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MFEprimer
Allows users to check primer specificity against genomic DNA and messenger RNA/complementary DNA sequence databases. MFEprimer is a tool that processes in four steps: (1) finds all of the binding-site positions of the 30 -end subsequence of a primer among all possible DNA template sequences; (2) evaluates the binding stability of the entire primer sequence using the nearest-neighbour (NN) model; (3) runs a virtual polymerase chain reaction (PCR) amplification; and (4) filters out the predicted amplicons by size and other parameters.
OligoAnalyzer
Provides useful predictions of oligonucleotide properties under various experimental conditions. The OligoAnalyzer is the central calculator where various kinds of information about an oligonucleotide sequence can be predicted. Selection of the analyze button results in the physical properties of the oligonucleotide, such as a complementary sequence, oligonucleotide length, content of G and C bases, melting temperature, extinction coefficient at 260 nm and molecular weight. OligoAnalyzer was designed to position locked nucleic acids (LNA) modifications within a sequence, so that the desired melting temperature of the duplex sequence is achieved.
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