Crate sigalign

SigAlign

SigAlign is a library for gap-affine sequence alignment tasks guided by explicit similarity cutoffs.

Quick Start

use sigalign::{
    Aligner,
    algorithms::Local,
    ReferenceBuilder,
};

// (1) Build `Reference`
let fasta =
br#">target_1
ACACAGATCGCAAACTCACAATTGTATTTCTTTGCCACCTGGGCATATACTTTTTGCGCCCCCTCATTTA
>target_2
TCTGGGGCCATTGTATTTCTTTGCCAGCTGGGGCATATACTTTTTCCGCCCCCTCATTTACGCTCATCAC"#;
let reference = ReferenceBuilder::new()
    .set_uppercase(true) // Ignore case
    .ignore_base(b'N') // 'N' is never matched
    .add_fasta(&fasta[..]).unwrap() // Add sequences from FASTA
    .add_target(
        "target_3",
        b"AAAAAAAAAAA",
    ) // Add sequence manually
    .build().unwrap();

// (2) Initialize `Aligner`
let algorithm = Local::new(
    4,   // Mismatch penalty
    6,   // Gap-open penalty
    2,   // Gap-extend penalty
    50,  // Minimum length
    0.2, // Maximum penalty per length
).unwrap();
let mut aligner = Aligner::new(algorithm);

// (3) Align query to reference
let query = b"CAAACTCACAATTGTATTTCTTTGCCAGCTGGGCATATACTTTTTCCGCCCCCTCATTTAACTTCTTGGA";
let result = aligner.align(query, &reference);
println!("{:#?}", result);

Core Structures

• Reference: A database for multiple target sequences.
  • Generated from ReferenceBuilder.
  • Purpose: Combining multiple sequences into one struct, indexing them to facilitate alignment processes.
  • Can be immutable while alignment.
• Aligner: An executor for alignment tasks.
  • Generated from Algorithm.
  • Purpose: Managing the workspace for alignment tasks.
  • Need to be mutable while alignment.

Parameters: Definition of alignment results

• Penalties
  • Mismatch penalty (u32)
  • Gap-open penalty (u32)
  • Gap-extend penalty (u32)
• Cutoffs
  • Minimum alignment length (MinL) (u32)
  • Maximum penalty per alignment length (MaxP) (f32)

Inputs and Outputs

• Inputs
  • Query: &[u8] (byte array)
  • Reference: ref(&) to Reference
• Outputs
  • QueryAlignment: A vector of TargetAlignment for each target sequence.
    • TargetAlignment: A vector of Alignment for each alignment.
      • Index: Index of the target sequence in Reference.
      • Alignment: Alignment results.
        • Penalty score
        • Length of alignment
        • Alignment position
        • Operations (Match, Substitution, Insertion, Deletion)

Modules

algorithms

Supported alignment algorithms.

results

Representation of the alignment outcomes.

utils

Utilities for SigAlign.

Structs

Aligner

An alignment executor.

Reference

A database for multiple target sequences.

ReferenceBuilder

Builder for Reference.

Enums

ReferenceBuildError

Error for building Reference.

ReferenceLoadError

Error for loading Reference.