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Re^6: Primer3 - BioPerl

by Anonymous Monk
on Apr 27, 2012 at 12:36 UTC ( #967613=note: print w/ replies, xml ) Need Help??


in reply to Re^5: Primer3 - BioPerl
in thread Primer3 - BioPerl

Try copying the src/primer3_config file from the primer3 build directory to /opt/primer3_config - it should look in there by default according to the docs (http://www.mcardle.wisc.edu/mprime/help/primer3/primer3_manual.htm)


Comment on Re^6: Primer3 - BioPerl
Re^7: Primer3 - BioPerl
by tinu329 (Initiate) on Apr 01, 2013 at 16:08 UTC

    I know its more than a year since the question is posted. Had to deal with the same problem and could solve using the below method. Thought of posting it, if it would be useful for anyone else. Thanks !!

    specify the PRIMER_THERMODYNAMIC_PARAMETERS_PATH in the input file for the primer3_core software

    cat inputfile.txt SEQUENCE_ID=example SEQUENCE_TEMPLATE=GTAGTCAGTAGACNATGACNACTGACGATGCAGACNACACACACACACACAG +CACACAGGTATTAGTGGGCCATTCGATCCCGACCCAAATCGATAGCTACGATGACG SEQUENCE_TARGET=37,21 PRIMER_TASK=generic PRIMER_PICK_LEFT_PRIMER=1 PRIMER_PICK_INTERNAL_OLIGO=1 PRIMER_PICK_RIGHT_PRIMER=1 PRIMER_OPT_SIZE=18 PRIMER_MIN_SIZE=15 PRIMER_MAX_SIZE=21 PRIMER_MAX_NS_ACCEPTED=1 PRIMER_PRODUCT_SIZE_RANGE=75-100 P3_FILE_FLAG=1 SEQUENCE_INTERNAL_EXCLUDED_REGION=37,21 PRIMER_EXPLAIN_FLAG=1 PRIMER_THERMODYNAMIC_PARAMETERS_PATH=/home/User/Softwares/primer3-2.3. +5/src/primer3_config/ =
    Thanks, Tinu

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