[][src]Crate aa_similarity

Substitution matrices for use in protein sequence analysis and alignment.

This crate implements the trait Similarity which provide the similarity() function for each substitution matrix. Similarity data from ftp://ftp.ncbi.nih.gov/blast/matrices/ is parsed and creates a match between all possible combination of 2 amino acids.

use aa_similarity::{Blosum62, Blosum65, Similarity, AminoAcid};
use std::convert::TryFrom;

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

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

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

Structs

Blosum30

implementation generated from ftp://ftp.ncbi.nih.gov/blast/matrices/BLOSUM30

Blosum35

implementation generated from ftp://ftp.ncbi.nih.gov/blast/matrices/BLOSUM35

Blosum40

implementation generated from ftp://ftp.ncbi.nih.gov/blast/matrices/BLOSUM40

Blosum45

implementation generated from ftp://ftp.ncbi.nih.gov/blast/matrices/BLOSUM45

Blosum50

implementation generated from ftp://ftp.ncbi.nih.gov/blast/matrices/BLOSUM50

Blosum55

implementation generated from ftp://ftp.ncbi.nih.gov/blast/matrices/BLOSUM55

Blosum60

implementation generated from ftp://ftp.ncbi.nih.gov/blast/matrices/BLOSUM60

Blosum62

implementation generated from ftp://ftp.ncbi.nih.gov/blast/matrices/BLOSUM62

Blosum65

implementation generated from ftp://ftp.ncbi.nih.gov/blast/matrices/BLOSUM65

Blosum70

implementation generated from ftp://ftp.ncbi.nih.gov/blast/matrices/BLOSUM70

Blosum75

implementation generated from ftp://ftp.ncbi.nih.gov/blast/matrices/BLOSUM75

Blosum80

implementation generated from ftp://ftp.ncbi.nih.gov/blast/matrices/BLOSUM80

Blosum85

implementation generated from ftp://ftp.ncbi.nih.gov/blast/matrices/BLOSUM85

Blosum90

implementation generated from ftp://ftp.ncbi.nih.gov/blast/matrices/BLOSUM90

Blosum100

implementation generated from ftp://ftp.ncbi.nih.gov/blast/matrices/BLOSUM100

Blosumn

implementation generated from ftp://ftp.ncbi.nih.gov/blast/matrices/BLOSUMN

Dayhoff

implementation generated from ftp://ftp.ncbi.nih.gov/blast/matrices/DAYHOFF

Identity

implementation generated from ftp://ftp.ncbi.nih.gov/blast/matrices/IDENTITY

Pam10

implementation generated from ftp://ftp.ncbi.nih.gov/blast/matrices/PAM10

Pam20

implementation generated from ftp://ftp.ncbi.nih.gov/blast/matrices/PAM20

Pam30

implementation generated from ftp://ftp.ncbi.nih.gov/blast/matrices/PAM30

Pam40

implementation generated from ftp://ftp.ncbi.nih.gov/blast/matrices/PAM40

Pam50

implementation generated from ftp://ftp.ncbi.nih.gov/blast/matrices/PAM50

Pam60

implementation generated from ftp://ftp.ncbi.nih.gov/blast/matrices/PAM60

Pam70

implementation generated from ftp://ftp.ncbi.nih.gov/blast/matrices/PAM70

Pam80

implementation generated from ftp://ftp.ncbi.nih.gov/blast/matrices/PAM80

Pam90

implementation generated from ftp://ftp.ncbi.nih.gov/blast/matrices/PAM90

Pam100

implementation generated from ftp://ftp.ncbi.nih.gov/blast/matrices/PAM100

Pam110

implementation generated from ftp://ftp.ncbi.nih.gov/blast/matrices/PAM110

Pam120

implementation generated from ftp://ftp.ncbi.nih.gov/blast/matrices/PAM120

Pam130

implementation generated from ftp://ftp.ncbi.nih.gov/blast/matrices/PAM130

