Link to this post | posted 09 Jun, 2024 19:08
delesall	I attach the cluster report for the AK phages from the SEA faculty meeting June 2024 148Kb

Link to this post | posted 09 Jun, 2024 19:05
delesall	I attach the four cluster reports for the AZ phages, one for each subcluster, done at SEA faculty meeting, June 2024 Edited 09 Jun, 2024 19:09 148Kb 146Kb 147Kb 146Kb

Link to this post | posted 02 Jun, 2024 13:21
delesall	To the best of my understanding, the classification that Genbank uses to replace what we submit is the ICTV classification - so that should satisfy your reviewer (even if it's not meaningful taxonomy in my opinion). Edited 04 Jun, 2024 00:25

Link to this post | posted 19 Dec, 2023 19:43
delesall	It also looks like the first 18 aa correspond to the beginning of Malithi gp 54, a 262 aa sequence. So maybe some HGT in ancestor of Sonah interrupted/broke this gene?

Link to this post | posted 11 Jun, 2023 22:20

delesall

Some Cluster B3 and B4 phages have an intein in the middle of their terminase gene. To learn about inteins see this paper: Kelley DS, Lennon CW; SEA-PHAGES; Belfort M, Novikova O. Mycobacteriophages as Incubators for Intein Dissemination and Evolution. mBio. 2016 Oct 4;7(5):e01537-16. doi: 10.1128/mBio.01537-16. PMID: 27703073; PMCID: PMC5050341. To visualize an example of terminase with or without an intein, create a phamerator map with phage Kronus and Casbah (both B3). Note that presence of an intern may lead to identical proteins being assigned to different phams.

Link to this post | posted 23 Mar, 2023 11:54
delesall	Does anybody know what a "Socket Error #11002" mean? Thanks

Link to this post | posted 16 Mar, 2023 23:44
delesall	I'll add my two cents to what Chris wrote. I ended up NOT calling this a helicase loader in Rofo, mostly because there was no evidence for a helicase near by. In SPP1 and related phages, the pattern is helicase loader followed by helicae!

Link to this post | posted 10 Sep, 2022 13:24
delesall	Hi Nikki Yes. It magically started working again the next day (Aug 2). I did nothing different. I also just blasted one gene with no issue! Good luck, V

Link to this post | posted 01 Aug, 2022 20:28
delesall	I did a whole genome BLASTp within DNAMaster last week - no problem. Today DNAMaster does not seem to connect to NCBI. I have all the right permissions. Anybody else with this issue?

Link to this post | posted 01 Aug, 2022 17:56
delesall	I did a whole genome BLASTp within DNAMaster last week - no problem. Today DNAMaster does not seem to connect to NCBI. I have all the right permissions. Anybody else with this issue?