Link to this post | posted 08 Oct, 2021 20:05

afreise

Hi everyone, Our former primary SEA-PHAGES faculty member, Jordan Parker, was an expedited submitter and had been doing things somewhat differently than the general SEA-PHAGES requirements. For example, she (and I) have been asking students to take notes using a customized template in the PECAAN "Notes" box. Jordan has since left UCLA and I am now the primary faculty for SEA-PHAGES at UCLA. Now that Jordan has left UCLA, I need to return to the standard SEA-PHAGES requirements for recording annotations since I am not an expedited submitter. Since we have been completing our annotations in PECAAN since I started teaching the course, I want to make sure I'm doing things correctly going forward. The PECAAN output actually does follow the DNA Master notes requirements exactly - so do I need to make edits to our template and/or have students fill things out differently as we complete our primary annotations in PECAAN? Or is the standardize PECAAN output sufficient? I have attached the output from PECAAN for PumpkinSpice so you can see the template we are using, if that is useful. Hopefully this is acceptable for PumpkinSpice, at least, since it was a huge genome and those students have since graduated! Thank you in advance for your guidance! 652Kb

Link to this post | posted 08 Sep, 2021 17:07
afreise	You are so welcome, Kyle! Let me know if you have any feedback, suggestions, or questions.

Link to this post | posted 30 Aug, 2021 21:25
afreise	Hi everyone, The comparative genomics lab manual we created at UCLA is now officially a QUBES resource. You can access the lab manual there as well as teaching/implementation notes. https://qubeshub.org/publications/2745/1 Happy analyses, Amanda

Link to this post | posted 19 Feb, 2021 01:35
afreise	awesome! thanks, Debbie!

Link to this post | posted 19 Feb, 2021 00:45

afreise

Hello SEA-PHAGES team, Some students doing characterization of cluster H phages noticed an interesting discrepancy in the lysin A gene of Predator (cluster H1). Many other phages, including others in H1, have lysin A genes in pham 52459. Predator also has this pham, but the small orpham 17367 immediately upstream is the one that has been annotated as lysin A (see Pham Map photo). The orpham has no hits in NCBI BLAST. Could this be an annotation error? Edited 19 Feb, 2021 00:46 1.02Mb

Link to this post | posted 09 Dec, 2020 17:05

afreise

Dear SEA-PHAGES colleagues, Jordan and I are giving the virtual poster symposium format a try at UCLA, and we'd be so glad to have you and your students attend! The symposium has 8 posters about phage bioinformatics research, as well as research by other students in our department. You can read the attached flyer for more details. The basics: UCLA Microbiology, Immunology, and Molecular Genetics Poster Symposium Friday, Dec 11, 2-4pm PST Padlet (Posters, Abstracts, and Video Abstracts):  https://padlet.com/mimg_undergradresearch/vtbd94431ogqvdf8 Zoom (for short presentations and Q&A): https://ucla.zoom.us/meeting/register/tJEqcO6pqjkqHNcwzZc8c4_YJHNaEXU5G4NA Note that you have two ways to interact: you can chat with the presenters on Zoom, and you can also leave comments and questions asynchronously on the Padlet itself. This is our first time trying this format out, but we're optimistic that it will showcase the students' work well and give everyone opportunities to learn and engage about phage research. Please let me know if you have questions! 120Kb

Link to this post | posted 17 Nov, 2020 19:51
afreise	Great! Thanks, Debbie.

Link to this post | posted 17 Nov, 2020 05:10

afreise

Hello all, We were excited to see that a phage of interest, former singleton Vibaki, has been clustered with phage Jinkies in new cluster FL. However, when I compared the two phages on Phamerator.org, the last ~10,000 bp of phage Jinkies (starting at 40k bp) has some nucleotide similarity with Vibaki and quite a lot of coding potential on Genemark-Self, but there are no genes annotated. This is also reflected on PhagesDB and in the Genbank entry. The last gene is gene 57, but there are close to 10,000bp after that with no genes annotated and plenty of coding potential. In PECAAN, Jinkies (noted as unclustered for now) was annotated up through gene #84, which makes much more sense to me based on the coding potential. Has there been an error with the final annotation files that were Phamerated and submitted to Genbank? It was submitted back in May 2020. Thanks for any insight!

Link to this post | posted 22 Oct, 2020 00:19
afreise	Thank you so much! The Starterator split of manual annotations between sites 12 and 15 threw me off, but you make an excellent point about the better conservation of site 12. Gene 2 does appear to be real and is very well conserved in the cluster. So it looks like this one is a weird overlap!

Link to this post | posted 19 Oct, 2020 22:23

afreise

A gene early in the genome, found in A2 phages, is often called as a VIP2-like toxin OR an ADP-ribosyltransferase. The start call for this gene is very polarizing. For example, in phage Smeagan, the gene is Gene 3 (stop site 2251): Either of the two recommended start sites, 1322 or 1661, result in either a large overlap (-94) or a large gap (245). The earlier one includes a region without coding potential; the later start cuts off a lot of coding potential. The -94 start site has a slightly better RBS score and Z-score. Starterator calls for this gene are split almost down the middle between the two recommended sites, with a slight bias toward choosing the site that results in the overlap. Any guidance on this one? Thanks all! Edited 19 Oct, 2020 22:24