def get_primer(seq,t1,l):
return primer3.bindings.designPrimers(
{
'SEQUENCE_ID': 'TEST',
'SEQUENCE_TEMPLATE': seq,
'SEQUENCE_TARGET': [t1,l]
},
{
'PRIMER_OPT_SIZE': 20,
'PRIMER_PICK_INTERNAL_OLIGO': 0,
'PRIMER_INTERNAL_MAX_SELF_END': 8,
'PRIMER_MIN_SIZE': 18,
'PRIMER_MAX_SIZE': 25,
'PRIMER_OPT_TM': 55.0,
'PRIMER_MIN_TM': 52.0,
'PRIMER_MAX_TM': 58.0,
'PRIMER_MIN_GC': 20.0,
'PRIMER_MAX_GC': 80.0,
'PRIMER_MAX_POLY_X': 100,
'PRIMER_INTERNAL_MAX_POLY_X': 100,
'PRIMER_SALT_MONOVALENT': 50.0,
'PRIMER_DNA_CONC': 50.0,
'PRIMER_MAX_NS_ACCEPTED': 0,
'PRIMER_MAX_SELF_ANY': 12,
'PRIMER_MAX_SELF_END': 8,
'PRIMER_PAIR_MAX_COMPL_ANY': 12,
'PRIMER_PAIR_MAX_COMPL_END': 8,
'PRIMER_PRODUCT_SIZE_RANGE': [400,500](/k821209/pipelines/wiki/400,500),
})
import primer3
c = primer3.bindings.designPrimers(
{
'SEQUENCE_ID': 'MH1000',
'SEQUENCE_TEMPLATE': seq,
},
{
'PRIMER_OPT_SIZE': 20,
'PRIMER_PICK_ANYWAY':1,
'PRIMER_MIN_SIZE': 18,
'PRIMER_MAX_SIZE': 25,
'PRIMER_TASK' : 'pick_cloning_primers'
})
- dg : deltaG (Gibbs free energy) of the structure (cal/mol)
- dh : deltaH (entropy) of the structure (cal/mol)
- ds : deltaS (enthalpy) of the structure (cal/K*mol)
- tm : Melting temperature of the structure in deg. C
primer3.calcHairpin('CCCCCATCCGATCAGGGGG')
# result : ThermoResult(structure_found=True, tm=34.15, dg=337.09, dh=-36300.00, ds=-118.13)
primer3.bindings.calcHeterodimer('ATGAACAAGAACAAGATTGATGT','TCAACGAGGAGAAATATGAGAT')
# result : ThermoResult(structure_found=True, tm=-29.81, dg=8441.74, dh=-71600.00, ds=-258.07)
primer3.bindings.calcHomodimer('ATGAACAAGAACAAGATTGATGT')
# result : ThermoResult(structure_found=True, tm=-2.60, dg=3158.73, dh=-98200.00, ds=-326.81)
#http://bioinfo.ut.ee/primer3/primer3web_help.htm#PRIMER_DNA_CONC
oligo_calc = primer3.thermoanalysis.ThermoAnalysis(mv_conc=50, dv_conc=1.5, dntp_conc=0.6, dna_conc=50, max_nn_length=60)
# 위 설정이 primer3 default
oligo_calc.calcTm(seq)