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BioMed Research International
Volume 2014 (2014), Article ID 690340, 10 pages
http://dx.doi.org/10.1155/2014/690340
Research Article

Characteristics and Prediction of RNA Structure

1School of Computer Science and Technology, Shandong Provincial Key Laboratory of Digital Media Technology, Shandong University of Finance and Economics, Jinan 250014, China
2Computational Biology Institute, George Washington University, Ashburn, VA 20147, USA
3School of Computer Science and Technology, Shandong Provincial Key Laboratory of Software Engineering, Shandong University, Jinan 250101, China

Received 28 February 2014; Accepted 11 June 2014; Published 6 July 2014

Academic Editor: Maria Cristina De Rosa

Copyright © 2014 Hengwu Li et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Supplementary Material

PKNOTS data set includes 116 sequences, that is 25 tRNA sequences randomly selected from Sprinzl tRNA database, HIV-1-RT-ligand RNA pseukonts, and some viral RNAs. Column len and base pair indicate the length and the number of the native base pairs of sequence. For each algorithm, the sensitivity and specificity are shown. Average is is the usual average of sensitivity and specificity values reported in the table.

TT2NE data set has 47 sequences from PseudoBase and PDB. In column ex, X indicates whether the native has been found experimentally. For each algorithm, the sensitivity and specificity are shown. Column g indicates the genus of the native structure and gT, gHK, gMQ, gPK, gLZ and gGM, are the respective genii of the predictions of TT2NE, HotKnots, McQfold, ProbKnot, LZ and GM. All Mfolds prediction have genus 0, as Mfold generates only structures without pseudoknots. Average 1 is the total number of base pairs correctly predicted in the whole database divided by respectively the total number of native base pairs (average sensitivity) and the total number of base pairs predicted (average specificity). Average 2 is the usual average of sensitivity and specificity values reported in the table (values used to perform the t-test).

Notice: TT2NE is shown the best value after several times folding with different parameters, so it is not the auto-computing value.

  1. Supplementary Materials