RNA Structure Evolution and Transducer Composition
نویسندگان
چکیده
Non-coding RNAs (ncRNAs) play important biological roles ranging from regulation of gene expression to translation of nucleotide sequence into proteins. Computational tools to analyze homologous ncRNAs and infer their shared structure are correspondingly important. We are developing constrained, tractable algorithms for simultaneous multiple sequence alignment and structural inference of small sets of homologous ncRNAs. Our methodology goes beyond simple point-substitution phylo-grammars by incorporating techniques previously available only for pairwise comparisons, including models of insertion and deletion events as well as large-scale structural evolution.
منابع مشابه
Evolutionary Triplet Models of Structured RNA
The reconstruction and synthesis of ancestral RNAs is a feasible goal for paleogenetics. This will require new bioinformatics methods, including a robust statistical framework for reconstructing histories of substitutions, indels and structural changes. We describe a "transducer composition" algorithm for extending pairwise probabilistic models of RNA structural evolution to models of multiple ...
متن کاملThe role of feldspar crystals zoning in interpreting the magmatic evolution of the Goushe granitoid Pluton (SE of Boroujerd)
The Goushe granitoid Pluton is located southeast of Boroujerd. The study area is composed of granite, granodiorite and the microgranular enclaves located in it with the granodiorite to quartzmonzodiorite combination. The microgranular enclaves presence along with evidence of the presence of the non-equilibrium textures such as dissolved margin and plagioclase zoning, sieve textures, mafic clots...
متن کاملRelation Between RNA Sequences, Structures, and Shapes via Variation Networks
Background: RNA plays key role in many aspects of biological processes and its tertiary structure is critical for its biological function. RNA secondary structure represents various significant portions of RNA tertiary structure. Since the biological function of RNA is concluded indirectly from its primary structure, it would be important to analyze the relations between the RNA sequences and t...
متن کاملA parameterization of RNA sequence space
RNA polymers are constructed from four distinct nucleotide bases. The sequence of these nucleotide bases determines both the folded conformation and the biological function of RNA. It recently has been established that disparately related functional classes of evolved RNA possess similar base composition biases despite a lack of sequence similarity, folded structure, or metabolic function. We h...
متن کاملComposition of functions with accumulating parameters
Many functional programs with accumulating parameters are contained in the class of macro tree transducers. We present a program transformation technique that can be used to solve the efficiency problems due to creation and consumption of intermediate data structures in compositions of such functions, where classical deforestation techniques fail. In order to do so, given two macro tree transdu...
متن کامل