منابع مشابه
Predicting RNA Secondary Structures Including Pseudoknots
RNA secondary structures play a vital role in modern genetics and a lot of time and e ort has been put into their study. It is important to be able to predict them with high accuracy, since methods involving manual analysis are expensive, time-consuming and error-prone. Predictions can also be used to guide experiments to reduce time and money requirements. Several algorithms have been develope...
متن کاملHotKnots: heuristic prediction of RNA secondary structures including pseudoknots.
We present HotKnots, a new heuristic algorithm for the prediction of RNA secondary structures including pseudoknots. Based on the simple idea of iteratively forming stable stems, our algorithm explores many alternative secondary structures, using a free energy minimization algorithm for pseudoknot free secondary structures to identify promising candidate stems. In an empirical evaluation of the...
متن کاملOn the page number of RNA secondary structures with pseudoknots.
Let S denote the set of (possibly noncanonical) base pairs {i, j } of an RNA tertiary structure; i.e. {i, j} ∈ S if there is a hydrogen bond between the ith and jth nucleotide. The page number of S, denoted π(S), is the minimum number k such that Scan be decomposed into a disjoint union of k secondary structures. Here, we show that computing the page number is NP-complete; we describe an exact ...
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: BRICS Report Series
سال: 2000
ISSN: 1601-5355,0909-0878
DOI: 10.7146/brics.v7i1.20129