This is now the backbone for Plasmid Designer

Plasmid is a genetics / bioinformatics framework.

It consists of two parts:

• libplasmid: Library for genetic code creation, editing and analysis
• plasmid-cli: CLI for genetic sequence processing

This is a work-in-progress.

I should also mention that I'm not at all trained in bioinformatics, bioengineering, or anything even remotely similar. I'm writing this library while I'm learning the concepts, so expect some rough edges.

GUI

The desktop application has moved to Plasmid Designer.

CLI

Pretty print DNA sequence

# Command
plasmid-cli pp "ATGTACCCGTATCTG"

# Output
# 5' ATGTACCCGTATCTG 3'
# 3' TACATGGGCATAGAC 5'
#     M  Y  P  Y  L

Match DNA sequence with IUPAC pattern

# Command
plasmid-cli match "ATGTACCCGTATCTG" "ATGNNNSSSW"

# Output
# 5' ATGTACCCGTATCTG 3'
#    ATGNNNSSSW   
# -> Matches: true

Export circular DNA as SVG

plasmid-cli export "ATGTACCCGTATCTG" --format svg > out.svg

libPlasmid

Modules

Module	Description
prelude	Exports all essential types and traits
dna	DNA Nucleotide Processing
rna	RNA Nucleotide Processing
eaa	Amino Acid Processing
seq	Genetic Sequence Editing and Analysis
uni	IUPAC Sequence Processing
vis	Visualization Tools
imp	Import Helpers
exp	Export Helpers
traits	Helpful Traits

Scope

• genetic sequence modeling
  • dna/rna nucleotides
  • dna/rna nucleotide triplets
  • dna/rna bp and anticodon handling
  • dna/rna iupac sequence matching
  • sequence alignment
  • dynamic dna/rna editing (seq module)
    • always keep nucleotide sequence
    • nucleotide triplet iterator
    • reverse complement iterator
    • push/pop nucleotides
    • push/pop codons
    • insert/remove nucleotides
    • substitute nucleotides
    • base-pair iterator
    • polypeptide iterator (lazy translation)
  • dna transcription
  • rna polypeptide translation
  • amino acid reverse transcription
  • genetic codes
    • ACGT (see DnaNucleotide)
    • ACGU (see RnaNucleotide)
    • ACGTWSMKRYBDHVN- (see IupacNucleotide)
• genetic sequence analysis
  • at-count, gc-count, at-ratio, gc-ratio, at/gc-ratio
  • hairpin detection
  • open reading frame detection
  • cut site detection
• annotation
  • general sequence annotation
  • auto-annotate cut sites
• visualization
  • simple text-based output
  • plasmid svg generation
• import / export
  • fasta
  • fastq
  • sam
  • svg
    • linear
    • circular
  • custom?

Examples

fn main() -> Result<(), Box<dyn std::error::Error>> {
  let dna = "ATGGTTCGGCAATTT";

  // Load DNA from string
  let mut seq = DnaSequence.from_str(dna)?;

  // Annotate restriction enzyme cut sites
  seq.annotate_restriction_enzymes();

  // Check if NdeI cut site exists
  if let Some(ann) = seq.annotation_iter().find(|ann| ann.text == "NdeI") {
    println!("Found NdeI cut site (start: {}; end: {})", ann.start, ann.end);
  }

  // Generate SVG of circular DNA
  let conf = SvgExportConfig::circular();
  let svg = SvgExport::new(conf, seq.as_nucleotides());
  println!("{}", svg.export()); // print svg code
}