DnaChisel

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See https://github.com/Edinburgh-Genome-Foundry/DnaChisel/issues/62#issuecomment-1106482376

veghp

Request: use updated codon usage tables

13

Hello, I have a request that should enhance the utility of DNA Chisel for codon optimization. When selecting Codon Usage Tables for species [not included](https://github.com/Edinburgh-Genome-Foundry/codon-usage-tables/tree/master/codon_usage_data/tables) in DNA Chisel, Kazusa Codon...

eggrandio

Sequence diversity in output from CodonOptimize

3

Hello! Thanks for this great tool. I am exploring using it on a project. Is there an existing way to get dnachisel to return a few codon optimized sequences, maybe...

jlerman44

Support for optimization of RNA structure

3

Even though the `AvoidHairpins` specification is a good compromise between speed and quality of the results, there are few tools available for optimizing RNA structure accurately (none actually usable programmatically,...

simone-pignotti

Feature: Add GC content variance constraint

8

Twist Bioscience has a GC variance constraint. Quote from their website: > Avoid extreme differences in GC content within a gene (i.e. the difference in GC content between the highest...

andrewshvv

Feature: Add "use_breach_form" field in "constraints_breaches_dataframe"

3

**Scenario:** I would like to use `constraints_breaches_dataframe` for generating my own report and upload `SeqRecord` in `Benchling` instead of the `.pdf`. **Problem:** For our customers, we need a bit more...

andrewshvv

Suggestion: rename biotools to tools

1

since there are tools like mathtools, renaming it and put Location to tools dir will make code more organized.

Lix1993

can I generate a sequence with a sequence with 'medium' score?

3

By default, dnachisel gives a 'best' sequence with score close to 0. I can get a 'worst' sequence by `new_score < score`. If i want a 'medium' sequence , i...

Lix1993

suggestion: put builtin_specification to Specification folder and split it into sub folders by specification type

3

like this: ``` └── Specification ├── builtin_specifications │   ├── alignment_related │   │   ├── AvoidBlast.py │   │   └── AvoidMatches.py │   ├── codons_related │   ├── pattern_related │   │   ├── AvoidChanges.py │   │  ...

Lix1993

AvoidPattern with regex

1

I ran into an issue recently where I was using a regex in my AvoidPattern and didn't realize that I needed to specify the size. What happened was that even...

deto