PrimerDigital

The FastPCR software is an integrated tools environment that provides comprehensive facilities for designing primers for most PCR applications including standard, long distance, inverse, real-time (LUX, TaqMan, molecular beacon and self-reporting), multiplex, group-specific (common primers for given N target related sequences) and unique (design of specific, unique primers for each sequence); overlap extension PCR (OE-PCR) multi-fragments assembling cloning with or without multiplexing; single primer PCR (design of PCR primers from close located inverted repeat), automatically SSR loci detection and direct PCR primers design, amino acid sequence degenerate PCR and much more.

Polymerase Chain Assembly (PCA), oligos assembly - created to automate the design of oligodeoxynucleotides for the PCR-based construction of long DNA molecules (the desired gene sequence is segmented into short oligo sequences of 20 to 100 nt in length).

The software selects 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-labelled oligonucleotides for probes and molecular beacon. The software utilize combinations of normal and degenerated primers for all tools and for the temperature melting calculation 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.

FastPCR is able to perform repeat search for single sequence or for comparisons of two sequences. 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 analysis and supports the clustering of sequences and consensus sequence generation and sequences similarity and conservancy analysis.



Reference
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.