Beacon Designer software introduction
Beacon Designer can help you design biological experiment analysis plans, allowing you to obtain a better data analysis platform when making some biological models. This software can be used in conjunction with some chemical formulas. You can load some chemical formulas into the software for annotation when analyzing biological data, and you can also convert the analyzed biological data into gene models for viewing. It is also very good at using PCR primer design. It uses a variety of biological reactions and DNA primer analysis techniques, and lets the software help you complete the analysis of later experimental data and report production!
Beacon Designer software features
1. FRET probe
FRET Probes - Design optimal FRET probes free of dimers, repeats and running sequences to ensure signal fidelity.
Multiple FRET probes and primers - Check that the FRET probe cross-hybridizes to all primers to prevent multiple reaction competition.
Evaluate pre-designed FRET probes and primers - allows you to design optimal FRET probes using SYBR® green primers.
Algorithm - Calculate Tm thermodynamic values using highly accurate SantaLucia nearest neighbors.
图形视图-显示探针二级结构的图形视图。
2. Scorpions® primer design
Scorpions® Primer - Optimally designed standard primers, Scorpions® Primers, Probes and Scorpions®, free of dimers, repeats and run sequences to ensure signal fidelity.
Allele Identification - Scorpions® are designed to detect wild and mutant alleles.
Multiplex Scorpions® and Primers - Check Scorpions® for cross-homology and all primers to prevent multiple reaction competition.
Pre-designed Scorpions® Primers - Allows the use of pre-designed probes/primers to design optimal primers/probes and scorpions.
Tm计算-高精度发夹Tm计算。
Graphical View - Graphical view of the Scorpions® Primer showing the design.
3. Primer design
Design primers - Design primer pairs optimized for SYBR®Green/Beacon/TaqMan®/FRET/Scorpions®/HRMA applications.
Algorithm - Calculates primer Tm using highly accurate SantaLucia nearest neighbor thermodynamic values.
Primer Rank – Rank primers based on primer efficiency. Comprehensive standard primers are screened based on their thermodynamic properties and secondary structure.
Automated Primer Multiplexing - Checks homology in primer pools to reduce primer dimers.
Pre-designed primers - Allows the use of previously designed primers for Beacon, TaqMan®, FRET, HRMA and SYBR® Green analyses.
Avoid secondary structures in templates - Automatically avoid secondary structures in templates when designing primers.
Avoid cross-homologies - Ensure signal fidelity by automatically avoiding homologies discovered using BLAST.
Primer Amplicon and Probe BLAST Search - BLAST search primers, amplicons and probes to verify the specificity of your design.
SNP Amplification Primers for Beacon, TaqMan®, FRET and HRMA chemistries are designed to amplify SNPs. SYBR® Green primers should be designed so that the allele-discriminating nucleotide is located at the 3' terminal base of one of the primers. HRMA analysis can be designed to amplify SNPs and all other types of mutations, such as substitutions, deletions, insertions, etc.
Consistent conditions - All primers in a run are optimized for the same PCR reaction conditions.
4. Explosion search
Selective cDNA amplification - Avoid gDNA contamination by designing primers that span exon/exon and exon-intron boundaries. Exonic regions were identified by interpreting GenBank header annotations. They can also be specified manually.
BLAST Search - BLAST searches the entire sequence and designs primers and amplicons to demonstrate specificity.
BLAST Database - Use standalone BLAST to search local custom databases, or connect directly to NCBI servers for public databases.
Repetitive and low-complexity regions - Optimize BLAST search parameters to detect repetitive and low-complexity regions when searching genome databases available at NCBI.
BLAST Results View - Provides a results view for searching BLAST on sequences, primer pairs, amplicons, and probes.
5. Database and data management
Design Modes - Beacon and TaqMan® designs are in separate modules: allows mode switching at runtime.
Projects - Create multiple projects. Data for multiple experiments can be easily managed by creating a separate project for each experiment.
Application Database - Maintains a local database for sequence information and search results.
Beacon Designer software features
Provides analysis functions for a variety of primers.
It can complete more genetic analysis on biological sequences.
Supports the use of genetic mutation sequences to be loaded into experiments for analysis.
Supports the use of DNA primer analysis to view changes in experimental data.
Supports the expansion of data changes and external molecules in bioanalysis.
Supports the establishment of sequence analysis of multiple genes.
Research data that can help you test amino acids.
It allows you to obtain better indicators when analyzing biological sequences.
Supports generating graphical display of tested single nucleotides.
Supports the production of biological chains and genetic models.
Beacon Designer update log
1. Modify user-submitted bugs
2.Add new features
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