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the programs on March 2019 and then reviewed on March 2020, the results would be different because the PECAAN data was out-of-date.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 Today Dex found 2 databases out of date and will upload them tonight.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

Link to this post | posted 23 Mar, 2020 20:04
debbie	Hi Nikki, If there is an intron in the tRNA, we are not calling the tRNA. There may have been times where we thought we could call them, but at the present time we are not calling them. debbie

Link to this post | posted 21 Mar, 2020 20:06

debbie

Hi all, I got curious about this, because technically I thought a heuristic model and one that is trained on self were the same thing. GenemarkS was written for 'bigger' genomes. I believe it is as suggested, that the decision as to what server a genome is sent to is its length. I picked a few genomes and ran GeneMarkS at phagesDB (with the buttons). It looks like smaller genomes, below 50k, are run through GeneMark's heuristic program and ones that are larger, greater than 50k, through the GeneMarkS program. (Check out the GeneMarkS output of PSullivan (49990 nt) and Pistachio (50006 nt). If you don't like the noise of the heuristic modeling, you can run GeneMark at their website using GeneMarkS. By the way, I have been working on a few papers with Graham, where repeat sequences are analyzed. These analyses have shown that 'capturing all coding potential' is not always the best answer. Happy annotating! Edited 21 Mar, 2020 20:11 209Kb 180Kb

Link to this post | posted 17 Mar, 2020 19:14
debbie	Chris, Thanks! Someday I will learn how to do the queries. debbie

Link to this post | posted 17 Mar, 2020 00:42
debbie	Lee, Do you have any Streptomyces phage genomes with a lysin B? debbie

Link to this post | posted 05 Mar, 2020 16:42
debbie	Yes, the tail length might reflect the differences. However, if the two genes are stitched back together, the tail would be the same length. It would be a great exercise to ask students to provide an explanation for how that could happen, by checking out the literature. Fin, right? debbie