Overview

UniPrime2 is an web service which automatically designs large sets of universal primers by simply inputting a GeneID reference.

Useful links

UniPrime2 is an experimentally validated, fully automated program that generates successful cross-species primers that take into account the biological aspects of the PCR. UniPrime2 automatically retrieves and aligns orthologous sequences from GenBank, identifies regions of conservation within the alignment and generates suitable primers that can amplify variable genomic regions. UniPrime2 differs from previous automatic primer design programs in that all steps of primer design are automated, saved and are phylogenetically limited. We have experimentally verified the efficiency and success of this program.

  • 1. Locus

    Initial sequence retrieval

  • 2. Ortho

    Search for orthologs

  • 3. Align

    Multi-species alignment

  • 4. Primer

    Primer design

  • 5. PCR

    Virtual PCR

Tutorial

Learn how to use Uniprime.

Tutorial sections

Before using UniPrime2, it is advised to read the following tutorial which consists of 3 main parts:

  • How to find the GeneID
    Describes how to find the locus GenBank GeneID.
  • Website overview
    The website overview describes all you have to know about the UniPrime2 website by highlighting the key parts.
  • Step by step
    This tutorial details each step of a full execution of UniPrime2.

Local installation

09-02-2010

The open-source software.

The Linux/Unix code is publicly available. Before installing UniPrime, your system must be compliant with the following requirements:

  • * BioPerl modules: UniPrime uses functionality provided in BioPerl modules.
  • * Primer3 is mandatory since UniPrime is based on Primer3.
  • * T-coffee is mandatory if you plan to use multi-alignment option.
  • * PostgreSQL is mandatory since UniPrime store all the sequences, alignments and primers in a database.
  • * Perl 5.005 or later.