README
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DnaDesign
DnaDesign is a Go project creating tools for automated genetic design, spanning from the lowest levels of DNA sequence manipulation to higher level functionality.
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Practical: DnaDesign tooling is meant to be used by practitioners of synthetic biology. Let's make something actually useful!
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Modern: DnaDesign is at the bleeding edge of technology. We are happy to adopt the newest advancements in synthetic biology, wasm, LLMs, and more to get our tools in the hands of people who need it.
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Ambitious: DnaDesign's goal is to be the most complete, open, and well used collection of computational synthetic biology tools ever assembled. If you like our dream and want to support us please star this repo, request a feature, or open a pull request.
Documentation
Contributing
Write good, useful code. Open a pull request, and we'll see if it fits!
License
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Copyright (c) 2023 Keoni Gandall
Other
DnaDesign is a fork of Poly at commit f76bf05 with a different mission focus.
Directories
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| Path | Synopsis |
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external
module
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Package DnaDesign is a Go package for engineering organisms.
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Package DnaDesign is a Go package for engineering organisms. |
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align
Package align is a package for aligning (comparing) DNA, RNA, and protein sequences.
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Package align is a package for aligning (comparing) DNA, RNA, and protein sequences. |
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align/matrix
Package matrix provides a variety of alignment scoring matrices for sequence alignment.
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Package matrix provides a variety of alignment scoring matrices for sequence alignment. |
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alphabet
Package alphabet provides structs for defining biological sequence alphabets.
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Package alphabet provides structs for defining biological sequence alphabets. |
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bio
Package bio provides utilities for reading and writing sequence data.
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Package bio provides utilities for reading and writing sequence data. |
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bio/fasta
Package fasta contains fasta parsers and writers.
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Package fasta contains fasta parsers and writers. |
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bio/fastq
Package fastq contains fastq parsers and writers.
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Package fastq contains fastq parsers and writers. |
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bio/genbank
Package genbank provides genbank parsers and writers.
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Package genbank provides genbank parsers and writers. |
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bio/pileup
Package pileup contains pileup parsers and writers.
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Package pileup contains pileup parsers and writers. |
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bio/rebase
Package rebase contains a rebase parser for rebase data dump #31.
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Package rebase contains a rebase parser for rebase data dump #31. |
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bio/slow5
Package slow5 contains slow5 parsers and writers.
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Package slow5 contains slow5 parsers and writers. |
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bio/uniprot
Package uniprot provides an XML parser for Uniprot data dumps.
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Package uniprot provides an XML parser for Uniprot data dumps. |
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checks
Package checks provides utilities to check for certain properties of a sequence.
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Package checks provides utilities to check for certain properties of a sequence. |
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clone
Package clone provides functions for cloning DNA sequences.
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Package clone provides functions for cloning DNA sequences. |
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fold
Package fold is a package for folding DNA and RNA sequences into secondary structures.
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Package fold is a package for folding DNA and RNA sequences into secondary structures. |
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mash
Package mash is for sketching sequence data to make it easier to compare to other sequence.
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Package mash is for sketching sequence data to make it easier to compare to other sequence. |
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primers
Package primers provides utilities for creating primers and DNA barcodes.
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Package primers provides utilities for creating primers and DNA barcodes. |
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primers/pcr
Package pcr designs and simulates simple PCR reactions.
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Package pcr designs and simulates simple PCR reactions. |
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random
Package random provides functions to generate random DNA, RNA, and protein sequences.
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Package random provides functions to generate random DNA, RNA, and protein sequences. |
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seqhash
Package seqhash contains the seqhash algorithm.
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Package seqhash contains the seqhash algorithm. |
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synthesis
Package synthesis provides utilities for preparing DNA to be synthesized.
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Package synthesis provides utilities for preparing DNA to be synthesized. |
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synthesis/codon
Package codon is a package for optimizing codons for expression when synthesizing DNA.
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Package codon is a package for optimizing codons for expression when synthesizing DNA. |
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synthesis/fix
Package fix fixes synthetic DNA molecules in preparation for synthesis.
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Package fix fixes synthetic DNA molecules in preparation for synthesis. |
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synthesis/fragment
Package fragment optimally fragments DNA for GoldenGate systems.
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Package fragment optimally fragments DNA for GoldenGate systems. |
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transform
Package transform provides functions for transforming sequences.
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Package transform provides functions for transforming sequences. |
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transform/variants
Package variants contains a function for generating all variants of a sequence.
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Package variants contains a function for generating all variants of a sequence. |
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py
module
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