aa-similarity

Usage

Add the following to your Cargo.toml

[dependencies]
aa-similarity = "0.1.0"

Examples

use aa_similarity::{Blosum65, Similarity, AminoAcid};

assert_eq!(
    Blosum65::similarity(
        AminoAcid::GlutamicAcid,
        AminoAcid::AsparticAcid
    ),
    2
);

aa-similarity re-exports AminoAcid from aa-name. Amino acids from an alignment can be converted from chars or string like so:

use aa_similarity::{Blosum62, Similarity, AminoAcid};

let ala = AminoAcid::try_from('A')?;
let tyr = AminoAcid::try_from('Y')?;

assert_eq!(Blosum62::similarity(ala, tyr), -2);

See: aa-name.

Supported matrices

Source: ftp://ftp.ncbi.nih.gov/blast/matrices/

• Blosum30

• Blosum35

• Blosum40

• Blosum45

• Blosum50

• Blosum55

• Blosum60

• Blosum62

• Blosum65

• Blosum70

• Blosum75

• Blosum80

• Blosum85

• Blosum90

• Blosum100

• Blosumn

• Dayhoff

• Identity

• Pam10

• Pam20

• Pam30

• Pam40

• Pam50

• Pam60

• Pam70

• Pam80

• Pam90

• Pam100

• Pam110

• Pam120

• Pam130

• Pam140

• Pam150

• Pam160

• Pam170

• Pam180

• Pam190

• Pam200

• Pam210

• Pam220

• Pam230

• Pam240

• Pam250

• Pam260

• Pam270

• Pam280

• Pam290

• Pam300

• Pam310

• Pam320

• Pam330

• Pam340

• Pam350

• Pam360

• Pam370

• Pam380

• Pam390

• Pam400

• Pam410

• Pam420

• Pam430

• Pam440

• Pam450

• Pam460

• Pam470

• Pam480

• Pam490

• Pam500

Contributing

The project is maintained by Jean Manguy. Please submit a bug report or a feature request on the Github issues page.

License

aa-similarity is distributed under the terms of both the MIT license and the Apache License (Version 2.0).

See LICENSE-APACHE and LICENSE-MIT for details.