Degenerate primer design bioinformatics tools

Degenerate primer design software tools | qPCR analysis

Degenerate primers are a mixture of similar, but not identical primers that are used to amplify a same gene from different organisms. Alternatively, degenerate primers are used when primer design is based on protein sequence, as several different codons can code for one amino acid. Degenerate primers design tools for qPCR are able to calculate and generate primer sequences using specific algorithms.

Primer Premier

Scans automatically target DNA sequences and designs primers in regions of low degeneracy that are free of secondary structures (hairpins, dimers and false priming sites). Primer Premier searches for optimal polymerase chain reaction (PCR), multiplex and single nucleotide polymorphism (SNP) genotyping primers via a nearest neighbor algorithm. It supports multiplex assays and can automatically describe BLAST search results.

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