Mfold web server for nucleic acid folding and hybridization prediction.
Journal: 2003/August - Nucleic Acids Research
ISSN: 1362-4962
PUBMED: 12824337
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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Nucleic Acids Res 31(13): 3406-3415

Mfold web server for nucleic acid folding and hybridization prediction

Department of Mathematical Sciences, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
Tel: +1 5182766902; Fax: +1 5182764824; Email: ude.ipr@mrekuz
Department of Mathematical Sciences, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
Received 2003 Feb 14; Revised 2003 Apr 7; Accepted 2003 Apr 7.

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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ACKNOWLEDGEMENTS

This work was supported, in part, by grant #GM54250 from the National Institutes of Health. I thank Gerald Johns for hardware and systems support in the early days of the server at Washington University. All of the graphics applications (except for naview) were written by Darrin Stewart, who also wrote the ‘cgi’ scripts for interactive viewing of plots. I thank Art Sanderson (Vice President of Research at RPI), for connecting me with the Academy of Electronic Media and for supporting this project; Bill Shumway, for initiating and facilitating interactions with IBM Research; and Alex Yu, who has done so much work in assembling the hardware, organizing the web server layout, porting applications and in keeping the server running day in and day out. Finally, I thank IBM Research for the SUR grant that gave us a thirty-fold increase in computer power for housing this valuable resource.

ACKNOWLEDGEMENTS

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