link to this post | posted 30 Mar, 2020 12:07
debbie	Kyle, Yes! Have you made a phage page for Gole? That is the first step. Second step is to email Dan with the request to post the sequence there. Cool! debbie

Link to this post | posted 30 Mar, 2020 02:57

debbie

Kyle, 1.The 'missing' gene is a tRNA call. As you investigate, you should be able to discern the discrepancy and what to call. It is tricky. It is not uncommon that the numbers between Phamerator and your DNA Master files do not match. In this case you are talking about the right end of the genome, sometimes the discrepancy is at the left end. So you are lucky. Remember that Glimmer and GeneMark make predictions on a 'random sample' of the genome. Because the 'samples' can be different, the auto-annotation can be different. This is important because it is part of the rationale of why we do the work that we do. Remember in the workshop, I asked that you always orient your self to the stop codon, because all other numbers can be different. 2. What are the end types of your genome? Can you figure out your question about the last 2 genomes once you know that? You will want to be very careful how you annotate both ends of your genome. Have you evaluated the ORF at 63636-64280 (reverse direction)? I am not sure that this is/isn't a gene, but I would strongly consider it. Great genes to consider! debbie