Then perform a BLAST search of the desired sequence followed by a template structure search which avoids secondary structure while designing primers. To give a summary of using the Beacon Designer software: First, select the desired sequence and the type of probe you wish to design (i.e.
BEACON DESIGNER FREE EDITION SOFTWARE
The software also allows hundreds of SNPs to be loaded for designing probes for multiplex detection By entering a stretch of sequence or the gene’s accession number, the software can directly access and upload the sequence from Entrez.
If we are designing primers and probes for a known sequence, this can be done in just a few clicks. The software can also generate reports in which it mentions important points characteristics such as Tm, delta G, product size, sequence and as well as providing a ranking of the predicted performance of the primers and probes. Specific sequences can be retrieved using accession numbers.
The software opens a separate window for the BLAST results results include the any sequence hits for the primer-pair, amplicon and probe. We can also BLAST the primer and probe sequences through the Beacon Designer software. For example, primers used in SYBR® Green detection can also be used in a TaqMan® assay. The main feature I like about the software is that we can also use previously designed primers with chemistries different from what they were originally designed for. Primers are also screened for there thermodynamic properties, for secondary structures, and cross homologies (i.e. In addition, the software also gives a rating to the primers based upon their priming efficiency. The Tm calculation for the primer pair is also based on the Santa Lucia values. In addition to probe design, Beacon Designer can also design the forward and reverse primers for Molecular Beacons, TaqMan®, FRET and SYBR® Green qPCR experiments. All these feature are also available with FRET probes and primers for SYBR® Green detection. A TaqMan® probe graphical view is also available. The Tm calculation for TaqMan® probes is based upon the SantaLuia values Tm calculations utilize “nearest neighbor” thermodynamic values. Beacon Designer also allows for the design of multiplex assays. Just like Molecular Beacon, TaqMan® probes are free of repeats and do not dimerize. The software can also design and optimize primers and probes for TaqMan® assays. The software also gives us a graphical view of the Beacons probe. The Tm calculation is highly accurate it is calculated by connecting to the mfold server. For example, for Molecular Beacons probes, Beacon Designer has an automatic Tm adjustment in which it automatically selects the optimal length such that the probe does not dimerize or form hairpin structures. The software is fully loaded with a number of features which make it the best option for primer and probe design. This software allows us to design Molecular Beacons probes for standard qPCR and for Nucleic Acid Sequence Based Amplification (NASBA), TaqMan® probes for standard qPCR and as well as locked nucleic acid (LNA)- substituted TaqMan® probes, other FRET (fluorescent resonance energy transfer) probes, and SYBR® Green primers for real-time detection of PCR products. For me, Beacon Designer is the best way to design qPCR primers and probes. Designing primers and probes for quantitative (also known as real-time) PCR (qPCR) is not an easy task because both the primer and probe sequences need to be considered during design.
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