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Add RBS design functionality #1

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jeffreybarrick opened this issue Aug 9, 2021 · 0 comments
Open

Add RBS design functionality #1

jeffreybarrick opened this issue Aug 9, 2021 · 0 comments
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enhancement New feature or request

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@jeffreybarrick
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jeffreybarrick commented Aug 9, 2021

Right now OSTIR will predict the translation initiation rate for a start codon given the surrounding mRNA sequence. It does not have the "reverse" capability of designing (or mutating) a sequence that has a desired translation initiation rate.

I'd propose adding a separate module with a function run_ostir_design() that will output mRNA/RBS sequences that have predicted translation initiation rates in a specified range for a given open-reading frame. It should also probably be implemented as a separate command-line script named ostir-design or similar. There will need to be some way of specifying the constraints on the sequence and/or where mutation of the sequence is allowed.

@jeffreybarrick jeffreybarrick added the enhancement New feature or request label Aug 9, 2021
@jeffreybarrick jeffreybarrick changed the title Add design functionality Add RBS design functionality Aug 15, 2021
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