[BioPython] Emboss eprimer3

[Stefanie Lück]

Hi!

I have some questions about eprimer3 from Emboss which I use over Python to design primers in a batch mode:

1) I'm using the GCclamp function (value=1). Is it possible to limit the G or C's at the end to maximum of one G or C? 

2) Is there a setting to get the original primer3 output? The emboss output is for hundrets of primers not very usefull and many informations are missing.

The primer 3 file looks like this:

PRIMER_SEQUENCE_ID=HF15E08r
SEQUENCE=GCATGTAATAATGCCAAAGCTCACAGCTGCAGTTGAATCTTGGGACCCGCGGAGCGAGAATGTACCAATCCATGTATGGGTACACCCATGGCTGCCAACTCTAGGGCAAAGGATAGATACACTGTGCCACTCTATCCGGTACAAGCTGAGTAGTGTCCTCCAATTATGGCAAGCTCACGATTCATCAGCTTATGCTGTGCTATCTCCATGGAAGGGTGTATTTGATCCAGCAAGTTGGGAAGACTTGATAGTGCGTTATATCATTCCTAAACTGAAAATGGCACTCCAGGAGTTCCAGATTAACCCAGCAAGCCAAAAGTTTGACCAGTTTAACTGGGTTATGATCTGGGCTTCTGCTGTCCCGGTACACCATATGGTCCATATGTTGGAAGTTGATTTCTTTAGCAAGTGGCAGCTGGTTTTGTACCATTGGCTGAGCTCACCAAATCCTGATTTCAATGAGATAATGAATTGGTAT
PRIMER_PRODUCT_SIZE_RANGE=500-1000 450-500 400-450 350-400 300-350 250-300 200-250 150-200
PRIMER_OPT_TM=60.0
PRIMER_MIN_TM=58.0
PRIMER_MAX_TM=65.0
PRIMER_MAX_DIFF_TM=3.0
PRIMER_DNA_CONC=420
PRIMER_NUM_RETURN=1
PRIMER_PAIR_PENALTY=0.8691
PRIMER_LEFT_PENALTY=0.708329
PRIMER_RIGHT_PENALTY=0.160746
PRIMER_LEFT_SEQUENCE=GCATGTAATAATGCCAAAGC
PRIMER_RIGHT_SEQUENCE=TTGAAATCAGGATTTGGTGA
PRIMER_LEFT=0,20
PRIMER_RIGHT=458,20
PRIMER_LEFT_TM=59.292
PRIMER_RIGHT_TM=60.161
PRIMER_LEFT_GC_PERCENT=40.000
PRIMER_RIGHT_GC_PERCENT=35.000
PRIMER_LEFT_SELF_ANY=7.00
PRIMER_RIGHT_SELF_ANY=8.00
PRIMER_LEFT_SELF_END=2.00
PRIMER_RIGHT_SELF_END=2.00
PRIMER_LEFT_END_STABILITY=8.5000
PRIMER_RIGHT_END_STABILITY=7.9000
PRIMER_PAIR_COMPL_ANY=5.00
PRIMER_PAIR_COMPL_END=3.00
PRIMER_PRODUCT_SIZE=459

Thanks in advance!
Stefanie