MoonBio

MoonBio is a lightweight bioinformatics library for MoonBit. It provides basic data structures and alignment algorithms to process DNA/RNA sequences, primarily targeting WASM environments.

Features

• Sequence Ops: Basic types and operations for DNA/RNA (e.g., reverse complement, transcription).
• Parsers: A simple zero-allocation FASTA file reader.
• Alignment Algorithms:
  • Needleman-Wunsch (Global)
  • Smith-Waterman (Local)
  • Levenshtein Distance

Quick Start

git clone https://github.com/caassien/cassien-.git
cd cassien-
moon test

Usage Example

import cassien/moonbio/align

fn main {
  // simple needleman-wunsch alignment
  let res = align.needleman_wunsch("GATTACA", "GCATGCU", 1, -1, -1)
  
  println(res.score)
  println(res.alignment_a)
  println(res.alignment_b)
}

TODO / Roadmap

• FASTQ parsing
• MSA (Multiple Sequence Alignment)
• HMM-based motif discovery

License

MIT