SEA-PHAGES | All posts created by mkdennis

Link to this post \| posted 14 Jan, 2023 16:43
mkdennis	debbie Hi Megan, I agree that Ciao sequence in the first 4-8 amino acids is unlike others in the pham. However, the gene does stop at 42523. So the only start to call is 42699. I think that starterator shows the data well. in addition, check the GeneMark using smeg and tb as the target. You will see that the best coding potential is in the frame identified. Make sense? debbie Hi Debbie, Yes, this makes sense - thanks! I was thinking about this in a chicken-or-egg way. Does a strong RBS which we "know" was previously used as a start site override coding potential, even though the frameshift has separated it from most of the coding potential, or is the coding potential enough for the ribosome to use a different/less favorable RBS (and how does the ribosome "know" where the coding potential is? philosophical questions of gene expression ). From your reply it sounds like we should favor the latter, which makes sense.

Link to this post | posted 14 Jan, 2023 16:43

debbie
Hi Megan,
I agree that Ciao sequence in the first 4-8 amino acids is unlike others in the pham.
However, the gene does stop at 42523. So the only start to call is 42699.
I think that starterator shows the data well.
in addition, check the GeneMark using smeg and tb as the target. You will see that the best coding potential is in the frame identified.
Make sense?
debbie

Hi Debbie,

Yes, this makes sense - thanks!

I was thinking about this in a chicken-or-egg way. Does a strong RBS which we "know" was previously used as a start site override coding potential, even though the frameshift has separated it from most of the coding potential, or is the coding potential enough for the ribosome to use a different/less favorable RBS (and how does the ribosome "know" where the coding potential is? philosophical questions of gene expression smile

).

From your reply it sounds like we should favor the latter, which makes sense.

Posted in: Annotation → 2022 Genomics Workshop Follow-up Annotation: Ciao

Link to this post \| posted 28 Dec, 2022 21:58
mkdennis	Hi Debbie & all, I'm looking at the start for the reverse gene w/ a stop at 42523 in Ciao and came across something interesting. Pippin_68 and Ciao_66 are virtually identical AA sequences, except for the first 4-8 AA's, and the frameshift mutation that occurred in Ciao to generate this is making me question which frame the "real" start codon is actually in. It made more sense with pictures and formatting that's hard to achieve in a forum post, so PDF is attached, including my question about which of two possible starts to call. Thanks! 282Kb

Link to this post | posted 28 Dec, 2022 21:58

mkdennis

Hi Debbie & all,

I'm looking at the start for the reverse gene w/ a stop at 42523 in Ciao and came across something interesting. Pippin_68 and Ciao_66 are virtually identical AA sequences, except for the first 4-8 AA's, and the frameshift mutation that occurred in Ciao to generate this is making me question which frame the "real" start codon is actually in.

It made more sense with pictures and formatting that's hard to achieve in a forum post, so PDF is attached, including my question about which of two possible starts to call.

Thanks!

Posted in: Annotation → 2022 Genomics Workshop Follow-up Annotation: Ciao

Recent Activity

All posts created by mkdennis