SigAlign

Similarity-guided Align

1. Have only five simplified parameters
   • Gap-affine penalties (3)
     1. Mismatch penalty
     2. Gap-open penalty
     3. Gap-extend penalty
   • Similarity cut-offs (2)
     1. Minimum length
     2. Maximum penalty per length
2. Give non-exceptional result
3. Reproducible by dynamic programming (DP) matrix

Quick Start

use sigalign::wrapper::{
    DefaultAligner,
    DefaultReference,
};

// (1) Build `Reference`
let fasta =
br#">record_1
ACACAGATCGCAAACTCACAATTGTATTTCTTTGCCACCTGGGCATATACTTTTTGCGCCCCCTCATTTA
>record_2
TCTGGGGCCATTGTATTTCTTTGCCAGCTGGGGCATATACTTTTTCCGCCCCCTCATTTACGCTCATCAC"#;
let reference = DefaultReference::from_fasta_bytes(fasta).unwrap();

// (2) Make `Aligner`
let mut aligner = DefaultAligner::new_local(
    4,   // Mismatch penalty
    6,   // Gap-open penalty
    2,   // Gap-extend penalty
    50,  // Minimum aligned length
    0.2, // Maximum penalty per length
).unwrap();

// (3) Align query to reference
let query = b"CAAACTCACAATTGTATTTCTTTGCCAGCTGGGCATATACTTTTTCCGCCCCCTCATTTAACTTCTTGGA";
let result = aligner.align_query(&reference, query).unwrap();
println!("{}", result.to_json());