def gc(self):
'''Returns GC content'''
return round(_GC(str(self.seq)), 1)
def program(self):
r'''Returns a string containing a text representation of a proposed
PCR program using Taq or similar polymerase.
::
Taq (rate 30 nt/s)
Three-step| 30 cycles | |Tm formula: Biopython Tm_NN
94.0°C |94.0°C | |SaltC 50mM
__________|_____ 72.0°C |72.0°C|
04min00s |30s \ ________|______|
| \ 46.0°C/ 0min 1s|10min |
| \_____/ | |
| 30s | |4-8°C
'''
# Primer melting temperatures are calculated with the Tm_NN formula from
# biopython
# simple salt concentration correction is used and the template concentration
# is ignored. dnac1 = primer concentration
tmf = _Tm_NN(str(self.forward_primer.footprint),
dnac1=self.fprimerc,
Na=self.saltc)
tmr = _Tm_NN(str(self.reverse_primer.footprint),
dnac1=self.fprimerc,
Na=self.saltc)
# Ta calculation according to
# Rychlik, Spencer, and Rhoads, 1990, Optimization of the anneal
# ing temperature for DNA amplification in vitro
# http://www.ncbi.nlm.nih.gov/pubmed/2243783
# The formula described uses the length and GC content of the product and
# salt concentration (monovalent cations).
#GC_prod=GC(str(self.seq))
tmp = 81.5 + 0.41*_GC(str(self.seq)) + 16.6*_math.log10(self.saltc/1000.0) - 675/len(self)
tml = min(tmf,tmr)
ta = 0.3*tml+0.7*tmp-14.9
# Taq polymerase extension rate is set to 30 nt/s
# see https://www.thermofisher.com/pt/en/home/life-science/pcr/pcr-enzymes-master-mixes/taq-dna-polymerase-enzymes/taq-dna-polymerase.html
taq_extension_rate = 30 # seconds/kB PCR product length
extension_time_taq = int(round(taq_extension_rate * len(self) / 1000)) # seconds
f = _textwrap.dedent(r'''
Taq ({rate} nt/s) 35 cycles
| 95.0°C |95.0°C | |tm:
|_________|_____ 72.0°C |72.0°C|Salt {saltc:2} mM
| 03min00s|30s \ ________|______|fp {forward_primer_concentration:3} µM
| | \ {ta}°C/{0:2}min{1:2}s| 5min |rp {reverse_primer_concentration:3} µM
| | \_____/ | |GC {GC_prod}%
| | 30s | |{size} bp'''[1:].format(rate=taq_extension_rate,
forward_primer_concentration=self.fprimerc/1000,
reverse_primer_concentration=self.rprimerc/1000,
ta=round(ta,1),
saltc=self.saltc,
*divmod(extension_time_taq,60),
size= len(self.seq),
GC_prod= int(self.gc()) ))
return _pretty_str(f)
def gc(self):
"""Return GC content."""
return round(_GC(str(self.seq)) / 100.0, 3)
def gc(self):
"""Returns GC content"""
return round(_GC(str(self.seq)), 1)