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检索条件"主题词=RNA secondary structure prediction"

共 132 条记录，以下是91-100 订阅

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Computational and Bioinformatics Methods for Microrna Gene prediction

Computational and Bioinformatics Methods for MicroRNA Gene P...

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作者： Jens Allmer

Micrornas (mirnas) have attracted ever-increasing interest in recent years. Since experimental approaches for determining mirnas are nontrivial in their application, computational methods for the prediction of mirnas have gained popularity. Such methods can be grouped into two broad categories (1) performing ab initio predictions of mirnas from primary sequence alone and (2) additionally employing phylogenetic conservation. Most methods acknowledge the importance of hairpin or stem–loop structures and employ various methods for the prediction of rna secondary structure. Machine learning has been employed in both categories with classification being the predominant method. In most cases, positive and negative examples are necessary for performing classification. Since it is currently elusive to experimentally determine all possible mirnas for an organism, true negative examples are hard to come by, and therefore the accuracy assessment of algorithms is hampered. In this chapter, first rna secondary structure prediction is introduced since it provides a basis for mirna prediction. This is followed by an assessment of homology and then ab initio mirna prediction methods. less

关键词： structure prediction Gene prediction Machine Learning rna secondary structure prediction mirna Homology-based prediction Ab initio prediction mirna prediction accuracy Multiple sequence alignment-based prediction

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Single-Molecule FRET Studies of rna Structural Rearrangements and rna-rna Interactions

Single-Molecule FRET Studies of RNA Structural Rearrangement...

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作者： Ewelina M. Małecka Boyang Hua Sarah A. Woodson

rna-guided regulation of gene expression is found in all cell types. In this mode of regulation, antisense interactions between the regulatory rna and its target are typically facilitated by a protein partner. Single-molecule fluorescence microscopy is a powerful tool for dissecting the conformational states and intermediates that contribute to target recognition. This chapter describes protocols for studying target recognition by bacterial small rnas and their chaperone Hfq on the single-molecule level, using a total internal reflection fluorescence microscope. The sections cover the design of suitable rna substrates for srna-mrna annealing reactions, preparation of internally labeled mrna for detecting conformational changes in the target, and key steps of the data analysis. These protocols can be adapted to other rna-binding proteins that chaperone rna interactions. less

关键词： Single-molecule FRET Data analysis FRET Fluorescence Microscopy TIRF Microscopy rna secondary structure prediction Total Internal Reflection Microscopy Passivation Single-molecule fluorescence Small rna TIRF rna chaperone Hfq Antisense-rna interactions

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GCG: The Analysis of rna secondary structure

GCG: The Analysis of RNA Secondary Structure

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作者： Reinhard Dölz

The prediction of rna secondary structure differs significantly from that of protein secondary structure. The latter is based on crystallographic data, and by using a variety of empiric or semiempiric parameters, a prediction is achieved. rna secondary structure prediction, on the other hand, is based on an energy calculation. Each nucleotide sequence can be calculated using a table of energies for stacking and loop destabilizing energies. The GCG program (1) foldrna is the program of M. Zuker (2), using the energies published by Turner (3). The algorithm and its usage are explained in Chapter 23 in Part II. This chapter shows the use of the foldrna program as implemented in the GCG package, including the broad range of output visualization provided. less

关键词： Protein secondary structure rna secondary structure prediction

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Computational Design of rna Libraries for In Vitro Selection of Aptamers

Computational Design of RNA Libraries for In Vitro Selection...

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作者： Yaroslav G. Chushak Jennifer A. Martin Jorge L. Chávez Nancy Kelley-Loughnane Morley O. Stone

Selection of aptamers that bind a specific ligand usually begins with a random library of rna sequences, and many aptamers selected from such random pools have a simple stem–loop structure. We present here a computational approach for designing a starting library of rna sequences with increased formation of complex structural motifs and enhanced affinity to a desired target molecule. Our approach consists of two steps: (1) generation of rna sequences based on customized patterning of nucleotides with increased probability of forming a base pair and (2) a high-throughput virtual screening of the generated library to select aptamers with binding affinity to a small-molecule target. We developed a set of criteria that allows one to select a sequence with potential binding affinity from a pool of random sequences and designed a protocol for rna 3D structure prediction. The proposed approach significantly reduces the rna sequence search space, thus accelerating the experimental screening and selection of high-affinity aptamers. less

