Mfold web server for nucleic acid folding and hybridization prediction

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'.

Figure 1

This figure reproduces part of the initial results page for an RNA folding. Some input is reproduced in the text area. Various hyperlinks lead to the actual folding results.

Figure 2

Two complementary DNA sequences have been concatenated by linking them with six Ns. The two loops are labeled ‘1’ and ‘2’. Loop ‘1’ is an exterior loop, which is correct, but loop ‘2’ is a hairpin loop instead of an exterior loop.