Primer3

Overview

Primer3 is a widely used program for designing PCR primers (PCR = “Polymerase Chain Reaction”). PCR is an essential and ubiquitous tool in genetics and molecular biology. Primer3 can also design hybridization probes and sequencing primers.

PCR is used for many different goals. Consequently, primer3 has many different input parameters that you control and that tell primer3 exactly what characteristics make good primers for your goals.

Version 2.3.5 is installed.

Restrictions on use

The software is open source and available to all users.

Set up procedure

To access the software please load the modulefile:

module load apps/gcc/primer3/2.3.5

primer3_config dir

The primer3_config directory does not reside in one of the expected default locations on the CSF. Instead we have set this globally for all users with the file $PRIMER3_HOME/csf2.p3.settings which contains the following:

Primer3 File - http://primer3.sourceforge.net
P3_FILE_TYPE=settings

PRIMER_THERMODYNAMIC_PARAMETERS_PATH=/opt/gridware/apps/gcc/primer3/2.3.5/primer3_config/
=

Without this file the software fails to run. See the example below to ensure your job uses this file.

Running the application

Please submit all work to batch.

Serial batch job submission

• Make sure you have the modulefile loaded.
• Create a batch submission script/file, for example:

#!/bin/bash
#$ -cwd
#$ -V

primer3_core -p3_settings_file $PRIMER3_HOME/csf2.p3.settings -format_output formatted_seqs.txt

• Submit the job: qsub scriptname

Parallel batch job submission

Primer3 does not run in parallel on the CSF.

Further info

• Primer3 website
• Primer3 2.3.5 manual
• Information about changes to default values post version 2.2.3 (Note that this link goes to the 2.3.4 manual, not the 2.3.5).