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Debbie Jacobs-Sera posted in Calling start in FC phage Phrampa
Choice of join in frameshift
| Link to this post | posted 12 Mar, 2021 04:56 | |
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I am trying to do the programmed translational frameshift in a Microbacterium EA6 phage, Juicer. I attended the 2020 Hackathon and saw Claire's excellent post in this forum about doing it in PECAAN, but I think I have two possible candidates for the join and would appreciate suggestions. I have screengrabs of the two regions along with the GM output in the attached document. I'm thinking the join should be 10397 OR 10367. Both are -1 and have listed slippery sequences around a Glycine. Should I be trying to BLAST the protein sequence with a related phage (Chepli)? |
921Kb| Link to this post | posted 12 Mar, 2021 07:45 | |
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Here's the other phage: Gordonia GiKK cluster CT. I'm just not getting the frameshift yet. |
| Link to this post | posted 12 Mar, 2021 15:21 | |
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Here is how I would call Juicer's frameshift. I use the six-frame translation in DNA Master to find the slippery sequence. I'll look at GiKK next. debbie |
| Link to this post | posted 12 Mar, 2021 15:36 | |
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Here is how I would call GiKK's frameshift. |
| Link to this post | posted 01 Apr, 2021 20:36 | |
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Thank you Debbie!!!!! |