Package org.biojava.nbio.core.alignment.matrices

Class SubstitutionMatrixHelper

java.lang.Object

org.biojava.nbio.core.alignment.matrices.SubstitutionMatrixHelper

All Implemented Interfaces:

Serializable

public class SubstitutionMatrixHelper
extends Object
implements Serializable

Static utility to access substitution matrices that come bundled with BioJava. All matrices were downloaded from ftp://ftp.ncbi.nih.gov/blast/matrices/

Author:

Mark Chapman, Paolo Pavan

See Also:

• Serialized Form

Method Summary

Modifier and Type	Method	Description
static SubstitutionMatrix<AminoAcidCompound>	getAminoAcidSubstitutionMatrix(String name)	Returns a substitution matrix for amino acids given by the name name.
static SubstitutionMatrix<AminoAcidCompound>	getBlosum100()	Returns Blosum 100 matrix by Henikoff & Henikoff
static SubstitutionMatrix<AminoAcidCompound>	getBlosum30()	Returns Blosum 30 matrix by Henikoff & Henikoff
static SubstitutionMatrix<AminoAcidCompound>	getBlosum35()	Returns Blosum 35 matrix by Henikoff & Henikoff
static SubstitutionMatrix<AminoAcidCompound>	getBlosum40()	Returns Blosum 40 matrix by Henikoff & Henikoff
static SubstitutionMatrix<AminoAcidCompound>	getBlosum45()	Returns Blosum 45 matrix by Henikoff & Henikoff
static SubstitutionMatrix<AminoAcidCompound>	getBlosum50()	Returns Blosum 50 matrix by Henikoff & Henikoff
static SubstitutionMatrix<AminoAcidCompound>	getBlosum55()	Returns Blosum 55 matrix by Henikoff & Henikoff
static SubstitutionMatrix<AminoAcidCompound>	getBlosum60()	Returns Blosum 60 matrix by Henikoff & Henikoff
static SubstitutionMatrix<AminoAcidCompound>	getBlosum62()	Returns Blosum 62 matrix by Henikoff & Henikoff
static SubstitutionMatrix<AminoAcidCompound>	getBlosum65()	Returns Blosum 65 matrix by Henikoff & Henikoff
static SubstitutionMatrix<AminoAcidCompound>	getBlosum70()	Returns Blosum 70 matrix by Henikoff & Henikoff
static SubstitutionMatrix<AminoAcidCompound>	getBlosum75()	Returns Blosum 75 matrix by Henikoff & Henikoff
static SubstitutionMatrix<AminoAcidCompound>	getBlosum80()	Returns Blosum 80 matrix by Henikoff & Henikoff
static SubstitutionMatrix<AminoAcidCompound>	getBlosum85()	Returns Blosum 85 matrix by Henikoff & Henikoff
static SubstitutionMatrix<AminoAcidCompound>	getBlosum90()	Returns Blosum 90 matrix by Henikoff & Henikoff
static SubstitutionMatrix<AminoAcidCompound>	getGonnet250()	Returns PAM 250 matrix by Gonnet, Cohen & Benner
static SubstitutionMatrix<AminoAcidCompound>	getIdentity()	Gets identity matrix where matches score 1 and mismatches score -10000
static SubstitutionMatrix<AminoAcidCompound>	getMatrixFromAAINDEX(String matrixName)	Returns any matrix from the AAINDEX database file
static SubstitutionMatrix<NucleotideCompound>	getNuc4_2()	Returns Nuc 4.2 matrix by Lowe Only the first nucleotide sequence to align can contain ambiguous nucleotides
static SubstitutionMatrix<NucleotideCompound>	getNuc4_4()	Returns Nuc 4.4 matrix by Lowe Both of the nucleotide sequences to align can contain ambiguous nucleotides
static SubstitutionMatrix<AminoAcidCompound>	getPAM250()	Returns PAM 250 matrix by Dayhoff

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Method Details

getMatrixFromAAINDEX

public static SubstitutionMatrix<AminoAcidCompound> getMatrixFromAAINDEX(String matrixName)

Returns any matrix from the AAINDEX database file

Parameters:

matrixName -

Returns:

a SubstitutionMatrix

getIdentity

public static SubstitutionMatrix<AminoAcidCompound> getIdentity()

Gets identity matrix where matches score 1 and mismatches score -10000

Returns:

getBlosum100

public static SubstitutionMatrix<AminoAcidCompound> getBlosum100()

