SEA-PHAGES | All posts created by nietof

Link to this post \| posted 30 Sep, 2024 18:12
nietof	viknesh nietof Hi everyone Has anybody successfully isolated phages from soils stored frozen after sampling? Thank you Fernando Wanted to share that no faculty has shared with me that they've tried this. Hi Vic thanks for the reply,I found a citation from an seaphages abstract, I think from a student or faculty at UPitt, that isolated phages from frozen soils during the winter of 2023. But she isolated them actually from outdoor frozen soils. I was going to try to isolate from soils in storage at -80C. thank you F

Link to this post | posted 30 Sep, 2024 18:12

viknesh
nietof
Hi everyone
Has anybody successfully isolated phages from soils stored frozen after sampling?
Thank you
Fernando

Wanted to share that no faculty has shared with me that they've tried this.

Hi Vic
thanks for the reply,I found a citation from an seaphages abstract, I think from a student or faculty at UPitt, that isolated phages from frozen soils during the winter of 2023. But she isolated them actually from outdoor frozen soils. I was going to try to isolate from soils in storage at -80C.
thank you
F

Posted in: Phage Discovery/Isolation → Isolating from frozen soils

Link to this post \| posted 30 Sep, 2024 14:51
nietof	Hi everyone Has anybody successfully isolated phages from soils stored frozen after sampling? Thank you Fernando

Posted in: Phage Discovery/Isolation → Isolating from frozen soils

Link to this post \| posted 11 Apr, 2024 17:42
nietof	Hi everyone We have a putative holin in Alkhayr cluster O gene 66 in PECAAN. Both TmHmm and Sosui show two tmb domains, strong matches in BLAST to other phages in this cluster and others but HHPred doesnt yield robust matches to a holin protein. It has Lysin a and b upstream. I assume it is a Holin but I am not sure why HHPred doesnt find matches.

Posted in: Cluster P Annotation Tips → Assignment of gp28 as holin

Link to this post \| posted 11 Apr, 2024 17:42
nietof	Hi everyone We have a putative holin in Alkhayr cluster O gene 66 in PECAAN. Both TmHmm and Sosui show two tmb domains, strong matches in BLAST to other phages in this cluster and others but HHPred doesnt yield robust matches to a holin protein. It has Lysin a and b upstream. I assume it is a Holin but I am not sure why HHPred doesnt find matches.

Posted in: Cluster P Annotation Tips → Assignment of gp28 as holin

Link to this post \| posted 03 Apr, 2024 15:07
nietof	lhughes It opened fine for me just now. Lee I just checked and it works for me now too. Thank you F

Posted in: Phamerator → Is Phamerator down?

Link to this post \| posted 03 Apr, 2024 13:27
nietof	Hi everyone Anybody having problems accessing phamerator. I haven't been able to access it since yesterday. It doesn't go beyond the sign in page. Thank you Fernando

Posted in: Phamerator → Is Phamerator down?

Link to this post \| posted 03 Apr, 2024 13:23
nietof	Hi We are annotating a cluster O phage, Alkhayr. Our sequence is not canonical. Furthermore, HHPred doesn't support calling TAC as a function for either one of the gene products (gene 50 and 51). I have attached the HHPred matches for gene T, gene 50. Regards F 210Kb

Posted in: Cluster O Annotation Tips → Tail Assembly Chaperones and Programmed Ribosmal Frameshift Call

Link to this post \| posted 12 Jan, 2024 16:43
nietof	Feliz "jubilacion" David!!! Thank you for your leadership. Fernando

Posted in: General Message Board → A Message from David Asai

Link to this post \| posted 20 Aug, 2022 02:00
nietof	debbie Fernando, Yes, the immunity repressor is called correctly in those genomes. And yes, that area is omitted in Caviar, so you most likely have a lytic phage. Likely a derivative a temperant one. debbie Debbie Thank you Fernando

Posted in: Cluster A Annotation Tips → Cluster A3 Immunity Repressor?

Link to this post \| posted 15 Jul, 2022 15:06
nietof	debbie In calling the immunity repressor of a phage JF2 (gp71), we came across a peculiar finding. It seems that the immunity repressor's open reading frame has less coding potential than another open reading frame in that area. Don't be fooled! JF2's immunity repressor shows hits in HHPred to the HTH DNA binding site (N-terminus). Read Pope, et al 2011a for info about Bxz2's broken repressor. However, our gene doesn't match that N terminus either. Many (did I say many?) phages have miscalled the open reading frame as the immunity repressor. Be careful. We will fix as soon as we can. debbie Hi Debbie Is the immunity repressor called correctly in Norbert_70 and Lambert1_73. We annotated Caviar and it has a 552 base pair deletion in that region and therefore doesn't have an immunity repressor gene. Please advise Thank you Fernando

Link to this post | posted 15 Jul, 2022 15:06

nietof

debbie
In calling the immunity repressor of a phage JF2 (gp71), we came across a peculiar finding. It seems that the immunity repressor's open reading frame has less coding potential than another open reading frame in that area. Don't be fooled! JF2's immunity repressor shows hits in HHPred to the HTH DNA binding site (N-terminus).
Read Pope, et al 2011a for info about Bxz2's broken repressor. However, our gene doesn't match that N terminus either.
Many (did I say many?) phages have miscalled the open reading frame as the immunity repressor. Be careful. We will fix as soon as we can.

debbie

Hi Debbie
Is the immunity repressor called correctly in Norbert_70 and Lambert1_73. We annotated Caviar and it has a 552 base pair deletion in that region and therefore doesn't have an immunity repressor gene.
Please advise
Thank you
Fernando

Posted in: Cluster A Annotation Tips → Cluster A3 Immunity Repressor?

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