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ayaanhossain / nrpcalc

Non-Repetitive Parts Calculator - Automated design and discovery of non-repetitive genetic parts for engineering stable genetic systems
MIT License
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Feature/status request: NRPcalc for CDS's #2

Closed eyesmo closed 3 years ago

eyesmo commented 3 years ago

Hi! Howard mentioned you're working on a nonrepetitive parts calculator for protein coding sequences. How's that going? Would love to use it for some projects. I've found it difficult to use the regular nrpcalc for this task--most queries end up with no solved sequences, and no indication what regions of the sequence are causing problems.

hsalis commented 3 years ago

Hello Isaac,

The prototype is done & tested. I can prepare the web interface (sometime this week) & throw it up on our test server for your usage.

Regarding the solution space: If Lmax is too small and/or if the CDS is very polymeric, then the # of non-repetitive CDSs will indeed be small. Though I routinely received 10+ non-repetitive CDSs with 300 randomly generated AA sequences with an Lmax of 20. But an Lmax of 15 reduced the solution set to 2-3 CDSs. So your best strategy is to start off with a high Lmax. On the website, it will automatically calculate the solution set with lower and lower Lmax until some threshold is reached.

Thanks, Howard

~~ Howard Salis Associate Professor Biological Engineering and Chemical Engineering Penn State University

Email: salis@psu.edu Phone: 814-865-1931 Lab web site: http://salislab.net Design your DNA: http://salislab.net/software

On Sun, Mar 7, 2021 at 7:25 PM Isaac Larkin notifications@github.com wrote:

Hi! Howard mentioned you're working on a nonrepetitive parts calculator for protein coding sequences. How's that going? Would love to use it for some projects. I've found it difficult to use the regular nrpcalc for this task--most queries end up with no solved sequences, and no indication what regions of the sequence are causing problems.

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hsalis commented 3 years ago

And it's done. I'll DM you our test server URL. Let me know how it goes.