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All posts created by nietof

| posted 11 Apr, 2024 17:42
default avatar
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
| posted 11 Apr, 2024 17:42
default avatar
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
| posted 03 Apr, 2024 15:07
default avatar
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?
| posted 03 Apr, 2024 13:27
default avatar
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?
| posted 03 Apr, 2024 13:23
default avatar
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
| posted 12 Jan, 2024 16:43
default avatar
nietof
Feliz "jubilacion" David!!!
Thank you for your leadership.
Fernando
Posted in: General Message Board → A Message from David Asai
| posted 20 Aug, 2022 02:00
default avatar
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?
| posted 15 Jul, 2022 15:06
default avatar
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?
| posted 15 Jul, 2022 15:06
default avatar
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?
| posted 02 Jun, 2022 15:20
default avatar
nietof
Dan
One last question, are you using the 300-cycle kit at 2x150 paired end reads that you are running on the MiSeq?
Thank you
Fernando
Posted in: Sequencing, Assembling, and Finishing Genomes → MiSeq protocol and info