util.bio.calc
Class NucleicAcid

java.lang.Object
  util.bio.calc.NucleicAcid

public class NucleicAcid

extends java.lang.Object

Nucleic Acid parameter calculator and converter static methods.

Field Summary

static double[][]	dH delta H values for dinucleotide pairs.
static double[][]	dS delta S values for dinucleotide pairs.

Constructor Summary

NucleicAcid()

Method Summary

static int	baseNumber(char b) Returns 0 for a, 1 for c, 2 for g, 3 for t, -1 for everything else.
static double	calcDefaultNearestNeighborTm(java.lang.String seq) Calculates a nearest neighbor Oligo Tm at 50nM oligo, 50mM Salt, also corrects case for real method.
static double	calculateBasicOligoTm(java.lang.String seq) Calculate basic Oligo Tm
static double	calculateFractionGC(java.lang.String DNA) Calculates a GC concentration, case insensitive.
static double	calculateMolecularWtDNA(int[] gatcn) Calculates molecular weight of a DNA sequence given an int[] of gatcn's, no 5' phosphate
static double	calculateMolecularWtRNA(int[] gaucn) Calculates molecular weight of a RNA sequence given an int[] of gaucn's, no 5' phosphate
static double	calculateSaltAdjustedOligoTm(java.lang.String seq) Calculate salt adjusted Oligo Tm
static double	convertToMicroMolarDNA(java.lang.String seq, double ngPerUl) coverts ng/ul to uM given a DNA sequence
static double	convertToMicroMolarRNA(java.lang.String seq, double ngPerUl) coverts ng/ul to uM given an RNA sequence
static double	convertToNgPerUlDNA(java.lang.String seq, double uM) coverts uM to ng/ul given a DNA sequence
static double	convertToNgPerUlRNA(java.lang.String seq, double uM) coverts uM to ng/ul given an RNA sequence
static java.lang.String	formatNumberOneFraction(double num) Takes a double returns a String with one fractional digit 9.54443 -> 9.5
static java.lang.String	formatPercentOneFraction(double num) Takes a double in percent returns a String with one fraction 0.85842 -> 85.8%
static double	getTotalDelta(double[][] delta, java.lang.String seq) Returns the total delta given a lower case DNA sequence.
static double	nearestNeighborOligoTm(java.lang.String seqLowerCase, double oligoConcentration, double saltConcentration) Calculates nearest neighbor tm given a DNA oligonucleotide.

Methods inherited from class java.lang.Object

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

Field Detail

dH

public static final double[][] dH

delta H values for dinucleotide pairs. For tmNN().

dS

public static final double[][] dS

delta S values for dinucleotide pairs. For tmNN().

Constructor Detail

NucleicAcid

public NucleicAcid()

Method Detail

convertToMicroMolarDNA

public static double convertToMicroMolarDNA(java.lang.String seq,
                                            double ngPerUl)

coverts ng/ul to uM given a DNA sequence

convertToNgPerUlDNA

public static double convertToNgPerUlDNA(java.lang.String seq,
                                         double uM)

coverts uM to ng/ul given a DNA sequence

convertToMicroMolarRNA

public static double convertToMicroMolarRNA(java.lang.String seq,
                                            double ngPerUl)

coverts ng/ul to uM given an RNA sequence

convertToNgPerUlRNA

public static double convertToNgPerUlRNA(java.lang.String seq,
                                         double uM)

coverts uM to ng/ul given an RNA sequence

calculateMolecularWtDNA

public static double calculateMolecularWtDNA(int[] gatcn)

Calculates molecular weight of a DNA sequence given an int[] of gatcn's, no 5' phosphate

calculateMolecularWtRNA

public static double calculateMolecularWtRNA(int[] gaucn)

Calculates molecular weight of a RNA sequence given an int[] of gaucn's, no 5' phosphate

calculateFractionGC

public static double calculateFractionGC(java.lang.String DNA)

Calculates a GC concentration, case insensitive.

formatPercentOneFraction

public static java.lang.String formatPercentOneFraction(double num)

Takes a double in percent returns a String with one fraction 0.85842 -> 85.8%

formatNumberOneFraction

public static java.lang.String formatNumberOneFraction(double num)

Takes a double returns a String with one fractional digit 9.54443 -> 9.5

calculateBasicOligoTm

public static double calculateBasicOligoTm(java.lang.String seq)

Calculate basic Oligo Tm

calcDefaultNearestNeighborTm

public static double calcDefaultNearestNeighborTm(java.lang.String seq)

Calculates a nearest neighbor Oligo Tm at 50nM oligo, 50mM Salt, also corrects case for real method.

calculateSaltAdjustedOligoTm

public static double calculateSaltAdjustedOligoTm(java.lang.String seq)

Calculate salt adjusted Oligo Tm

nearestNeighborOligoTm

public static double nearestNeighborOligoTm(java.lang.String seqLowerCase,
                                            double oligoConcentration,
                                            double saltConcentration)

Calculates nearest neighbor tm given a DNA oligonucleotide. Concentrations are in moles, suggest 0.00000005 for oligo (50nM) and 0.05 salt (50mM). Lower case is faster, only gatcGATC, nothing else. Tm = {(DH-3.4)/(DS+1.9872ln(1/[primer])} + 16.6*log10([Na+]) Ğ273.15

getTotalDelta

public static double getTotalDelta(double[][] delta,
                                   java.lang.String seq)

Returns the total delta given a lower case DNA sequence. For tmNN().

baseNumber

public static int baseNumber(char b)

Returns 0 for a, 1 for c, 2 for g, 3 for t, -1 for everything else. For tmNN().