First, a library of hairpin RNAs was constructed by exhausting all possible combinations of base pairs in the 5-bp stem, provided that the following requirements were met: (1) in the GS, each base pair belongs to ‘strong’ base pairs (defined as WC base pairs or G ∙ U wobbles...
base-pair with transcript targets, marking or identifying them for the synthesis of the more abundant antisense, secondary 22G-RNAs by RNA-dependent RNA polymerases (RdRPs)18,19,20,21,22,23. 22G-RNAs silence mobile elements, pseudogenes, non-annotated loci, and select endogenous, germline gene...
The rules for converting an RNA structure into a dual graph are as follows: (1) An RNA stem with more than one complementary base pair is represented as a vertex (•). (2) An edge (∩ or —) represents a single-strand that may occur in segments connecting the secondary elements (e...
The connectivity matrix is constructed following the cooperativity rules of nucleation for RNA hairpin formation and base-pair stacking. Attractive neural patterns correspond to stable RNA secondary structures. Moreover, the Gibbs probability of a pattern coincides with the Boltzmann weight of the ...
Note that the structure for x (above, in black) has what is most likely an unconserved base pair C·G in the second stem of the structure. Full size image Parameterization Given the set of pairSCFG production rules above, we need to determine all the necessary probability parameters. As ...
Its rules are written to record and distinguish the situation where a helix (1) ends with a base pair, (2) already has a single unpaired base to its right or left, or (3) has several unpaired bases on either side. No dangle energies are added in cases (1) and (3), and in case...
Ifseveralsequencesareexpectedtoshareacommonstructure,highlyaccuratepredictions oftheconsensusstructurecanbeobtainedbycombiningthermodynamicruleswithan analysisofsequencevariationandcovariation.Suchamethodisimplementedinthe RNAalifoldprogram(Hofackeretal.,2002;seeBasicProtocol2). Finally,theauthorsoftheViennaRNApackage...
21.2The5′EndofEukaryoticmRNAIsCapped •A5′capisformedbyaddingaGtotheterminalbaseofthetranscriptviaa5′–5′link.•Thecappingprocesstakesplaceduringthetranscription,whichmaybeimportantfortranscriptionreinitiation.FIGURE02:EukaryoticmRNAhasamethylated5’cap 21.2The5′EndofEukaryoticmRNAIsCapped •The5′...
(生物化学)RNA sythesis
(SCFGs). Mathematical models in which base pairings in an RNA molecule are described as a set of production rules, each augmented with a probability. Machine learning methods Algorithms that use empirical data (called the training set) to capture characteristics of unknown underlying phenomena and ...