util.bio.calc
Class NucleicAcid

java.lang.Object
  extended byutil.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+]) 273.15


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().