def add_PCR_conditions(feature):
try:
feature.qualifiers['C_Na'] = str(C_Na)+ ' mM'
feature.qualifiers['C_Mg'] = str(C_Mg)+ ' mM'
feature.qualifiers['C_dNTP'] = str(C_dNTP)+' mM'
feature.qualifiers['C_DNA'] = str(C_DNA)+ ' nM'
feature.qualifiers['C_Primer'] = str(C_Prim)+' uM'
feature.qualifiers['C_DMSO'] = str(C_DMSO)+' %'
except Exception, e:
print 'add_PCR_conditions:'
print_exception(e)
def add_PCR_conditions(feature):
try:
feature.qualifiers['C_Na'] = str(C_Na) + ' mM'
feature.qualifiers['C_Mg'] = str(C_Mg) + ' mM'
feature.qualifiers['C_dNTP'] = str(C_dNTP) + ' mM'
feature.qualifiers['C_DNA'] = str(C_DNA) + ' nM'
feature.qualifiers['C_Primer'] = str(C_Prim) + ' uM'
feature.qualifiers['C_DMSO'] = str(C_DMSO) + ' %'
except Exception, e:
print 'add_PCR_conditions:'
print_exception(e)
The thermodynamics of DNA structural motifs. Annual review of biophysics and
biomolecular structure, 33, 415-40. doi:10.1146/annurev.biophys.32.110601.141800
2) von Ahsen, N., Wittwer, C. T., & Schütz, E. (2001). Oligonucleotide melting
temperatures under PCR conditions: nearest-neighbor corrections for Mg(2+),
deoxynucleotide triphosphate, and dimethyl sulfoxide concentrations with
comparison to alternative empirical formulas. Clinical chemistry, 47(11), 1956-61.
'''
from math import sqrt, log
from UnifiedNN import *
from StringTools import print_exception
try:
from Bio.SeqFeature import SeqFeature, FeatureLocation
except Exception, e:
print_exception(e)
raise ImportError('The BioPython must be installed in your system.')
#utility functions
def print_exception(e):
print "Exception occurred: " + str(type(e)) + " : " + e.__str__()
###############################################################################
#standard PCR conditions
C_Mg = 1.5 #mM
C_Na = 50 #mM; should be above 0.05M and below 1.1M
C_dNTP = 0 #mM
C_DNA = 50 #nM; DNA template concentration
C_Prim = 0.1 #uM; Primer concentration
C_DMSO = 0 #percent
The thermodynamics of DNA structural motifs. Annual review of biophysics and
biomolecular structure, 33, 415-40. doi:10.1146/annurev.biophys.32.110601.141800
2) von Ahsen, N., Wittwer, C. T., & Schütz, E. (2001). Oligonucleotide melting
temperatures under PCR conditions: nearest-neighbor corrections for Mg(2+),
deoxynucleotide triphosphate, and dimethyl sulfoxide concentrations with
comparison to alternative empirical formulas. Clinical chemistry, 47(11), 1956-61.
'''
from math import sqrt, log
from UnifiedNN import *
from StringTools import print_exception
try:
from Bio.SeqFeature import SeqFeature, FeatureLocation
except Exception, e:
print_exception(e)
raise ImportError('The BioPython must be installed in your system.')
#utility functions
def print_exception(e):
print "Exception occurred: " + str(type(e)) + " : " + e.__str__()
###############################################################################
#standard PCR conditions
C_Mg = 1.5 #mM
C_Na = 50 #mM; should be above 0.05M and below 1.1M
C_dNTP = 0 #mM
C_DNA = 50 #nM; DNA template concentration