• Intro

  • step_01
  • step_02
  • step_03
  • step_04
  • step_05
  • step_06
  • step_07
  • step_08
  • step_09
  • step_10
  • step_11
  • step_12
  • step_13
  • step_14
  • step_15
  • step_16
  • step_17
  • step_18
  • step_19
  • step_20
  • step_21
  • step_22
  • step_23
  • step_24

  • Credits

    UC Davis

    Step 18: Oligo design

    Final steps of our SNP/INDEL pipeline are oligo (primer) design for PCR based molecular markers.

    We are using Primer3 program and contig_target_May_01_2003.pl Perl script to generate a set of oligos (primers) for PCR.

    contig_target_May_01_2003.pl script takes as an input two files:
    1. Table generated by Py_ContigViewer with info about region of interest
    2. Tab-delimited file with consensus sequences

    This web page describes briefly how to generate a table with "target" info. Next web page - how to obtain tab-delimited file with consensus sequences and "step 20" - how to run contig_target_May_01_2003.pl script and description of its output.

    Detailed description of Py_ContigViewer is available here. Below, just example screenshots for three selected contigs and table with "target" info generated by the viewer:

    By using "Add to list" function "primer_picker.in" table has been generated with "target" info for three selected contigs.