Beacon designer

Beacon designer

Infobox Software
name = Beacon Designer



caption =
developer = Premier Biosoft
latest release version = 5.0
latest release date = 3 June 2008
latest preview version =
latest preview date =
operating system = Windows, Macintosh
platform =
genre = Bioinformatics
license = commercial
website = http://www.premierbiosoft.com
Beacon Designer is a software that runs on Windows and Macintosh operating systems and designs primers and probes for real time PCR (polymerase chain reaction). The software is currently in its 7th version of development and supports following real time PCR chemistries for primer and probe design

1. TaqMan
2. Molecular beacon
3. SYBR Green
4. Scorpions
5. FRET
6. Locked nucleic acid
7. NASBA

The program has an in-built support for homology avoidance using the standard web BLAST service or the set-up of a desktop BLAST feature for identification of regions that are significantly cross homologous with the target gene sequence. The software is supposed to design critical primers and probes for complex differential gene expression and allele discrimination assays. [http://www.biorad.com/LifeScience/pdf/Bulletin_2448.pdf]

Avoidance of the cross homology renders specificity to the primers in question and they are highly targeted and only amplify the intend sequence and no other targets. [http://ajpgi.physiology.org/cgi/content/full/290/5/G1016Tjalling Bosse, Herbert M. van Wering, Marieke Gielen, Lauren N. Dowling, John J. Fialkovich, Christina M. Piaseckyj, Frank J. Gonzalez, Taro E. Akiyama, Robert K. Montgomery, Richard J. Grand and Stephen D. Krasinski]
Beacon Designer has been used in workshops and conferences related to real time PCR study as a reference software [http://www.k-state.edu/gene-exp/rtpcr08.pdf]

The software also supports the design of multiplex PCR reactions with the selection of a reference gene. [http://jcm.asm.org/cgi/reprint/43/9/4585.pdf]

The author company, Premier Biosoft has also launched a simple version for evaluation of oligos for real time PCR primers and probes (support limited to TaqMan and SYBR Green primers) by the name Beacon designer free version. [ [http://www.protocol-online.org/prot/Research_Tools/Online_Tools/Oligo_Design/Real-Time_PCR_Primer/ Oligo Design/Real-Time PCR Primer ] ]


References


External Links

* [http://www.premierbiosoft.com/molecular_beacons/index.html Beacon Designer Homepage]

* [http://www.premierbiosoft.com/qpcr/index.html Beacon Designer Free Edition]


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