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 …

rust 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

```rust extern crate seal;

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

fn main() { let strx = "The quick brown fox jumps over the lazy dog."; let stry = "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<InMemoryAlignmentMatrix> =
    AlignmentSet::new(sequence_x.len(), sequence_y.len(), strategy, |x, y| {
        sequence_x[x] == sequence_y[y]
    })
    .unwrap();

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

rust let alignment in alignment_set.local_alignment(); let alignment in alignment_set.global_alignment();

Enumerate all locally/globally optimal alignments

rust for alignment in alignment_set.local_alignments() { // … } for alignment in alignment_set.global_alignments() { // … }

Contributing

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

License

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