Expand description
§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§
- Amino
Acid - One variant for each amino acid
- Substitution
Matrix - One variant per matrix