OligoCalc

OligoCalc is a web-based tool designed to assist researchers in the design and analysis of oligonucleotide sequences. It provides a suite of functionalities for calculating various properties of DNA and RNA sequences, making it a valuable resource for molecular biology, genetics, and related fields.

The primary functions of OligoCalc include calculating the melting temperature (Tm) of oligonucleotide duplexes, which is crucial for optimizing PCR and hybridization experiments. It can also determine the molecular weight, extinction coefficient, and base composition of a given sequence. The tool supports the calculation of Tm for different salt concentrations, which can significantly influence hybridization stability.

OligoCalc also offers features for primer design, such as checking for potential self-complementarity, hairpins, and primer dimers, which can lead to unwanted amplification or non-specific binding. Users can input a DNA or RNA sequence and specify parameters like primer length, GC content, and Tm range to identify suitable primer candidates. Furthermore, it can predict the thermodynamic stability of RNA secondary structures, aiding in the understanding of RNA folding and function.

The web interface of OligoCalc is generally user-friendly, allowing researchers to input sequences directly or upload them from files. The results are presented in a clear and organized manner, often with graphical representations where applicable. This accessibility and comprehensive feature set have made OligoCalc a widely used and cited tool in scientific literature.