Pam140

implementation generated from ftp://ftp.ncbi.nih.gov/blast/matrices/PAM140

Pam150

implementation generated from ftp://ftp.ncbi.nih.gov/blast/matrices/PAM150

Pam160

implementation generated from ftp://ftp.ncbi.nih.gov/blast/matrices/PAM160

Pam170

implementation generated from ftp://ftp.ncbi.nih.gov/blast/matrices/PAM170

Pam180

implementation generated from ftp://ftp.ncbi.nih.gov/blast/matrices/PAM180

Pam190

implementation generated from ftp://ftp.ncbi.nih.gov/blast/matrices/PAM190

Pam200

implementation generated from ftp://ftp.ncbi.nih.gov/blast/matrices/PAM200

Pam210

implementation generated from ftp://ftp.ncbi.nih.gov/blast/matrices/PAM210

Pam220

implementation generated from ftp://ftp.ncbi.nih.gov/blast/matrices/PAM220

Pam230

implementation generated from ftp://ftp.ncbi.nih.gov/blast/matrices/PAM230

Pam240

implementation generated from ftp://ftp.ncbi.nih.gov/blast/matrices/PAM240

Pam250

implementation generated from ftp://ftp.ncbi.nih.gov/blast/matrices/PAM250

Pam260

implementation generated from ftp://ftp.ncbi.nih.gov/blast/matrices/PAM260

Pam270

implementation generated from ftp://ftp.ncbi.nih.gov/blast/matrices/PAM270

Pam280

implementation generated from ftp://ftp.ncbi.nih.gov/blast/matrices/PAM280

Pam290

implementation generated from ftp://ftp.ncbi.nih.gov/blast/matrices/PAM290

Pam300

implementation generated from ftp://ftp.ncbi.nih.gov/blast/matrices/PAM300

Pam310

implementation generated from ftp://ftp.ncbi.nih.gov/blast/matrices/PAM310

Pam320

implementation generated from ftp://ftp.ncbi.nih.gov/blast/matrices/PAM320

Pam330

implementation generated from ftp://ftp.ncbi.nih.gov/blast/matrices/PAM330

Pam340

implementation generated from ftp://ftp.ncbi.nih.gov/blast/matrices/PAM340

Pam350

implementation generated from ftp://ftp.ncbi.nih.gov/blast/matrices/PAM350

Pam360

implementation generated from ftp://ftp.ncbi.nih.gov/blast/matrices/PAM360

Pam370

implementation generated from ftp://ftp.ncbi.nih.gov/blast/matrices/PAM370

Pam380

implementation generated from ftp://ftp.ncbi.nih.gov/blast/matrices/PAM380

Pam390

implementation generated from ftp://ftp.ncbi.nih.gov/blast/matrices/PAM390

Pam400

implementation generated from ftp://ftp.ncbi.nih.gov/blast/matrices/PAM400

Pam410

implementation generated from ftp://ftp.ncbi.nih.gov/blast/matrices/PAM410

Pam420

implementation generated from ftp://ftp.ncbi.nih.gov/blast/matrices/PAM420

Pam430

implementation generated from ftp://ftp.ncbi.nih.gov/blast/matrices/PAM430

Pam440

implementation generated from ftp://ftp.ncbi.nih.gov/blast/matrices/PAM440

Pam450

implementation generated from ftp://ftp.ncbi.nih.gov/blast/matrices/PAM450

Pam460

implementation generated from ftp://ftp.ncbi.nih.gov/blast/matrices/PAM460

Pam470

implementation generated from ftp://ftp.ncbi.nih.gov/blast/matrices/PAM470

Pam480

implementation generated from ftp://ftp.ncbi.nih.gov/blast/matrices/PAM480

Pam490

implementation generated from ftp://ftp.ncbi.nih.gov/blast/matrices/PAM490

Pam500

implementation generated from ftp://ftp.ncbi.nih.gov/blast/matrices/PAM500

Enums

AminoAcid

One variant for each amino acid

SubstitutionMatrix

One variant per matrix

Traits

Similarity