Crate sigalign

SigAlign

SigAlign is a library designed to handle gap-affine pairwise sequence alignment tasks guided by easy-to-understand similarity cutoffs.

Quick Start Example

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

// (1) Build `Reference`
let fasta =
br#">target_1
ACACAGATCGCAAACTCACAATTGTATTTCTTTGCCACCTGGGCATATACTTTTTGCGCCCCCTCATTTA
>target_2
TCTGGGGCCATTGTATTTCTTTGCCAGCTGGGGCATATACTTTTTCCGCCCCCTCATTTACGCTCATCAC"#;
let reference = DefaultReference::from_fasta_bytes(fasta).unwrap();

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

// (3) Perform alignment
let query = b"CAAACTCACAATTGTATTTCTTTGCCAGCTGGGCATATACTTTTTCCGCCCCCTCATTTAACTTCTTGGA";
let result = aligner.align_query(&reference, query).unwrap();
println!("{:#?}", result);

Core Structures

The core of SigAlign is built around two central structures: Reference and Aligner. The Reference serves as a database for multiple target sequences, while the Aligner is responsible for executing the alignment tasks. The basic workflow is as follows:

1. Instantiate Reference and Aligner
2. Pass the Reference and query sequence to the Aligner.

Inputs and Outputs

Inputs

• Sequences
  • Target sequences
  • Query sequence
• Regulators
  • Penalties
    • Mismatch penalty
    • Gap-open penalty
    • Gap-extend penalty
  • Cutoffs
    • Minimum length (ML)
    • Maximum penalty per length (MPL)

Outputs

• Alignment Results
  • Penalty score
  • Length of alignment
  • Alignment position
  • Operation history

Module Navigation

• wrapper: For ease of use, SigAlign provides a wrapper module which offers DefaultReference and DefaultAligner. These structures come with additional convenience methods.
• reference, aligner: Detailed implementations of Aligner and Reference are found in their respective modules: reference and aligner. Customizing each structure according to your usage requirements can help optimize performance.

Modules

• aligner
  Provides the Aligner struct, an alignment worker that performs sequence alignment.
• reference
  Provides the Reference struct, a database for multiple targeted sequences.
• results
  Alignment results.
• utils
  Utilities.
• wrapper
  Easy to use wrappers.