seal

Synopsis

A Rust implementation of Needleman-Wunsch & Smith-Waterman sequence alignment.

Motivation

The aim of this crate is to provide a memory- and time-efficient implementation of Needleman-Wunsch as well as Smith-Waterman sequence alignment using a unified API.

Getting Started

Add the most recent version of seal to your dependencies in your project's Cargo.toml.

Then add …

extern crate seal;

… to your crate's root file (e.g. lib.rs, main.rs).

Once that's done you're ready to play!

Example

extern crate seal;

use seal::pair::{SmithWaterman, NeedlemanWunsch, AlignmentSet, Alignment, MemoryBacking, Step};

fn main() {
    let str_x = "The quick brown fox jumps over the lazy dog.";
    let str_y = "The brown dog jumps over the very lazy snail.";

    let strategy = NeedlemanWunsch::new(1, -1, -1, -1);
    // Alternatively:
    // let strategy = SmithWaterman::new(2, -1, -1, -1);

    let sequence_x: Vec<char> = str_x.chars().collect();
    let sequence_y: Vec<char> = str_y.chars().collect();
    let set = AlignmentSet::new(sequence_x.len(),
                                sequence_y.len(),
                                strategy,
                                MemoryBacking::MemoryBacked,
                                |x, y| sequence_x[x] == sequence_y[y]);

    let print_alignment = |alignment: Alignment| {
        for step in alignment.steps() {
            match step {
                Step::Align { x, y } => {
                    if sequence_x[x] == sequence_y[y] { print!("=") } else { print!("!") }
                },
                Step::Delete { .. } => print!("-"),
                Step::Insert { .. } => print!("+"),
            }
        }
        println!("\n");
    };

    println!("Local alignment:");
    let local_alignment = set.local_alignment();
    print_alignment(local_alignment);

    println!("Global alignment:");
    let global_alignment = set.global_alignment();
    print_alignment(global_alignment);

    // Local alignment:
    // ====------======!=!================+++++=====
    // 
    // Global alignment:
    // ====------======!=!================+++++=====!!!++=
}

See the examples directory for more in-depth examples.

API Reference

An AlignmentSet contains all optimal alignments for a given pair of sequences.

Retrieving a single locally/globally optimal alignment:

let alignment in set.local_alignment();
let alignment in global_alignment();

Enumerate all locally/globally optimal alignments:

for alignment in set.local_alignments() {
	// …
}

Contributing

Please read CONTRIBUTING.md for details on our code of conduct, and the process for submitting pull requests to us.

Versioning

We use SemVer for versioning. For the versions available, see the tags on this repository.

Authors

• Vincent Esche – Initial work – Regexident

See also the list of contributors who participated in this project.

License

This project is licensed under the MPL-2.0 – see the LICENSE.md file for details.