Class Bioinformatics

java.lang.Object

org.episteme.natural.biology.Bioinformatics

public final class Bioinformatics
extends Object

Basic bioinformatics algorithms for sequence analysis.

Method Summary

Modifier and Type	Method	Description
static Real	smithWaterman(String seq1, String seq2, Real match, Real mismatch, Real gap)	Calculates the local alignment score between two sequences using the Smith-Waterman algorithm.

Methods inherited from class Object

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

Method Details

smithWaterman

public static Real smithWaterman(String seq1,
 String seq2,
 Real match,
 Real mismatch,
 Real gap)

Calculates the local alignment score between two sequences using the Smith-Waterman algorithm.

Parameters:

seq1 - First sequence (e.g., DNA string).

seq2 - Second sequence.

match - Score for a match.

mismatch - Penalty for a mismatch.

gap - Penalty for a gap.

Returns:

The maximum alignment score.