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Beacon Designerâ„¢ automates the design of real time primers and probes
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Beacon Designer™

Upgrades

Beacon Designer™ 8.13 Released

Latest changes to the genomic databases at the NCBI-BLAST along with fixes to reported problems are accommodated.

Beacon Designer™ 8.12 Released

The latest changes at the NCBI BLAST, including latest genomic databases and fixes to reported problems are also accommodated.

The upgrade offers compatibility with Mavericks, Mac OS X 10.9.

Beacon Designer™ 8.10 Released

The upgrade accommodates the latest genomic databases available at the NCBI BLAST server and fixes to reported problems. The version is now compatible with Windows 8.

Beacon Designer™ 8.02 Released

The latest changes at the NCBI BLAST, including latest genomic databases and fixes to reported problems are also accommodated.

Beacon Designer™ 8.01 Released

The latest changes at the NCBI BLAST, including latest genomic databases and fixes to reported problems are also accommodated.

The upgrade offers compatibility with Windows 64bit OS.

Beacon Designer™ 8.00 Released

Beacon Designer now enables primer design across exon-exon and exon-intron junctions to selectively amplify cDNA from a mixture. The primers are designed such that at least one of the primers from the pair spans one of the junctions selected by the user.

Primer and probe design parameters can now be saved as a template for repeated use. The saved template of parameters can be called for future searches. It would not only make the design easy and convenient for large number of sequences but also facilitate in saving time for your research.

Beacon Designer™ 7.92 Released

The upgrade offers compatibility with Lion, Mac OS X 10.7.

The latest changes at the NCBI BLAST, including latest genomic databases and fixes to reported problems are also accommodated.

Beacon Designer™ 7.91 Released

The upgrade accommodates the changes at the NCBI BLAST server, the latest databases available for BLAST and fixes to reported problems.

Beacon Designer™ 7.90 Released

Beacon Designer now supports HRMA primer design for all mutation types including deletions, insertions, substitutions and mixed mutations, along with SNPs. The program reports amplicons and their melting temperatures for both the wild as well as the mutant alleles.

Multiplex assays are now supported for five sequences fully utilizing all the five real time PCR cycler channels. Additionally, the oligos designed for the five sequences are checked by the program for cross hybridization and their multiplexing ability.

Assays designed can now be sorted on either primer or probe rating. If the search results are sorted on the basis of primer rating, the assay with the best sense/anti-sense rating is displayed. Similarly, if the search results are sorted taking into consideration the probe rating, the assay with best rated probe is displayed.

Projects created in Beacon Designer can be exported in a zipped format for easy collaboration.

Beacon Designer™ 7.80 Released

Beacon Designer™ now enables better control over TaqMan design. Parameters such as the GC%, Avoiding G base at the 5' end of the probe, avoiding more Gs than Cs in the probe, avoiding T base at the 3' end of the primer are settable to ensure an efficient design.

Designing multiplex assays is a lot easier. The design parameters have now been optimized, based on empirical and theoretical evidence, to improve the success in a multiplex reaction.

Beacon Designer™ now offers improved SNP assay evaluation. Given a wild or mutant TaqMan® probe, the program first checks if it is designed to detect the SNP selected and proceeds to design compatible SNP flanking primers. Similarly, given a forward or reverse SNP flanking primer, a compatible primer and TaqMan® probe are designed. For SYBR® Green assays, the program checks if either of the two primers span the SNP to be detected.

The upgrade accommodates the most recent changes at the BLAST server, including support for the latest genomic databases. Users can now choose the regions of homologies to avoid by providing setting the percent identity and e-value.

Beacon Designer™ 7.70 Released

Beacon Designer can now design primers for High Resolution Melting Analysis (HRMA). The primers are designed flanking a SNP of interest to generate the shortest possible amplicons with detectable melting temperature variation. The HRMA primers are designed avoiding template secondary structures, assuring efficient primer extension. The primers designed can be BLAST searched against nucleotide databases at NCBI to check their specificity. Pre-designed or published primers can also be analyzed.

Beacon Designer™ 7.61 Released

The upgrade offers compatibility with Snow Leopard, Mac OS X 10.6. It also accommodates the changes at the NCBI BLAST server and fixes to reported problems.

Beacon Designer™ 7.60 Released

The upgrade accommodates the changes at the NCBI BLAST server, the latest databases available for BLAST and fixes to reported problems.

Beacon Designer™ 7.51 Released

The upgrade includes fixes to reported problems.

Beacon Designer™ 7.50 Released

Given a primer sequence, Beacon Designer can now design a compatible probe and primer, enabling the use of pre-designed, pre-tested oligos.

Amongst a host of other improvements, Beacon Designer now boasts of a new improved Scorpion design module. The thermodynamic values are so chosen to give you improved scorpion design results. For the TaqMan® and SYBR® Green modules, the set of design parameters are now so chosen that they greatly improve the success of an assay.

The new export functionality enables you to export the oligos designed along with the template from the "sequences view" pane making it easier to manipulate the design to better meet your experimental needs.

Support for all the genomic databases available at NCBI is also updated.

Beacon Designer™ 7.21 Released

The upgrade includes fixes to reported problems.

Beacon Designer™ 7.20 Released

Beacon Designer™ now provides suitable control primers and probes for MethyLight assays by designing them for unmethylated and untreated DNA sequences. Amongst a host of other improvements, Beacon Designer™ now graphically displays the regions of homology and secondary structures and where the designed oligos are located with respect to these. To adjust the similarity threshold according to the type of technology or your own stringency criterion, Beacon Designer™ now enables you to set either the e value, the identity or both. Based upon the values chosen, the hits reported will be avoided during oligo design.

