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 facilities for designing any kind of PCR primers for standard, long distance, inverse, real-time PCR (LUX and self-reporting), multiplex PCR, group-specific PCR (common primers for given N target sequences), unique PCR (design of specific (unique) PCR primers for each sequence); 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 consists of a data editor; build-in commands for probe/primers design and build automation tools. The software selects the best primers with the widest range of melting temperatures that allows designing qualified primers for all PCR tasks.
The “in silico” (virtual) PCR primers or probe searching, comprehensive pairs and individual primers analysis tests are included. The “in silico” oligonucleotide search is helpful for discovering target binding sites with the temperature melting calculation.
A long oligonucleotide can be designed for microarray analyses and dual-labeled oligonucleotides for probes such as molecular beacons. 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.

Reference
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.
Kalendar R, Lee D, Schulman AH 2009. FastPCR Software for PCR Primer and Probe Design and Repeat Search. Genes, Genomes and Genomics, 3(1): 1-14.