A global sampling approach to designing and reengineering RNA secondary structures
نویسندگان
چکیده
منابع مشابه
A global sampling approach to designing and reengineering RNA secondary structures
The development of algorithms for designing artificial RNA sequences that fold into specific secondary structures has many potential biomedical and synthetic biology applications. To date, this problem remains computationally difficult, and current strategies to address it resort to heuristics and stochastic search techniques. The most popular methods consist of two steps: First a random seed s...
متن کاملDesigning RNA Secondary Structures is Hard
An RNA sequence is a word over an alphabet on four elements {A,C,G,U} called bases. RNA sequences fold into secondary structures where some bases match one another while others remain unpaired. Pseudoknot-free secondary structures can be represented as well-parenthesized expressions with additional dots, where pairs of matching parentheses symbolize paired bases and dots, unpaired bases. The tw...
متن کاملA novel approach to represent and compare RNA secondary structures
Structural information is crucial in ribonucleic acid (RNA) analysis and functional annotation; nevertheless, how to include such structural data is still a debated problem. Dot-bracket notation is the most common and simple representation for RNA secondary structures but its simplicity leads also to ambiguity requiring further processing steps to dissolve. Here we present BEAR (Brand nEw Alpha...
متن کاملPredicting RNA secondary structures with pseudoknots by MCMC sampling.
The most probable secondary structure of an RNA molecule, given the nucleotide sequence, can be computed efficiently if a stochastic context-free grammar (SCFG) is used as the prior distribution of the secondary structure. The structures of some RNA molecules contain so-called pseudoknots. Allowing all possible configurations of pseudoknots is not compatible with context-free grammar models and...
متن کاملBayesian sampling of evolutionarily conserved RNA secondary structures with pseudoknots
MOTIVATION Today many non-coding RNAs are known to play an active role in various important biological processes. Since RNA's functionality is correlated with specific structural motifs that are often conserved in phylogenetically related molecules, computational prediction of RNA structure should ideally be based on a set of homologous primary structures. But many available RNA secondary struc...
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ژورنال
عنوان ژورنال: Nucleic Acids Research
سال: 2012
ISSN: 1362-4962,0305-1048
DOI: 10.1093/nar/gks768