org.strbio.mol
Class Primer

java.lang.Object
  org.strbio.mol.Primer

public class Primer
extends java.lang.Object

Class to represent a single primer.

Version:

1.0, 6/16/06

Author:

JMC

Field Summary

java.lang.String	dna the DNA sequence
int	index index of primer within larger DNA sequence (e.g., chromosome)
double	tm calculated melting temperature

Constructor Summary

Primer()
new primer with no info

Primer(Primer p)
copy another primer

Method Summary

void	calcTm() calculate tm using Melting
static Primer	design(java.lang.String dna, double minTm, int minLength) make a primer with melting temperature of at least N degrees, for a given sequence
static Primer	design(java.lang.String dna, java.lang.String start, double minTm, int minLength) Design a primer that has a specified start pattern.
Primer	reverseComplement() returns complement of this one
void	reverseIndex(int dnaLength) reset index to be the index from the other end of the DNA (usueful if you reverse complement)

Methods inherited from class java.lang.Object

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

Field Detail

dna

public java.lang.String dna

the DNA sequence

tm

public double tm

calculated melting temperature

index

public int index

index of primer within larger DNA sequence (e.g., chromosome)

Constructor Detail

Primer

public Primer()

new primer with no info

Primer

public Primer(Primer p)

copy another primer

Method Detail

reverseComplement

public Primer reverseComplement()

returns complement of this one

reverseIndex

public void reverseIndex(int dnaLength)

reset index to be the index from the other end of the DNA (usueful if you reverse complement)

calcTm

public void calcTm()

calculate tm using Melting

design

public static final Primer design(java.lang.String dna,
                                  double minTm,
                                  int minLength)

make a primer with melting temperature of at least N degrees, for a given sequence

design

public static final Primer design(java.lang.String dna,
                                  java.lang.String start,
                                  double minTm,
                                  int minLength)

Design a primer that has a specified start pattern. Nucleotides that don't match will not be considered in determining melting temperature.