FastPCR is an integrated tool for automatic and manual PCR primers or probe design, alignment and any repeat searching.

Provided for non-commercial research and education use only. Not for reproduction or distribution or commercial use.

FastPCR is a free software for Microsoft Windows (WINE compatible for Linux and Mac) and is based on a new approach in the design of PCR primers for standard and long PCRs, inverse PCR,  direct amino acid sequence degenerate PCR, multiplex PCR, in silico PCR, unique PCR primers design and group-specific PCR (common primers for multiple sequences), single primering PCR, automatically SSR loci detection and direct PCR primers design; for sequence alignments, clustering and any kind repeat sequence, MITE elements, LTR-retrotransposons, and SSR loci searching; restriction enzyme analysis.

At this moment the program is for OS Microsoft Windows, for Linux and Mac "Wine" as a compatibility layer for running Windows programs and it is a completely free alternative implementation of the Windows API also for use native Windows DLLs.

FastPCR software can simultaneously work with multiple nucleic acid or protein sequences. The multiplex PCR primers design and "in silico" PCR are also supported. The FastPCR program is an ideal software for personal databases homology searches which are similar to the basic local alignment search tool (BLAST) algorithm (a segment-to-segment alignment principle). The program includes various bioinformatics tools and supports the clustering of sequences. A new repeats search theory was developed and applied to the program, which makes the accomplishment of all DNA repeat types searches fast and powerful. 

The temperature melting calculation for normal and degenerated nucleotide combinations based on the nearest neighbour thermodynamic parameters is included.

FastPCR software has several specific, ready-to-use templates for many PCR and sequencing applications:

•    Standard, inverse, long, real-time PCR analysis - identification of the optimal primers for PCR, hybridization, or sequencing;
•    Multiplex PCR primers design - fast primer design with a cross-dimer test for high sensitive multiplex PCRs;
•    Group-specific PCR primers design - design of universal PCR primers for all sequences (there is no need for a multiple DNA alignment);
•    Unique PCR primers design - design of specific PCR primers for each sequence;
•    Degenerate PCR - primers design directly on an amino acid sequence;
•    Bisulphite modified genome sequence - design of specific PCR primers for in silico bisulphite conversion for both strands - only cytosines not followed by guanidine (CpG methylation) will be replaced by thymines;
•    Automatically SSR loci detection and direct PCR primers design;
•    In silico PCR and probe search - prediction of probable PCR products and search of potential mismatching location of the specified primer(s)/probe (s);
•    TaqMan and Molecular Beacons probes and other probes design;
•    LUX (self-quenched) primers design for quantitative PCR;
•    Self-Reporting DNA/DNA primers for qPCR analysis;
•    Primer Secondary structure analysis - self-dimer and cross-dimer primer analyses; primer alignment and melting temperature calculation;
•    False priming analysis -  (the secondary (non-specific) binding test) primers checking for multiple annealing sites using sequence alignment algorithms;
•    Primer quality report - a unique way for PCR efficiency determination;
•    Comprehensive primer report - comprehensive pairs and individual primers analysis (Tm and dimer detection);
•    Multitask PCR primers and probes design - simultaneously design primers or probe with different parameters and for different targets within the same sequence; interaction different tasks.