SEA-PHAGES | All posts created by nietof

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

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 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

Link to this post \| posted 27 Apr, 2021 03:14
nietof	Hi everyone All of the sudden the scrolling bar in the six frame translation window is gone. THe rest of the components of the ribbon at the bottom are there, but I can't scroll through the sequence. I attached a picture of the window. I uninstalled and reinstalled DNA Master and it still happening. I am running on a PC with windows 10. thank you Fernando 223Kb

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

Link to this post \| posted 20 Feb, 2021 00:03
nietof	debbie I do not think that this protein (gene35 of Sarma624) has a reportable function. HHPred has no hits to an applicable function. Debbie thanks for confirming. regards F

Posted in: Functional Annotation → PLA2-like domain in Cluster B1s

Link to this post \| posted 20 Feb, 2021 00:03
nietof	debbie I do not think that this protein (gene35 of Sarma624) has a reportable function. HHPred has no hits to an applicable function. Debbie thanks for confirming. regards F

Posted in: Functional Annotation → PLA2-like domain in Cluster B1s

Link to this post \| posted 20 Feb, 2021 00:02
nietof	debbie I do not think that this protein (gene35 of Sarma624) has a reportable function. HHPred has no hits to an applicable function. Debbie thanks for confirming. regards F

Posted in: Functional Annotation → PLA2-like domain in Cluster B1s

Link to this post \| posted 19 Feb, 2021 23:39
nietof	Hey Retaking this thread. We are annotating Sarma624. Gene 35 blasted in phagesdb gets two hits with a PLA2-like protein domain function, Bigphil_35 and Mozy_42. It is a phospholipase A2 It doesn't appear in the list of accepted functions yet. Most of the other F1 phages have NKF for the same gene. The HHPred hits are all human actin binding protein or other not close to a phospholipase. I would be inclined to think BigPhil and Mozy's annotations are incorrect and thus to call it NKF for Sarma.

Link to this post | posted 19 Feb, 2021 23:39

nietof

Hey
Retaking this thread. We are annotating Sarma624. Gene 35 blasted in phagesdb gets two hits with a PLA2-like protein domain function, Bigphil_35 and Mozy_42. It is a phospholipase A2 It doesn't appear in the list of accepted functions yet. Most of the other F1 phages have NKF for the same gene. The HHPred hits are all human actin binding protein or other not close to a phospholipase. I would be inclined to think BigPhil and Mozy's annotations are incorrect and thus to call it NKF for Sarma.

Posted in: Functional Annotation → PLA2-like domain in Cluster B1s

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