OligoCalc: an online oligonucleotide properties calculator

Nucleic Acids Res. 2007 Jul;35(Web Server issue):W43-6. doi: 10.1093/nar/gkm234. Epub 2007 Apr 22.

Abstract

We developed OligoCalc as a web-accessible, client-based computational engine for reporting DNA and RNA single-stranded and double-stranded properties, including molecular weight, solution concentration, melting temperature, estimated absorbance coefficients, inter-molecular self-complementarity estimation and intra-molecular hairpin loop formation. OligoCalc has a familiar 'calculator' look and feel, making it readily understandable and usable. OligoCalc incorporates three common methods for calculating oligonucleotide-melting temperatures, including a nearest-neighbor thermodynamic model for melting temperature. Since it first came online in 1997, there have been more than 900,000 accesses of OligoCalc from nearly 200,000 distinct hosts, excluding search engines. OligoCalc is available at http://basic.northwestern.edu/biotools/OligoCalc.html, with links to the full source code, usage patterns and statistics at that link as well.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Algorithms
  • Animals
  • Base Composition*
  • Computational Biology / methods*
  • DNA / chemistry*
  • Humans
  • Internet*
  • Models, Chemical
  • Oligonucleotides / chemistry*
  • Oligonucleotides / genetics*
  • RNA / chemistry*
  • Software
  • Temperature
  • User-Computer Interface

Substances

  • Oligonucleotides
  • RNA
  • DNA