SEA-PHAGES | All posts created by nietof

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?

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

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

Link to this post \| posted 02 Jun, 2022 15:20
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

Link to this post \| posted 27 May, 2022 22:24
nietof	Dan Muchas gracias!!! Regards Fernando

Posted in: Sequencing, Assembling, and Finishing Genomes → MiSeq protocol and info

Link to this post \| posted 27 May, 2022 15:49
nietof	Hi, We just got a MiniSeq and plan to try our own sequencing. I would like to follow your protocol. Would you be able to share the protocol you use for sequencing? Any recommendations for the MiniSeq? Recommended coverage? Any information is greatly appreciated. regards, Fernando Edited 27 May, 2022 17:15

Posted in: Sequencing, Assembling, and Finishing Genomes → MiSeq protocol and info

Link to this post \| posted 27 Apr, 2021 14:56
nietof	Debbie I will check that out! In the meantime I went to pecaan to look at the six frames. thank you Fernando

Posted in: DNA Master → Scroll bar in six frame translation

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