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.