Beacon Designer 5.10 review
DownloadBeacon Designer helps design successful SYBR® Green, TaqMan®, LNA™ spiked TaqMan®, molecular beacon for both standard and NASBA assays and FRET assays by interpreting BLAST results for specificity and locating oligos avoiding template structures.
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Beacon Designer helps design successful SYBR® Green, TaqMan®, LNA™ spiked TaqMan®, molecular beacon for both standard and NASBA assays and FRET assays by interpreting BLAST results for specificity and locating oligos avoiding template structures.
Here are some key features of "Beacon Designer":
SYBR® Green Primer Design- Highly specific primers are designed by avoiding significant homologies found by automatically interpreting BLAST search results. Primer efficiency is enhanced by avoiding template secondary structures identified by connecting to the Mfold server.
Dual Labelled Probe Design: Dual-labeled fluorescent TaqMan®, molecular beacon or FRET probes can be designed with the help of Beacon Designer. For these assays, you can design new primers and probes or find probes compatible with previously designed SYBR® Green assays and save on synthesis costs.
TaqMan® probes and Molecular Beacon Multiplex experiments- Multiplex assays are designed by avoiding homologies with all primers and probes in the pool. This prevents competition in multiplex real time PCR reactions and assures high signal strength.
Allelic Discrimination- Design both wild and mutant probes for SNP genotyping assays.
LNA™ Probe Design- In addition to standard TaqMan® probes, Beacon Designer also designs the increasingly popular LNA™ or Locked Nucleic Acid™ substituted TaqMan® probes to improve real-time PCR assay success.
NASBA Assays- Beacon Designer designs molecular beacon probes for NASBA assays for single template, multiplex or alleleic discrimination.
BLAST Search- Both primers and templates/amplicons can be BLAST searched against genomic databases available at NCBI or against local custom databases. This function helps verify the primer specificity.
Avoid Template Structures- Automatically avoid secondary structures in the template identified by connecting to the Mfold server while designing primers.
Generate Report- Generate an attractively formatted report for the assays designed. It should be helpful in record keeping and for sharing information with colleagues.
Limitations:
The demo version is a fully functional product, except that it allows you to work only with the sequences supplied with the product.
What's New:
now includes comprehensive support for multiplexing.
The program is now equipped with innovative proprietary algorithms to design the most optimal primer-probe sets for multiplex reactions.
The sets are chosen by minimizing Tm mismatches and cross dimerization and are made available in a sortable list.
For multiplex assays, you can even design oligos for additional sequences that are compatible with the predesigned sets for certain sequences. This feature may be most useful for incorporating a well-proven reference or housekeeping gene in a reaction.
It is also possible to check the suitability of pre-designed primer sets for a multiplex reaction.
Requirements:
iMac Power PC G5 1.6 GHz
256 MB of available RAM
400 MB of available hard disk.
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