prerktag: prediction of rna knotted structures using tree adjoining grammars
نویسندگان
چکیده
background: rna molecules play many important regulatory, catalytic and structuralroles in the cell, and rna secondary structure prediction with pseudoknots is one themost important problems in biology. an rna pseudoknot is an element of the rna secondary structure in which bases of a single-stranded loop pair with complementary basesoutside the loop. modeling these nested structures (pseudoknots) causes numerous computational diffilties and so it has been generally neglected in rna structure predictionalgorithms.objectives: in this study, we present a new heuristic algorithm for the prediction of rnaknotted structures using tree adjoining grammars (named prerktag).materials and methods: for a given rna sequence, prerktag uses a genetic algorithm ontree adjoining grammars to propose a structure with minimum thermodynamic energy.the genetic algorithm employs a subclass of tree adjoining grammars as individuals bywhich the secondary structure of rnas are modeled. upon the tree adjoining grammars,new crossover and mutation operations were designed.the finess function is defied according to the rna thermodynamic energy function, which causes the algorithm convergence to be a stable structure.results: the applicability of our algorithm is demonstrated by comparing its iresults withthree well-known rna secondary structure prediction algorithms that support crossedstructures.conclusions: we performed our comparison on a set of rna sequences from the rnasepdatabase, where the outcomes show effiency and practicality of the proposed algorithm.
منابع مشابه
PreRkTAG: Prediction of RNA Knotted Structures Using Tree Adjoining Grammars
Background: RNA molecules play many important regulatory, catalytic and structural <span style="font-variant: normal; font-style: norma...
متن کاملModeling RNA Secondary Structures Using Tree Grammars
This paper proposes a grammatical tool, called tree adjunct grammar with tag for RNA ( denoted by TAG 2 RNA ), for representing secondary structures of RNAs, and shows some example TAG 2 RNA grammars for fairly complicated RNA secondary structures. We then demonstrate the appropriateness of the grammars for modeling RNA secondary structures by discussing its formal language and/or graph theoret...
متن کاملSynchronous Tree-Adjoining Grammars
The unique properties of tree-adjoining grammars (TAG) present a challenge for the application of TAGs beyond the limited confines of syntax, for instance, to the task of semantic interpretation or automatic translation of natural language. We present a variant of TAGs, called synchronous TAGs, which characterize correspondences between languages. The formalism's intended usage is to relate exp...
متن کاملContextual Tree Adjoining Grammars
n rhi.\' pape1; 1i:e introduce a formalism called contextual tree adjoining grammar (CTAG). (::TAG.~ are a generalization of multi bracketed contextual reivriting gramnwrs (MBICR) which combine tree adjoini11g grammars (TAGs) and co11textual grammars. The generalization is to add a mechanism similar to obligatory adjoi11i11g in TAGs. Here, we present the definition o.f the model and some result...
متن کاملمنابع من
با ذخیره ی این منبع در منابع من، دسترسی به آن را برای استفاده های بعدی آسان تر کنید
عنوان ژورنال:
iranian journal of biotechnologyناشر: national institute of genetic engineering and biotechnology
ISSN 1728-3043
دوره 11
شماره 1 2013
میزبانی شده توسط پلتفرم ابری doprax.com
copyright © 2015-2023