Link to this post | posted 13 Mar, 2022 14:39

susannepfeifer

Hello, We have a question about annotating a programmed frameshift. In BiggityBass, two genes (genes 21 (stop: 19523; pham 99210) and 22 (stop: 19933; pham 97251)) near the tape measure protein COULD be in a programmed frameshift but the DR phage Phamerator maps are not very consistent: 1. AnClar - NO programmed frameshift 2. AnarQue - NO programmed frameshift 3. CloverMinnie - YES programmed frameshift (different phams) 4. Ligma - NO programmed frameshift 5. Mariokart - NO programmed frameshift 6. NHagos - YES programmed frameshift 7. Yago84 - NO programmed frameshift 8. Sour - YES programmed frameshift In short, 5/8 annotated DR phages did not call a programmed frameshift(including AnClar and Yago84 which are the most similar to BiggityBass based on our BLAST hits) 2/8 annotated DR phages called a programmed frameshift on their corresponding genes 21 and 22 1/8 annotated DR phage called a programmed frameshift but the genes were part of a different pham The 5/8 annotated DR phages without programmed frameshifts were submitted fairly recently (2019-2022), while the 2/8 annotated DR phages with programmed frameshifts were submitted earlier (2018-2019). Since majority of the DR phages do not have it annotated, would it be a fair assessment that it is okay to leave genes 21 and 22 in BiggityBass as is (i.e., NO programmed frameshift)? Thank you in advance for your help! Susanne

Link to this post | posted 04 Aug, 2021 22:19
susannepfeifer	Thank you!

Link to this post | posted 03 Aug, 2021 17:07
susannepfeifer	Hi, The cluster K1 mycobacteriophage that we annotated with our students this past semester, Stinson, contains an immunity repressor (gene 44). As immunity repressor genes can down-regulate lytic gene expression, we were wondering whether Stinson-like phages might be able to lysogenize their hosts and whether any might have been found as prophages? Best, Susanne

Link to this post | posted 17 Mar, 2021 17:26
susannepfeifer	Thank you - that's really helpful!

Link to this post | posted 10 Mar, 2021 18:29
susannepfeifer	That's a good point though all SEA-PHAGES phages in GenBank should have undergone the same rigorous gene annotation, right?

Link to this post | posted 09 Mar, 2021 20:53

susannepfeifer

Dear SEA-PHAGES team, If time allows, we would like to perform a small comparative analysis this semester. As we are planning to submit a manuscript with our students, this raises the question whether we i) can include any phage that has been deposited in GenBank (by citing its accession number) or ii) should limit ourselves to comparisons with phages that have already been published in a peer-reviewed journal? Any advise would be greatly appreciated! Best, Susanne

Link to this post | posted 02 Mar, 2021 22:20
susannepfeifer	Thank you so much, Debbie!

Link to this post | posted 02 Mar, 2021 21:06

susannepfeifer

Dear all, We are currently annotating the genome of Stinson, a cluster K1 phage. Looking at the Phamerator maps of several previously annotated K1 phages, it seems that genes 19 and 20 are annotated "on top of each other" which seems odd (and I vaguely remember Welkin mentioning in one of the tutorial videos that this might be a sign that something is wrong with the annotation). Any insights would be highly appreciated! Best, Susanne 363Kb

Link to this post | posted 09 Apr, 2020 15:43
susannepfeifer	It does, thanks Dan!

Link to this post | posted 08 Apr, 2020 22:17
susannepfeifer	Thanks Debbie!