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Streamlining PCR Assay Design with the IDT PrimerQuest® Design Tool

Published: Wednesday, July 03, 2013
Last Updated: Wednesday, July 03, 2013
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Free online tool enhances PCR primer and probe design with new upgrades.

Integrated DNA Technologies (IDT) has launched a new and enhanced version of the open access PrimerQuest® online tool, for efficient PCR primer and probe design.

Selection parameters have been optimized with built-in presets for a diverse range of applications, to produce the very best primers and probes.

Compatibility with multiple sequence entry formats has been expanded and combined with a more intuitive user interface. These features streamline the process of setting up a PCR or qPCR experiment for both new and existing users.

The PrimerQuest design tool is ideal for a variety of sequencing and endpoint PCR applications, with updated default parameter pre-sets (GC clamp, Poly X and Pair max difference Tm), and overall improved parameter criteria for primer/probe size, Tm and GC%.

As the tool of choice for custom design applications, the PrimerQuest design tool, which is based on Primer 3, delivers designs derived from user-specified information such as reaction conditions (e.g., MgCl2 and dNTP concentrations).

Users can designate target locations, exon junctions or existing primer and probe locations to effortlessly obtain designs for specific experimental requirements.

In addition, the PrimerQuest tool can now be used for studies on any scale, supporting larger experimental designs via the batch load setting.

This feature can be used to analyze up to 50 sequences at a time, and primers can now be ordered in plate format for streamlining high-throughput PCR studies.

Integration of the PrimerQuest online tool with other software programs has been improved for maximum compatibility. Sequences can now be uploaded in Excel format, or can even be manually entered and manipulated.

Downloading in FASTA format using GenBank Accession ID allows efficient transfer and analysis, while a link out enables BLAST search of primers to quickly ensure specificity.

These new features are now more easily accessible with the updated user interface, incorporating a modernized look and easy one-click solutions, for intuitive control and selection of parameters.

With the updated PrimerQuest software, users are guaranteed maximum performance in PCR and qPCR experiments.


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