MFEprimer : Multiple factor evaluation of the specificity of PCR primers. This program is designed to evaluate the specificity of PCR primers based on known multiple factors including sequence similarity, stability at the 3’end of the primer, melting temperature, GC content, and number of binding sites between the primers and DNA templates. It can help the user to select more suitable primers before running either standard or multiplex PCR reactions.
The MRPrimerW server performs complete homology testing, supports batch design of primers for multi-target qPCR experiments, and ranks the resulting primers to return the top-1 best primers to the user.
HYDEN (HighlY DEgeNerate primers) is a program for designing pairs of degenerate primers for a given set of DNA sequences. HYDEN works well for large input sets of genomic sequences (e.g., hundreds of sequences of length 1Kbp).
FastPCR software has integrated tools environment that provide comprehensive facilities for designing primers for most PCR applications including standard, long distance, inverse, real-time, multiplex, unique and group-specific; overlap extension PCR (OE-PCR) multi-fragments assembling cloning; 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, Polymerase Chain Assembly (PCA) or oligos assembly and much more.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.
PrimerFactoryQt is a tool for searching and designing primers. The Primer Search is based on Bowtie, an ultrafast, memory-efficient alignment program for aligning short DNA sequence. You can build your specific oligo database and search it against your query sequence. Consequently you find out, where your available primers will bind. Laboriously quests or new ordering of oligos is not anymore required. In addition you can save the search hits as features in a genbank file format.
Beacon Designer automates the design of real time primers and probes. It is used by molecular biologists worldwide to design successful real time PCR assays. It saves the time and the money involved in failed experiments. Beacon Designer is a flexible solution to your real time primer and probe design needs and pays for itself many times over.