Support for all the genomic databases available at NCBI is also included.

Beacon Designer™ 7.03 Released

The upgrade accomodates the latest changes for folding templates at the mfold server.

Beacon Designer™ 7.02 Released

The upgrade includes fixes to reported problems.

Beacon Designer™ 7.01 Released

NCBI recently redesigned the BLAST pages, changing the default interface. The support for old pages was removed on June 11, 2007 and a few more databases were added. Beacon Designer™ is released to accomodate these changes. It also includes fixes to problems reported.

Beacon Designer™ 7.00 Released

Scorpions® Assays- Using Beacon Designer 7.00, you can now design scorpions® primers and probes. Scorpions® represent the most recent development in real-time PCR chemistry since this technology is not dependent on enzymatic cleavage of the probe. The stem-loop format is a common approach for specific detection of PCR products in which the probe element and primer element are physically coupled during the reaction. It is ideally suited for many applications that require rapid detection such as viral load testing and RNA profiling.

With Beacon Designer™ you can not only design scorpions® primers and probes with a click of a button but also use pre-designed/published primer sets and design compatible oligos. The scorpions® primers are screened for all possible secondary structures and scorpions® probes are checked for alternate structures.

Batch BLAST- You can now BLAST search multiple sequences.

All databases available at NCBI are now accessible through the program.

Beacon Designer™ 6.01 Released

The upgrade accommodates the changes at the NCBI BLAST server.

Beacon Designer™ 6.00 Patch Released

Includes fixes to the reported problems.

Beacon Designer™ 6.00 Released

MethyLight TaqMan® Assays- With Beacon Designer 6.00, you can design TaqMan® oligos for MethyLight assays. MethyLight assay is widely used for measuring DNA methylation levels and has been proved to be an efficient and highly sensitive technology. Beacon Designer™ designs quantitative Methylight assays which utilizes fluorescence-based real-time PCR (TaqMan®) technology for detecting methylated DNA.

A short note on DNA Methylation

Improved Sequence View- Included, in addition, is the ability to copy and paste sequences from the Sequence View. Beacon Designer™ displays the primers and probes on the sequence in the right pane. You can now copy and paste the primer, probe or entire sequence at the right click of the mouse.

All databases available at NCBI are now accessible through the program.

Beacon Designer™ 5.11 Released

Includes support for the latest genomic databases available at NCBI.

Beacon Designer™ 5.10 Released

Multiplex TaqMan® Assays- Beacon Designer™ 5.10 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 pre-designed 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.

The latest genomic databases available at NCBI are also supported.

Beacon Designer™ 5.01 Released

Beacon Designer™ connects to the NCBI server to BLAST search your sequences and automatically interpret the results to design specific primers. Version 5.01 includes support for the latest genomic databases available at NCBI.

New in Version 5.00 of Beacon Designer™

We are pleased to release version 5.00 of Beacon Designer™ which includes:

LNA™ Probe Design-In addition to standard TaqMan® probes, the increasingly popular LNA™ or Locked Nucleic Acid™ substituted TaqMan® probes can now be designed. Incorporation of the LNA™ bases significantly increases thermal stability, making shorter probes possible for standard reaction conditions. Furthermore, it improves hybridization specificity and enhances gene quantification and alleleic discrimination accuracy.

NASBA Beacon Design- Beacon Designer™ also helps you design molecular beacons for both standard as well as NASBA assays for single template, multiplex or alleleic discrimination. NASBA, short for Nucleic Acid Sequence Based Amplification, is gaining acceptance as a single-step isothermal RNA-specific amplification process. It amplifies mRNA in double-stranded DNA background without temperature cycling.

Settable Parameters for Mfold- You can now alter the temperature, Mg++ ion and monovalent ion (Na+) concentration in Beacon Designer™ for folding templates at the Mfold server.

Genomic Databases Support- Includes support for the latest databases available at NCBI for BLAST search.

Beacon Designer™ 4.02 Released

Beacon Designer™ connects to the NCBI server to BLAST search your sequences and automatically interpret the results to design specific primers.

NCBI's BLAST server underwent a few changes over the last few days.  One of the most significant being the availability of a new version of the BLAST formatter. To accommodate these changes we have released an upgrade. With this upgrade you will now be able to BLAST search your sequences seamlessly.

New in Beacon Designer™ 4.01

Beacon Designer™ connects to the highly accurate Mfold server to fold templates and calculate the beacon Tm. The Mfold server underwent a few changes over the last couple of days. To accommodate these changes we have released an upgrade. With this upgrade you will now be able to  fold templates and design molecular beacons.

New in Beacon Designer™ 4.00

  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 and fixes to reported problems.

New in Beacon Designer™ 3.00 and Later

The Human, Rat and Mouse genome databases on the BLAST server were reorganized by NCBI. The databases were further classified into genome (all assemblies) and genome (reference only). To accommodate these changes we released the upgrade.

Ability to BLAST search oligos and templates against all the nucleotide redundant databases available at NCBI to verify the specificity of design.

  1. Facility to BLAST search probes for specificity of design.
  2. Includes support for the latest genomic databases available at NCBI.
  3. Includes the changes at the Mfold server.
  4. Simplified web based activation scheme (Beacon Designer™ customers, please click here for details.
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