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

Link to this post | posted 04 Mar, 2020 19:42
debbie	Success! always a good day! debbie

Link to this post | posted 04 Mar, 2020 18:16

debbie

Bob, The simple answer is that yes, the tape measure in Magel is in two pieces. However, that does not imply a programmed frameshift as we see in the tail assembly chaperone genes. Much bench work would be needed to confirm that there is a ribosomal slippage. It would be great to say that the upstream gene is a particular domain of the tape measure gene, but I don't think that is obvious. However more investigation could help to elucidate if the upstream gene has a particular function that we could identify. debbie

Link to this post | posted 04 Mar, 2020 17:31
debbie	Maria, I just took your file and generated a GenBank file with no errors. Did you choose the "Bacteria and Plant Plastid Code" on the Description pane of Submit to GenBank? all of the genes you have errors for have GTG starts (I think). debbie

Link to this post | posted 03 Mar, 2020 17:50

debbie

Hi all, I am going to chime in here, but my understanding today is that every phage may not have the G/T programmed frameshift. In lots of cases we can only find homologues to G and nothing to T. If the downstream gene of the frameshift does not have homologues and you cannot find a slippery sequence as denoted in the review paper cited in the guide https://seaphagesbioinformatics.helpdocsonline.com/article-54 , do not 'force' a frameshift. I would not call 4Gs, not followed by 3 of something else as a slippery sequence (though we have done it in the past). Is that the case here? debbie

Link to this post | posted 01 Mar, 2020 13:01

debbie

Hi Greg and all, Delete the 2 N's in the sequence pane of the file. Then click the "Raw" button (top right corner). I could try to tell you what "Raw" means, but I do not know the origin. What this button does is some form of reformatting to the sequence (to endure there is no 'hidden' characters) that allows the change to be posted. (Also make sure that the little 'lock' icon in the bottom right corner is 'open (unlocked). debbie