Tools

Calculator

Biopolymer Calculator
A. Schepartz, Yale University 
Mongo Oligo Mass Calculator
The Nucleic Acids Masspec Toolbox, University of Utah 
Oligo Analyzer
Integrated DNA Technologies, Inc. and University of Pittsburgh School of Medicine

Thermal denaturation profile

Thermal denaturation profile of double stranded RNA or DNA (Poland's algorithm)
Uni-Dusseldorf, Germany 

DNA Hybridization Thermodynamics

HyTher^TM server
Nicolas Peyret and John SantaLucia, Jr, Wayne State University 

Extinction (absorption) coefficient

Extinction (absorption) coefficient of DNA
Richard Owczarzy 

Free energy

Compute the free energy of an RNA/DNA structure
M. Zuker, Washington University 

Secondary Structure Prediction and Comparison

DNA Secondary Structure Prediction (mfold)
M. Zuker, Washington University 
RNA Secondary Structure Prediction (mfold)
M. Zuker, Washington University 
RNAstructure, Version 3.5
a PC version of the Zuker algorithm -- D. Turner, University of Rochester 
Mix&match
D. Turner, University of Rochester 
Vienna RNA Package
Theoretical Biochemistry Group, University of Vienna 
Vienna RNA Secondary Structure Prediction
Theoretical Biochemistry Group, University of Vienna 

Primer selection

Primer3 -- Pick primers from a DNA sequence
Dr. Rozen, Whitehead Institute for Biomedical Research, MIT