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Oligonucleotide Analysis

Primer 3: WWW primer tool
Powerful PCR primer design program permitting one considerable control over the nature of the primers, including size of product desired, primer size and Tm range, and presence/absence of a 3’-GC clamp.

PCR Suite
Based on Primer 3, but has more stringent settings (to allow more working primersets) and a smaller range of parameters. The suite consists of four programs: Overlapping_Primers is for creating multiple overlapping PCR products in one sequence. Genomic_Primers designs primers around exons in genomic sequence. All you need is a GenBank file containing your gene. SNP_Primers designs primers around every SNP in a GenBank file. cDNA_Primers designs primers around open reading frames.

GeneFisher: Interactive Primer Design
Allows good control over primer design.

Oligonucleotide primer selection
Search for unique primers within a sequence

Reverse translation tool
This Java applet translates proteins into nucleotide sequences with adapted codon usage. This allows optimizing a sequence for expression in specific organisms.

Oligonucleotide Calculator
Java Script Oligo calculator (Netscape V2 or better).