cyanea-seq

Sequence types, I/O, and analysis for DNA, RNA, and protein sequences.

What's Inside

• Sequence types -- validated DnaSequence, RnaSequence, ProteinSequence with reverse complement, transcription, translation
• FASTA/FASTQ parsing -- streaming statistics via needletail, paired-end support, interleave/deinterleave
• K-mers -- iterator-based extraction, 2-bit packed encoding (4x compression)
• Indexing -- suffix array (SA-IS), FM-index, FMD-index (bidirectional, SMEM enumeration)
• Pattern matching -- 7 algorithms: Horspool, KMP, Shift-And, BNDM, BOM, Myers bitparallel, Ukkonen
• MinHash -- bottom-k and scaled FracMinHash sketching for rapid genome comparison
• Quality trimming -- TrimPipeline builder with adapter removal, sliding window, BWA-style, paired-end
• Motif scanning -- PSSM with const-generic alphabet, PWM, EM-based motif discovery
• ORF finding -- all 6 reading frames, configurable start/stop codons
• Codon tables -- 7 NCBI translation tables, codon usage analysis, CAI
• Sequence masking -- DUST (low-complexity), SEG (protein), tandem repeat detection
• RNA structure -- Nussinov, Zuker MFE, McCaskill partition function, dot-bracket notation
• Protein properties -- composition, hydrophobicity, pI, extinction coefficient, Chou-Fasman/GOR secondary structure, disorder prediction
• De Bruijn graphs -- k-mer graph construction, unitig extraction
• Assembly QC -- N50/L50/N90/L90, auN statistics
• Taxonomy -- taxonomic trees, LCA queries, Kraken-style k-mer classification
• Restriction enzymes -- 20 common enzymes, cut-site finding, in-silico digestion

Quick Start

[dependencies]
cyanea-seq = { version = "0.1", features = ["minhash"] }

use cyanea_seq::{DnaSequence, MinHash};

let seq = DnaSequence::new(b"ACGTACGTACGT").unwrap();
println!("GC: {:.1}%", seq.gc_content() * 100.0);
println!("RevComp: {:?}", seq.reverse_complement());

let sketch = MinHash::from_sequence(b"ACGTACGT", 4, 100).unwrap();

Feature Flags

Modules

See Also

• API Reference (STATUS.md)
• Architecture
• Build Guide