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June 25, 2003Nucleic Acids Research13,682 citationsOpen Access

Mfold web server for nucleic acid folding and hybridization prediction

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MZMichael Zuker

Key Points

  • To provide the broader scientific community with accessible, web-based software for predicting the secondary structure folding and hybridization of single-stranded RNA and DNA.
  • Integrated a suite of thermodynamic folding and hybridization algorithms into a centralized World Wide Web server utilizing universally accessible graphical user interfaces.
  • Engineered support for single-sequence comprehensive analyses as well as high-throughput bulk servers capable of processing hundreds of sequences simultaneously.
  • Generated detailed graphical visual outputs, including secondary structure plots with reliability information, single-strand frequency plots, and energy dot plots.
  • Enabled rapid multi-sequence processing via specialized bulk server pipelines to bypass local software installation and portability barriers.

Abstract

The abbreviated name, 'mfold web server', describes a number of closely related software applications available on the World Wide Web (WWW) for the prediction of the secondary structure of single stranded nucleic acids. The objective of this web server is to provide easy access to RNA and DNA folding and hybridization software to the scientific community at large. By making use of universally available web GUIs (Graphical User Interfaces), the server circumvents the problem of portability of this software. Detailed output, in the form of structure plots with or without reliability information, single strand frequency plots and 'energy dot plots', are available for the folding of single sequences. A variety of 'bulk' servers give less information, but in a shorter time and for up to hundreds of sequences at once. The portal for the mfold web server is http://www.bioinfo.rpi.edu/applications/mfold. This URL will be referred to as 'MFOLDROOT'.

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Cite This Study

Michael Zuker (2003) studied this question.

synapsesocial.com/papers/69da7e94387cf70698686c7ehttps://doi.org/10.1093/nar/gkg595
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