Monday, December 27, 2004

Beacon Designer 4.00 Released

If you're into qRT-PCR, Premierbiosoft's Beacon Designer (a primer-design software) version 4 just got released. Lots of primer design programs are available on the web, but this one is specialized in qRT-PCR (SYBR green primers, dual-labeled taqman primers and probes, molecular beacons).

It analyze secondary structures of the template / probes, it avoid regions of homology by doing BLAST analysis automatically... it's really a wonderful piece of software (I used it extensively in the past). Primers it design just work, everytime. Many new features we're added in version 4. Unfortunaly, it got a big problem... the price is very high! 2000$ USD for a license... you have to design quite a few primers to justify buying this (excellent) software. Too bad they don't have a toned down, cheaper version... Note that they do have a limited demo available for download. New features in version 4.00 include :

1. SYBR Green primer design mode: design primers for SYBR Green assays. If you choose, these primers can be exported to the TaqMan®, FRET or molecular beacon design modes to design compatible dual labeled probes.

2. FRET probe design mode: design optimal FRET probes and compatible primers using this module. A list of alternate primer and probes is made available for you to choose the most appropriate set for your needs. You will also be able to evaluate pre-designed primers and probes.

3. Ability to generate an attractive report of the designed assays: You will now be able to create an attractively formatted report for the assays you designed. It should be helpful in record keeping and for sharing information with colleagues. The report helps visualize the positions of the primers and probes on the sequence, includes a list of the alternate primers and probes, displays primers, probe, amplicon and sequence properties and the design parameters used.

4. Includes support for the latest databases available at NCBI for BLAST search.

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