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.
Primerize is a Web Server for primer designs of DNA sequence PCR assembly. Primerize is optimized to reduce primer boundaries mispriming, is designed for fixed sequences of RNA problems, and passed wide and stringent tests.
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.
PhiSiGns is a web-based and standalone application that provides a simple and convenient tool to identify signature genes and design primers for PCR amplification of related genes from environmental samples. PhiSiGns is intended for phage biologists who want to find common conserved genes in phages for evolution or phylogeny based studies, or who are interested in designing primers that can be used to explore environmental phage diversity.
PROBER is an oligonucleotide primer design software application that can generate highly specific probes for use in fluorescence in-situ hybridization (FISH) and other in-situ labeling methods by densely tiling relatively small genomic intervals. Generating Tiling Oligonucleotide Probes (TOPs) requires software capable of masking repetitive genomic sequences and saturating unique contiguous blocks with small (100-2000bp), DNA probes that will generate a single, strong fluorescent signal for regions as small as a single gene.
ProbeSpec is a utility for mapping the specificity of all candidate probes for a given sequence (e.g. transcript) against a background containing a large set of sequences (e.g. a transcriptome). Probe specificity is determined by the subsequence in the background that is most similar to its target, the specificity being set as the number of mismatches between the probe and the closest non-specific background sequence.
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).