NAME

primer3Design.pl

SYNOPSIS


  primer3Design.pl    -if         <input sequence fasta file>
                      -ic         <sequence coords file>
                      -ip         <primer3 parameter file>
                      -o          <primer output file>

                      -help
  Note:all given options are required except help
    PRIMER3_PATH environmental variable path to primer3_core executable must be set

DESCRIPTION

primer3Design.pl is a program that takes as inputs: a sequence file in fasta format ,a sequence coordinate file (in the format described below), and a primer3 parameter file. The program then calls primer3_core and outputs a primer output file( in the format described below).

options:

-if: A sequence file in fasta format. The sequence id represented by the first space separated field in the fasta header lines.

-ic: The sequence coordinates file used to direct primer3 and must have the following format:


       FASTA_TAG=(sequence id)
       TARGET_REGION=(start and length coords of region to design primers around)
       TEMPLATE=(Template id)
       LEFT_PRIMER_NAME=(example s00127c01594c01595_left)
       RIGHT_PRIMER_NAME=(example s00127c01594c01595_right)
       EXCLUDED_REGION=(start and len of region to exclude)
       EXCLUDED_REGION=(Note: there can be multiple regions)
    Example:
       FASTA_TAG=s00127c01594c01595
       TARGET_REGION=60727 50
       TEMPLATE=GDNA
       LEFT_PRIMER_NAME=s00127c01594c01595_left
       RIGHT_PRIMER_NAME=s00127c01594c01595_right
       EXCLUDED_REGION=1 59626
       EXCLUDED_REGION=60677 50
       EXCLUDED_REGION=60777 50
       EXCLUDED_REGION=61877 59335

-ip: Primer3 paramter file. Formated list of primer3 paramters.

    Example:
     PRIMER_NUM_RETURN=5
     PRIMER_MAX_END_STABILITY=9.0
     PRIMER_MAX_MISPRIMING=12.00
     PRIMER_PAIR_MAX_MISPRIMING=24.00
     ...
     PRIMER_IO_WT_SEQ_QUAL=0.0
     PRIMER_TASK=pick_pcr_primers
     PRIMER_FIRST_BASE_INDEX=1
     PRIMER_PICK_ANYWAY=1
     =

-o: Path to primer output file containing the designed primer information with the following format:


   name=(left primer name),(right)
   position=("left primer id" "left primer start" "left primer end"),(right)
   type=(sequencing type left),(right)
   sequence=(primer sequence left),(right)
   template=(template to use)
   date=(left primer design date),(right date) temp=(left temp),(right)

   Example:
   name=s00127c01594c01595_left,s00127c01594c01595_right
   position=s00127c01594c01595 60623 60643,s00127c01594c01595 60892 60912
   type=custom PCR,custom PCR
   sequence=CGGTtACGTCAaGGTTCGTT,GCAAAGTCCACCTGAATGGT
   template=GDNA1
   date=20090120:142243,20090120:142243 temp=60,60

VERSION

$Revision: 1.8 $

$Date: 2009-09-22 17:42:44 $

HISTORY