|Original author(s)||Ruslan Kalendar|
|Operating system||Windows, Linux (Wine)|
The FastPCR software is an integrated tools environment that provides comprehensive facilities for designing any kind of PCR primers for standard, long-distance, inverse, quantitative PCR (LUX and self-reporting), multiplex PCR, Xtreme Chain Reaction (XCR), group-specific PCR (common primers for phylogenetically related DNA sequences) and unique PCR (unique 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) or oligos assembly and much more.
- The software utilizes combinations of normal and degenerate primers for all tools and for the melting temperature calculation are based on the nearest neighbor thermodynamic parameters.
- The in silico 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. 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 PCR efficiency, primer's linguistic complexity, and dilution and resuspension calculator.
- Primers (probes) are analyzed for all primer secondary structures including G-quadruplexes detection (Hoogsteen base pairs), hairpins, self-dimers and cross-dimers in primer pairs.
- 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.
- Kalendar R, Khassenov B, Ramankulov Y, Samuilova O, Ivanov KI 2017. FastPCR: an in silico tool for fast primer and probe design and advanced sequence analysis. Genomics, 109: 312-319.
- Kalendar R, Muterko A, Shamekova M, Zhambakin K 2017. In silico PCR tools a fast primer, probe and advanced searching. Methods in Molecular Biology (Clifton, N.J.), 1620: 1-31.
- Kalendar R, Tselykh TV, Khassenov B, Ramanculov EM 2017. Introduction on using the FastPCR software and the related Java web tools for PCR, in silico PCR, and oligonucleotide assembly and analysis. Methods in Molecular Biology (Clifton, N.J.), 1620: 33-64.
- Kalendar R, Lee D, Schulman AH 2014. FastPCR software for PCR, in silico PCR, and oligonucleotide assembly and analysis. Methods in Molecular Biology (Clifton, N.J.), 1116: 271-302.
- Kalendar R, Lee D, Schulman AH 2011. Java web tools for PCR, in silico PCR, and oligonucleotide assembly and analysis. Genomics, 98(2): 137-144.