Link to this post | posted 06 Apr, 2022 16:44
debbie	Yes please! They should be identical to whatever is the beginning of the genome.

Link to this post | posted 06 Apr, 2022 16:32

debbie

Amaya, That is because I recently removed MuF from the function list because it does not describe a function. Originally we thought MuF was a minor capsid protein, but we have a bit of experimental evidence that it doesn't show up in the capsid. There are some papers about how rampant this gene (and its homologues) are found, but still haven't found ay good evidence of what it is. If you have evidence of the portal, please call it. I hope that helps, debbie

Link to this post | posted 06 Apr, 2022 16:29
debbie	All information is informative. I guess it depends on how you use it! It might be helpful to do a protein alignment. debbie

Link to this post | posted 06 Apr, 2022 16:25
debbie	No, I meant the phage pages, they describe the specific ends type of the phage genome. I am trying to remember a good resource that gives the biology behind this, but I am still thinking about that. Although, there will be some good info concerning this in one of Dan's videos. https://phagesdb.org/workflow/videos/phageterm/ debbie

Link to this post | posted 06 Apr, 2022 16:14

debbie

Hi. Genome organization is something that is worked out during the sequencing of phages. We are keen to make sure we have been precise with the ends of our phage genomes. The type of ends fall into 3 categories: Those with cos ends, meaning there is an overhang of sequence, usually about 10 bases long this 'sticks the genome together Those with no ends - because these phages use a head-full-packaging mechanism that puts in > the genome length, but the start/stop of that length is not the same in every genome Those with direct terminal repeats, meaning that that genome when it circularizes in the host will overlap for the length of the repeat - so even though you see identical genes at the front and back of a genome (and you SHOULD see identical genes because the sequence is identical) there will only be one copy of them in the working phage genome. The phage page is chocked full of information about the phage, check there to see how Ottawa and Kharcho's genomes are described! Best, debbie Edited 06 Apr, 2022 16:21

Link to this post | posted 01 Apr, 2022 19:45

debbie

Hi Shima, Each time Glimmer and GeneMark predict coding potential, they use a SAMPLE of the genome to create their profiles. So the output that is then displayed in Phamerator and DNA Master can be different because data was generated independently. In my world, that is a good thing. The math of Glimmer and GeneMark breaks down for small open reading frames, and requires personal attention. (It is why we do what we do.) The outputs are showing you that a human is going to have to discern where the gene is and support that call with the data in total. It is also why I use the STOP codon of an open reading frame to identify a gene, because all others numbers can be different. debbie

Link to this post | posted 31 Mar, 2022 15:00
debbie	Exactly!

Link to this post | posted 30 Mar, 2022 19:08
debbie	Hi Pam, In some of our older protocols at Pitt we have some plaque picture taking protocols found here: https://phagesdb.org/workflow/Toolbox/. We use a gel doc to photograph plates. debbie

Link to this post | posted 30 Mar, 2022 17:50
debbie	Hi Ann, No, I don't believe that sequence is a tRNA in the phage, but if you integrate it into smeg (you will find that it completes a tRNA gene in M. smegmatis (tRNA Thr (Msmeg_6152)). It is picked up by tRNAScanSE because it is likely half of a tRNA that is made when the phage is integrated as a prophage. There is nothing to call in the phage annotation for this. Make sense? debbie

Link to this post | posted 29 Mar, 2022 20:24

debbie

Hi Allison, There are a lot of routes that our phages take to integrate, and close to the integrase is a good way to address it. We - I mean Graham, has spent a lot of time looking for integration sites in the Mycobacteria and proving them biochemically. He is writing a review article that gives a great summary, so when it is available it will help a lot. In the meantime, the first thing you want to know is what kind of integrase you have. The large serine integrases can have an attachment site that is but 3 bases in length. so without some bench work, that is going to be difficult. The tyrosine integrases have arm extensions that make it more readily identifiable. You can look up Bxb1 integration (first author is Pallavi Ghosh). Some of our best data published is in M. abscessus (Dedrick, 2021) because we found the prophages and could see the sequences of the attL and attR in the hosts. Those reads should help to get you started. Some of our phages like to integrate into tRNAs. Being able to match the attP to an attB is also needed, so know in the host sequence will be needed. After you read the Dedrick papers, I think you will see why the answer to your questions are not simple. Having said all that, another paper in the works is a prophage finder, that will help identify attL and attR. So much to do!