关键词： rna structure prediction Virtual Screening rna secondary structure Analysis structure prediction SELEX High-throughput Screening AutoDock Docking Method Microarray rna secondary structure prediction Screening library design Patterned sequences rna–small molecule docking

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Engineering, delivery, and biological validation of artificial microrna clusters for gene therapy applications

Engineering, delivery, and biological validation of artifici...

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作者： Vivek Bhaskaran Yizheng Yao Fengfeng Bei Pierpaolo Peruzzi

The cellular machinery regulating microrna biogenesis and maturation relies on a small number of simple steps and minimal biological requirements and is broadly conserved in all eukaryotic cells. The same holds true in disease. This allows for a substantial degree of freedom in the engineering of transgenes capable of simultaneously expressing multiple micrornas of choice, allowing a more comprehensive modulation of microrna landscapes, the study of their functional interaction, and the possibility of using such synergism for gene therapy applications. We have previously engineered a transgenic cluster of functionally associated micrornas to express a module of suppressed micrornas in brain cancer for therapeutic purposes. Here, we provide a detailed protocol for the design, cloning, delivery, and utilization of such artificial microrna clusters for gene therapy purposes. In comparison with other protocols, our strategy effectively decreases the requirements for molecular cloning, because the nucleic acid sequence encoding the combination of the desired micrornas is designed and validated in silico and then directly synthesized as DNA that is ready for subcloning into appropriate delivery vectors, for both in vitro and in vivo use. Sequence design and engineering require 4–5 h. Synthesis of the resulting DNA sequence requires 4–6 h. This protocol is quick and flexible and does not require special laboratory equipment or techniques, or multiple cloning steps. It can be easily executed by any graduate student or technician with basic molecular biology knowledge. less

关键词： Molecular Cloning rna secondary structure prediction rna structure prediction Quantitative Reverse Transcription PCR Bacterial Transformation Restriction Enzyme Digestion FACS rna Extraction Real-time PCR Surgery Cell And Tissue Culture Genome Visualization TA cloning DNA Ligation Ensembl Homo sapiens Mycoplasma Lentivirus Mus musculus Lens HEK293 Gene delivery Gene therapy mirnas

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Targeting Noncoding rna Domains to Genomic Loci with CRISPR-Display: Guidelines for Designing, Building, and Testing sgrna–ncrna Expression Constructs

Targeting Noncoding RNA Domains to Genomic Loci with CRISPR-...

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作者： David M. Shechner

CRISPR-Display uses the S. pyogenes Cas9 protein to posttranscriptionally localize noncoding rna (ncrna) domains to any genomic site, by directly fusing these domains to the Cas9 sgrna cofactor. This versatile technology enables numerous applications for interrogating natural chromatin-regulatory ncrnas, or for utilizing artificial ncrna and ribonucleoprotein (RNP) devices at individual chromatin loci. To achieve these, a successful CRISPR-Display experiment requires that chimeric sgrna–ncrna fusions are stably expressed and incorporated into Cas9 complexes, and that they retain their ncrna “cargo” domains at the targeted genomic sites. Here, I describe a workflow for designing, building, and testing such chimeric sgrna–ncrna expression constructs. I detail strategies for choosing expression systems and sgrna insertion topologies, for assaying the incorporation of sgrna–ncrna fusions into functional Cas9 complexes, and for surveying the activities of ncrna domains at targeted genomic loci. This establishes an initial set of “best practices” for the design and implementation of CRISPR-Display experiments. less

关键词： CRISPR rna secondary structure prediction Gibson Assembly Enzymatic Cleavage Sanger Sequencing Cross-linking rna Immunoprecipitation (RIP) Transient Transfection Cell And Tissue Culture Cell Lysis Sonication rna Extraction Real-time PCR Quantitative Reverse Transcription PCR Luciferase Reporter Assay FISH Recombinant Protein Expression Confocal Microscopy Molecular Cloning DNA Ligation Data analysis Pull-down Assay HEK293T lncrna Noncoding rna CRISPR-Display Extended sgrna rna Aptamer rna Devices lncrna reconstitution Anti-FLAG Anti-rabbit