Returns Blosum 100 matrix by Henikoff & Henikoff

Returns:

Blosum 100 matrix

getBlosum30

public static SubstitutionMatrix<AminoAcidCompound> getBlosum30()

Returns Blosum 30 matrix by Henikoff & Henikoff

Returns:

Blosum 30 matrix

getBlosum35

public static SubstitutionMatrix<AminoAcidCompound> getBlosum35()

Returns Blosum 35 matrix by Henikoff & Henikoff

Returns:

Blosum 35 matrix

getBlosum40

public static SubstitutionMatrix<AminoAcidCompound> getBlosum40()

Returns Blosum 40 matrix by Henikoff & Henikoff

Returns:

Blosum 40 matrix

getBlosum45

public static SubstitutionMatrix<AminoAcidCompound> getBlosum45()

Returns Blosum 45 matrix by Henikoff & Henikoff

Returns:

Blosum 45 matrix

getBlosum50

public static SubstitutionMatrix<AminoAcidCompound> getBlosum50()

Returns Blosum 50 matrix by Henikoff & Henikoff

Returns:

Blosum 50 matrix

getBlosum55

public static SubstitutionMatrix<AminoAcidCompound> getBlosum55()

Returns Blosum 55 matrix by Henikoff & Henikoff

Returns:

Blosum 55 matrix

getBlosum60

public static SubstitutionMatrix<AminoAcidCompound> getBlosum60()

Returns Blosum 60 matrix by Henikoff & Henikoff

Returns:

Blosum 60 matrix

getBlosum62

public static SubstitutionMatrix<AminoAcidCompound> getBlosum62()

Returns Blosum 62 matrix by Henikoff & Henikoff

Returns:

Blosum 62 matrix

getBlosum65

public static SubstitutionMatrix<AminoAcidCompound> getBlosum65()

Returns Blosum 65 matrix by Henikoff & Henikoff

Returns:

Blosum 65 matrix

getBlosum70

public static SubstitutionMatrix<AminoAcidCompound> getBlosum70()

Returns Blosum 70 matrix by Henikoff & Henikoff

Returns:

Blosum 70 matrix

getBlosum75

public static SubstitutionMatrix<AminoAcidCompound> getBlosum75()

Returns Blosum 75 matrix by Henikoff & Henikoff

Returns:

Blosum 75 matrix

getBlosum80

public static SubstitutionMatrix<AminoAcidCompound> getBlosum80()

Returns Blosum 80 matrix by Henikoff & Henikoff

Returns:

Blosum 80 matrix

getBlosum85

public static SubstitutionMatrix<AminoAcidCompound> getBlosum85()

Returns Blosum 85 matrix by Henikoff & Henikoff

Returns:

Blosum 85 matrix

getBlosum90

public static SubstitutionMatrix<AminoAcidCompound> getBlosum90()

Returns Blosum 90 matrix by Henikoff & Henikoff

Returns:

Blosum 90 matrix

getGonnet250

public static SubstitutionMatrix<AminoAcidCompound> getGonnet250()

Returns PAM 250 matrix by Gonnet, Cohen & Benner

Returns:

Gonnet 250 matrix

getNuc4_2

public static SubstitutionMatrix<NucleotideCompound> getNuc4_2()

Returns Nuc 4.2 matrix by Lowe Only the first nucleotide sequence to align can contain ambiguous nucleotides

Returns:

Nuc 4.2 matrix

getNuc4_4

public static SubstitutionMatrix<NucleotideCompound> getNuc4_4()

Returns Nuc 4.4 matrix by Lowe Both of the nucleotide sequences to align can contain ambiguous nucleotides

Returns:

Nuc 4.4 matrix

getPAM250

public static SubstitutionMatrix<AminoAcidCompound> getPAM250()

Returns PAM 250 matrix by Dayhoff

Returns:

PAM 250 matrix

getAminoAcidSubstitutionMatrix

public static SubstitutionMatrix<AminoAcidCompound> getAminoAcidSubstitutionMatrix(String name)

Returns a substitution matrix for amino acids given by the name name. Searches first in the default AAINDEX file (see @link getMatrixFromAAINDEX(String)), then in the classpath in src/main/resources/matrices. Example names:

• blosum62
• JOND920103
• pam250
• gonnet250

Parameters:

name - Either a common name or an AAINDEX name

Returns:

a SubstitutionMatrix or null if no matrix is found