edu.rit.compbio.seq

Class Blosum62

java.lang.Object

edu.rit.compbio.seq.Blosum62

public class Blosum62
extends java.lang.Object

Class Blosum62 provides the BLOSUM-62 substitution matrix for protein sequence alignment. The expression Blosum62.matrix[x][y] is the score when amino acid x is aligned with amino acid y, where x and y are amino acids in the range 0..27 from a ProteinSequence.

The BLOSUM-62 substitution matrix is taken from http://www.ncbi.nlm.nih.gov/Class/BLAST/BLOSUM62.txt.

Field Summary

Fields

Modifier and Type	Field and Description
static int[][]	matrix The BLOSUM-62 protein substitution matrix.

Method Summary

Methods inherited from class java.lang.Object

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

Field Detail

matrix

public static final int[][] matrix

The BLOSUM-62 protein substitution matrix.