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prediction of Plant mirna Genes

Prediction of Plant miRNA Genes

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作者： Matthew W. Jones-Rhoades

This chapter presents procedures for the computational identification of plant mirna genes. In the first procedure, homologs of known mirnas are identified in a database of genomic or cDNA sequence. In the second procedure, previously unidentified mirna families are predicted through the analysis of secondary structure, evolutionary conservation, and targeting potential. less

关键词： Gene prediction Genomics Deep Sequencing Northern Blot PCR rna secondary structure prediction microrna discovery

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Optimal tiling for the rna base pairing problem 02

Optimal tiling for the RNA base pairing problem

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Proceedings of the fourteenth annual ACM symposium on Parallel algorithms and architectures

作者： Francisco Almeida Rumen Andonov Daniel Gonzalez Luz M. Moreno Vincent Poirriez Casiano Rodriguez D.E.I.O.C. La Laguna Spain INRIA Rennes France University of Valenciennes D.E.I.O.C. La Laguna

ISBN: (纸本)9781581135299

Dynamic programming is an important combinatorial optimization technique that has been widely used in various fields such as control theory, operations research, computational biology and computer science. Many authors have described parallel dynamic programming algorithms for the family of multistage problems. More scarce is the literature for the more general class of problems where dependences appear between non-consecutive stages. Among the important problems falling in this class is the rna base pairing problem. In this study we propose a new parallel scheme for a large class of recurrences with triangular iteration space and nonuniform dependences that includes the rna base pairing problem. We derive two different instances of this scheme that correspond to an horizontal and a vertical traverse of the iteration domain. We develop and extend the tiling approach for this particular class. We formulate and analytically solve the optimization problem determining the tile size that minimizes the total execution time of the tiled program on a distributed memory parallel machine. Our analyze is based on the BSP model, which assures the portability of the obtained results. The computational experiments carried out on the CRAY T3E behave according to the predictions of our theoretical model.

关键词： loop partitioning BSP model MPI rna secondary structure prediction SPMD dynamic programming granularity on distributed memory machines

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Computational prediction of Microrna Targets

Computational Prediction of MicroRNA Targets

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作者： Xiaowei Wang

One critical step in mirna functional studies is to identify the gene targets that are directly regulated by mirnas. In this chapter, we describe a computational algorithm and an online database, miRDB, for mirna target prediction. In miRDB, flexible Web search interface has been developed for the retrieval of target prediction results generated by the newly developed computational algorithm. In addition, a wiki editing interface has been established to allow anyone with Internet access to make contributions on mirna functional annotation. All data stored in miRDB are freely accessible at http://*** . less

关键词： Machine Learning rna secondary structure prediction Statistical Calculation Data analysis Microarray GenBank

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Identification of micrornas and Other Tiny Noncoding rnas by cDNA Cloning

Identification of microRNAs and Other Tiny Noncoding RNAs by...

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作者： Victor Ambros Rosalind C. Lee

Micrornas (mirnas) and other small rnas can be identified by cloning and sequencing cDNAs prepared from the ∼22-nt fraction of total rna. Methods are described for the construction of cDNA libraries from small noncoding rnas through the use of T4 rna ligase, reverse transcriptase, and polymerase chain reaction. cDNAs are cloned in λ or plasmid vectors, and the sequences are compared to annotated genomic sequence databases, and analyzed by rna folding programs to distinguish mirna sequences from other small rnas of similar size. Northern blot hybridization is used to confirm the expression of small rnas in vivo. less

关键词： Northern Blot PCR Fractionation Total rna Extraction Gel Electrophoresis Shadowing (Histology) Reverse Transcription PCR Directional Cloning NCBI BLAST rna secondary structure prediction Library Preparation Database Search Electroblotting cDNA sequencing DNA Ligation rna folding rna ligase microrna noncoding rna SMART cDNAs

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