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| posted 09 Apr, 2018 16:08
We are working on the frameshift in the C1 phage Cane17 (gp123 and gp124). The DNA Master file is attached. We've used C1 phages Phox and ZygoTaiga as a reference. I have narrowed down the frameshift to occur somewhere between 72802-72805 in Cane17 where the shift is in one of the As in a sequence of 4 As. Phox and ZygoTaiga do not agree on which A is the correct one to be counted twice. I think that choosing any of the 4 As gives the same result. Is there a way to be more certain which A is the correct frameshift site?

Also, in DNA Master I get the error "72290 - 72817 and share a 5' (upstream) coordinate". That error makes sense after adding the frameshift, and I've read forum posts from others getting the same error. Is there a way to get rid of this error?
| posted 09 Apr, 2018 17:14
We are having the same problem with Burrough (C1 phage). When we validated after doing the programmed frameshift, we see:

71426-71953 share a 5' (upstream) coordinate
| posted 09 Apr, 2018 20:20
I'll jump in and Pitt can tell us if this answer isnt' correct:

I consider that message not an "error message" but instead a notification. DNA Master is notifying me that these two genes share a start. In the case of a frameshift, that is what I wanted so everything is fine. In other cases, this helps me to catch duplicate genes that were accidentally left in the feature list.

| posted 13 Apr, 2018 14:38
YEp, thanks, LEe— not an error.

For the exact slip coordinate, I usually pick the middle nucleotide of the slippery sequence.
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