Primer Premier - Primer Design Software

A Comprehensive PCR Primer Design Software

Primer Design for Standard PCR Assays

Primer Premier is the most comprehensive software to design and analyze PCR primers.

Primer Premier's search algorithm finds optimal PCR, multiplex and SNP genotyping primers with the most accurate melting temperature using the nearest neighbor thermodynamic algorithm. Primers are screened for secondary structures, dimers, hairpins, homologies and physical properties before reporting the best ones for your sequence, in ranked order. Equipped with a handy calculator, you can easily manipulate sequences and analyze the results of your primer design.

Load the gene of interest from NCBI, select a search range, sit back and let Primer Premier pick the best possible primers for you.

Primer Design for SNP Genotyping Assays

With Primer Premier, you can load sequences from dbSNP and have the primers designed flanking the SNP selected. Hundreds of unpublished SNPs can also be loaded by specifying them as variation features in standard GenBank/dbSNP files. After specifying the SNPs, primers can be designed to amplify them for detection using a probe-based chemistry.

Multiplex Primer Design

For a multiplex experiment, Primer Premier enables you to design multiplex primers by launching a primer search in batch mode and then checking the cross reactivity of the primers designed. Primer Premier checks for all the possible reactivity and displays the most stable structure formed by each oligo. This functionality reduces false priming and ensures a strong signal strength.

Automatic Homology & Template Structure Avoidance

Primer Premier automatically interprets the BLAST search results and avoids those regions to design primers that have significant cross homologies with the database. These homologous regions are highlighted in the sequence view and are avoided during primer search.

Primer extension may be hindered due to the presence of template structures at extension temperature. To avoid all such regions, where the template may fold upon itself, the program utilizes a proprietary algorithm to check for possible secondary structures within the template at a folding temperature you specify. The regions involved in the formation of a secondary structure are underlined in the sequence view and are avoided while designing primers.

Avoiding homologous regions makes the oligos highly specific and avoiding template structures improves the efficiency of the designed primers.

Manual Primer Search

Primer Premier offers complete control over primer design to the user. Using the manual primer search option, a user can select any position on the template sequence to design a sense or an anti-sense primer. Primer Premier instantly calculates and displays the properties of the new primers. The primers finally selected by a user are then shown in the Sequence View on the Main window.

Edit Template Sequence

The template sequence is editable and can be changed by a user. Bases can be modified using the standard Cut/Copy/Paste functions. Unwanted regions of sequences can be removed by using the Delete button. Users can comment or annotate a sequence and save them for future reference.

Software Link: Primer Premier -  Primer Design Software

Read more

Vector NTI - Sequence analysis software

Vector NTI® Advance software is the most highly integrated, multifunctional desktop sequence analysis application suite available today and provides superior integration, data management, and scalability.

Details

Vector NTI Advance® offers unparalleled, multi-modular, integrated sequence analysis and data management tools. The software contains a comprehensive set of data analysis and management tools, implemented across five application modules.

Detailed Pricing

$4,995 for a commercial license $2,998 for an academic license 

 

Software Link: Vector NTI - Sequence analysis software

Read more

PrimerPlex - PCR Oligo designing Software

Oligo Design for Multiplex PCR & High Throughput SNP Genotyping and Analysis

PrimerPlex is an efficient and sophisticated tool for designing oligos for multiplex assays. Multiplex assays facilitate amplification of multiple targets in a single reaction vessel, reducing both the time and cost of experimentation.

PrimerPlex designs oligos for multiplex PCR assays and for suspension array based systems such as Luminex 100, Luminex 200 and Bio-Plex 200. Such systems offer a versatile platform for multiplexed nucleic acid detection in a 96-well format. PrimerPlex designs specific capture probes for direct hybridization assays and primers for Allele Specific PCR Extension (ASPE) assays.

The multiplex assays are used for gene expression analysis (end point detection using gel electrophoresis) and for high throughput SNP applications such as genotyping, pathogen detection, strain typing, and haplotyping. To ensure specificity, the oligos are designed after avoiding the regions of homologies identified by a BLAST search. PrimerPlex then checks the oligos for cross reactivity and minimizes Tm mismatches to give you the best possible multiplex set. In the process, it analyzes millions of possible multiplex primer sets in a few seconds and presents a list of alternate sets to you as well.

Design Options

Multiplex PCR Primer Design
PrimerPlex designs standard primers for a 30-plex multiplex PCR assay. It uses proprietary algorithms to design optimal primer sets under uniform reaction conditions for up to 30 targets. Primer sets are identified after screening all the primers in a pool and minimizing Tm mismatches. All the multiplex primer sets are analyzed for cross hybridization to ensure specific amplification and high signal strength.


Direct Hybridization Assays

PrimerPlex designs optimal allele specific capture probes for high throughput SNP genotyping assays. The probes are designed such that the mutations are at their centers to maximize differentiation. Each one of the probes designed is checked for its suitability in a multiplex reaction. For amplifying the templates, the program designs SNP flanking primers as well. This functionality makes PrimerPlex the only software product capable of designing probes for 100 individual targets for a multiplex assay.


ASPE Assays

Another approach to detect mutations is to use a solution-based sequence specific enzymatic reaction such as Allele Specific Primer Extension (ASPE) to determine the target genotype. PrimerPlex designs highly specific primers for multiplexed ASPE assays. The ASPE primers are designed such that the mutations lies at their 3' end. PrimerPlex also designs primers to amplify the target sequence for ASPE assays.

Software Link : PrimerPlex - PCR Oligo designing Software

Read more

OLIGO - Primer Analysis Software

OLIGO Primer Analysis Software is the essential tool for designing and analyzing sequencing and PCR primers, synthetic genes, and various kinds of probes including siRNA and molecular beacons.

Based on the most up-to date nearest neighbor thermodynamic data, Oligo's search algorithms find optimal primers for PCR, including TaqMan, highly multiplexed, consensus or degenerate primers. Multiple file batch processing is possible. It is also an invaluable tool for site directed mutagenesis.
For each primer or primer pair, Oligo's various analysis windows show a multitude of useful data, such as DNA and RNA secondary structure, dimer formation, false priming and homology, internal stability, composition and physical properties. With Oligo you can analyze open reading frames down to predicted molecular weight and pKa of proteins, and search for restriction enzyme sites, not only in DNA but also in reverse-translated proteins.

The first version of the software appeared on the market in 1989. It went through several modifications, and the last one, the change from version 6 to 7, was the most comprehensive. Oligo 7 can automatically select multiplex primers, process sequence files in batch modes, automatically design PCR primers to cover multiple DNA regions in just one search and automatically find primer/probe sets for real time PCR or finds nested primers sets. Oligo search protocols (scoring system) may be customized in detail, so you may optimize the results according to your specific needs.

OLIGO's comprehensive functionality matches several other commercial primer design applications put together, so you can design probes for high throughput analysis, multiplex them or focus on one set of primers/probes and optimize it for a new, not yet published application.

Unlike other vendors who license software for a certain period of time, Oligo is supported as long as you use it. We still help customers who use Oligo 5, released in the mid 90's. Our pricing is not hidden.

Software Link : OLIGO - Primer Analysis Software

Read more