Oligo Analyzer

The Oligo Analyzer software is an easy-to-use Windows tool for analyzing DNA oligonucleotides such as PCR primers, developed by Teemu Kuulasmaa at the University of Kuopio in Finland. The program was written in Delphi and runs as a classic desktop application, so the calculations do not depend on any online service. The software allows users to quickly analyze the properties of their oligonucleotides and make informed decisions about their design and use.

Features:

• Analyze PCR primers: Oligo Analyzer determines the main properties of a primer, such as its length, melting temperature (Tm), GC content (GC%) and molecular weight. All you have to do is type or paste the primer sequence and let the program calculate the results.

Oligo Analyzer quickly calculates primer properties such as Tm, GC content, loops and dimers, helping to check primers and primer pairs before PCR.

• Create, edit and save primer projects: Oligo Analyzer has a simple project window that allows users to add as many primers as they need, give each of them a name and edit their sequences. The software also allows users to save projects and analysis results to files and open them again later.

• Calculate the Tm of an oligonucleotide: Oligo Analyzer calculates the melting temperature (Tm) of a primer based on its sequence. This value is essential for choosing a suitable annealing temperature and for matching the forward and reverse primers of a PCR reaction. The results are shown in the main window next to the sequence, so several primers can be compared quickly.

• Detect primer loops: the program checks whether a primer can fold back on itself and form loops (hairpins). Such structures can reduce the efficiency of the primer, so this check helps to reject problematic sequences before they are ordered.

• Detect primer dimers: Oligo Analyzer checks whether a primer can bind to itself or to another primer and form primer dimers. Primer dimers are a common cause of weak or unwanted PCR products, so the check saves time in the laboratory.

• Check primer pair compatibility: the Pair with function places two primers together, so users can compare their properties and see whether they work well as a forward and reverse pair in the same reaction.

• Check primers for multiplex PCR: users can define as many primers as they want and compare them all together with the Multiplex and Multiplex all functions. This helps to select sets of primers that are suitable for multiplex PCR applications.

• Keep notes: a separate Notes tab lets users write comments about the primers and keep them together with the project, while the Options tab sits next to the primer list in the same window.

• Format, find and print results: the results area supports bold, italic and underlined text, the Find command searches the results, and the analysis can be printed directly from the File menu for documentation.

• Licence and status: Oligo Analyzer is freeware for academic purposes, and a free registration removed the reminder window of the program. It is no longer developed, and its original website at the University of Kuopio is no longer online. The same author also released Oligo Explorer, a companion tool that searches a DNA sequence for suitable primers and primer pairs.