PrimerDigital

FastPCR is an integrated tool for PCR primers or probe design, in silico PCR, oligonucleotide assembly and analyses, alignment and repeat searching

• The FastPCR software is an integrated tools environment that provides comprehensive and professional facilities for designing any kind of PCR primers for standard, long distance, inverse, real-time PCR (LUX and self-reporting), multiplex PCR, group-specific (universal primers for phylogenetically related DNA sequences) and unique (specific primers for each from phylogenetically related DNA sequences), overlap extension PCR (OE-PCR) multi-fragments assembling cloning; single primer PCR (design of PCR primers from close located inverted repeat), automatically detecting SSR loci and direct PCR primer design, amino acid sequence degenerate PCR, Polymerase Chain Assembly (PCA) and much more.
• The “in silico” (virtual) PCR primers or probe searching or in silico PCR against whole genome(s) or a list of chromosome - prediction of probable PCR products and search of potential mismatching location of the specified primers or probes. Searching multiple targets simultaneously within a certain range. The “in silico” oligonucleotide search is helpful for discovering target binding sites with the temperature melting and PCR annealing temperature calculation.
• A long oligonucleotide can be designed for microarray analyses and dual-labeled oligonucleotides for probes such as molecular beacons.
• Comprehensive primer test, the melting temperature calculation for standard and degenerate oligonucleotides, primer's PCR efficiency and linguistic complexity, dilution and resuspension calculator.
• Primers (probes) are analyzed for all primer secondary structures including the alternative hydrogen bonding to Watson-Crick base pairing such as G/C-quadruplexes or wobble base pairs (like G-G, G-T, G-A), hairpins, self-dimers and cross-dimers in primer pairs. The software utilizes combinations of normal and degenerated primers for all tools and for the melting temperature calculation are based on the nearest neighbour thermodynamic parameters.
• FastPCR has the capacity to handle long sequences and sets of nucleic acid or protein sequences and it allowed the individual task and parameters for each given sequences and joining several different tasks for single run. It also allows sequence editing and databases analysis.
• Efficient and complete detection of various types of repeats developed and applied to the program with a visualisation.
• The program includes various bioinformatics tools for analysis of sequences with GC or AT skew, CG content and purine-pyrimidine skew, the linguistic sequence complexity; generation random DNA sequence, restriction I-II-III types enzymes and homing endonucleases analysis, find or create restriction enzyme recognition sites for coding sequences and supports the clustering of sequences and consensus sequence generation and sequences similarity and conservancy analysis.