We present an integrative approach, SeqFold, that combines high-throughput RNA structure profiling data with computational prediction for genome-scale reconstruction of RNA secondary structures. SeqFold transforms experimental RNA structure information into a structure preference profile (SPP) and uses it to select stable RNA structure candidates representing the structure ensemble. Under a hig...

Influenza A is a negative sense RNA virus of significant public health concern. While much is understood about the life cycle of the virus, knowledge of RNA secondary structure in influenza A virus is sparse. Predictions of RNA secondary structure can focus experimental efforts. The present study analyzes coding regions of the eight viral genome segments in both the (+) and (-) sense RNA for co...

Multiple context-free grammar (mcfg) [10] is a natural extension of context free grammar (cfg) and inherits many good properties of cfg. For example, the class of languages generated by mcfg (called multiple context-free languages or mcfl) is a substitution closed full AFL and the membership problem for mcfl L is solvable in O(n) time where n is the length of an input string and e is a constant...

Transcriptomics experiments and computational predictions both enable systematic discovery of new functional RNAs. However, many putative noncoding transcripts arise instead from artifacts and biological noise, and current computational prediction methods have high false positive rates. I discuss prospects for improving computational methods for analyzing and identifying functional RNAs, with a...

This thesis focus on the prediction of RNA secondary structure using stochastic context-free grammars (SCFG). The RNA secondary structure prediction problem consists of predicting a 2-dimensional structure from a 1-dimensional nucleotide sequence. The theory behind SCFG is explained and an overview of the research literature on various methods in the field of secondary structure prediction is g...

CC-BY-NC 4.0 International license peer-reviewed) is the author/funder. It is made available under a The copyright holder for this preprint (which was not. Abstract The RNA pseudoknot is a conserved secondary structure encountered in a number of ribozymes, which assume a central role in the RNA world hypothesis. However, RNA folding algorithms could not predict pseudoknots until recently. Analy...

The three-domain system is a biological classification of RNA. In bioinformatics, predicting the domain of RNA is helpful in the research of DNA and protein. By reviewing the related literature, we notice that many researches are conducted for domain prediction with only the primary structure. However, compared with the primary structure, the secondary structure of an RNA contains more discrimi...

MOTIVATION RNAs play an important role in many biological processes and knowing their structure is important in understanding their function. Due to difficulties in the experimental determination of RNA secondary structure, the methods of theoretical prediction for known sequences are often used. Although many different algorithms for such predictions have been developed, this problem has not y...

RNA was first explored and understood as a messenger molecule, relaying DNA encodings of amino acids during protein synthesis. Beyond messenger RNA, however, a class of RNA known as non-coding RNA plays fundamental roles in transcriptional and translational gene regulation. As the biological mantra goes, form fits function, and these regulatory roles depend on the 3-D structure of the RNA molec...