Beacon Designer Changelog

What's new in Beacon Designer 8.13 Build 813001

Jun 18, 2014
  • Latest changes to the genomic databases at the NCBI-BLAST along with fixes to reported problems are accommodated.

New in Beacon Designer 8.12 (Jun 18, 2014)

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

New in Beacon Designer 8.10 Build 810002 (Jun 22, 2013)

  • 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.

New in Beacon Designer 8.02 (Jun 22, 2013)

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

New in Beacon Designer 8.01 (Jun 22, 2013)

  • 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.

New in Beacon Designer 8.80 (Jun 22, 2013)

  • 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.

New in Beacon Designer 7.92 (Jun 22, 2013)

  • 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.

New in Beacon Designer 7.91 (Jun 22, 2013)

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

New in Beacon Designer 7.90 (Jun 22, 2013)

  • 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.

New in Beacon Designer 7.80 (Jun 22, 2013)

  • 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.

New in Beacon Designer 7.70 (Jun 22, 2013)

  • 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.