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elkebir-group / derna

RNA sequence design for a target protein sequence
BSD 3-Clause "New" or "Revised" License
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build: bioconda version is obsolete #3

Open h-ahl opened 2 months ago

h-ahl commented 2 months ago

The bioconda version (1.0.2) is obsolete, as has issues in it preventing it from optimising CAI as intended. E.g. maximal CAI optimisation does not lead to a CAI of 1.

xinyu-g commented 1 week ago

Thank you for bringing this issue to our attention. We will be working on updating the bioconda version asap. To help us better understand the issue, could you provide us with the sequence(s) you used?

h-ahl commented 1 week ago

Hi, @xinyu-g. Having some issues sharing the sequences in question due to legal restrictions. This should be a general issue though; you can evaluate it by generating a pareto front e.g. using LinearDesign and DERNA (Zuker) using the same codon table

xinyu-g commented 1 week ago

@h-ahl That might make it a little challenging on my side to debug the potential issue. I have not seen such problem with the sequences I have run. For instance, using the P15421 sequence given in the sweep example in the README, I got the attached results, where lambda = 1e-05 gave me a CAI of 1.

P15421_sweep.csv

I also tried using fixed lambda on another sequence (O14880) with the following command

./derna -i ../data/uniprotSeq/O14880.fasta -o O14880.fasta_fixed_lambda.txt -m 1 -s 2 -l 1e-5

And derna returned lambda: 1e-05,O: -0.2035,cai: 0,cai_s: 1,mfe: -20350,combined: -0.2035 which also gave a CAI of 1.

xinyu-g commented 3 days ago

@h-ahl Hi, I wanted to follow up on the issue. Have you had a chance to run the sequences using your own codon table, now that the issue with loading a custom codon table has been resolved? It’s possible that the default codon table derna uses is different from the one you’re using to evaluate the sequences, which could be causing the problem.

h-ahl commented 17 hours ago

Hi, @xinyu-g - I've asked my colleague to follow up on this. The issue shouldn't be codon table related, but thank you very much for resolving that issue