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()

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()
- 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. If the required matrix does not exist, null is returned. Example names:
  
  blosum62
  
  JOND920103
  
  pam250
  
  gonnet250
  Parameters:
  
  name - Either a common name or an AAINDEX name

Class SubstitutionMatrixHelper

Method Summary

Methods inherited from class java.lang.Object

Method Details

getMatrixFromAAINDEX

getIdentity

getBlosum100

getBlosum30

getBlosum35

getBlosum40

getBlosum45

getBlosum50

getBlosum55

getBlosum60

getBlosum62

getBlosum65

getBlosum70

getBlosum75

getBlosum80

getBlosum85

getBlosum90

getGonnet250

getNuc4_2

getNuc4_4

getPAM250

getAminoAcidSubstitutionMatrix