dnadesign

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Restriction Enzymes from Rebase

3

## Describe the desired feature/enhancement I'd like the ability to use many more restriction sites much like biopython's Restriction package. ### Is your feature request related to a problem? I'm...

rmcl

https://github.com/Koeng101/dnadesign/blob/85e882045b7cd1e61284431e5e3b8985243f1fbd/lib/synthesis/codon/codon.go#L264C1-L267C5 ```go for _, feature := range sequence.Features { if feature.Type == "CDS" { if _, ok := feature.Attributes["pseudo"]; ok { continue } seq, _ := feature.GetSequence() codingRegionsBuilder.WriteString(seq) genes++ }...

Koeng101

Minimal API with AI

4

My dream for DnaDesign is to integrate AI systems for designing DNA - the other API request is a means to this end. However, I want the end-to-end pipeline to...

Koeng101

vcf turns out to help with some of my sequencing. I like having pileup as a backup, though, for manual viewing. Generating vcf with bcftools is a good way to...

Koeng101

Megamash cannot call complicated sequences

10

`seq_recovery=0.4152_0` for example, cannot be processed into a megamash table because it doesn't have any unique 16mers. This is because of a flawed assumption: ESPECIALLY in protein variant libraries, 16mer...

Koeng101

Api

4

API adds an OpenAPI interface to DnaDesign. This allows other programs to work with DnaDesign. In particular, we have a focus on supporting an embedded lua environment and python interactivity....

Koeng101

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7200061/ We mapped the sequencing reads to the dual-barcode sequences with 56 bp in length using Minimap2 (v2.11) [[26](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7200061/#R26)] by -k7 -A1 -m42 -w1 options.

Koeng101

Document LinearFold+mfe and make linters work

1

I merged much of linearfold directly from https://github.com/allyourbasepair/rbscalculator - and so, not only are the linters *very* unhappy, but there are lots of missing spots for better documentation (though vivek...

Koeng101

Genbank improvements

1

Referencing https://github.com/bebop/poly/issues/434 @carreter is asking for a full rewrite there, but I think I disagree. Useful link to the [spec](https://www.ncbi.nlm.nih.gov/genbank/release/current/). - Feature.GetSequence() always returns a nil error value [link](https://github.com/bebop/poly/issues/352) This...

Koeng101

PCR simulation should have circularity as an aspect of the sequence itself, not of the entire function

1

[link](https://github.com/bebop/poly/issues/225) This should obviously be implemented.

Koeng101