Download or read book RNA Sequence Structure and Function Computational and Bioinformatic Methods written by Jan Gorodkin and published by Humana. This book was released on 2014-03-18 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: The existence of genes for RNA molecules not coding for proteins (ncRNAs) has been recognized since the 1950's, but until recently, aside from the critically important ribosomal and transfer RNA genes, most focus has been on protein coding genes. However, a long series of striking discoveries, from RNA's ability to carry out catalytic function, to discovery of riboswitches, microRNAs and other ribo-regulators performing critical tasks in essentially all living organisms, has created a burgeoning interest in this primordial component of the biosphere. However, the structural characteristics and evolutionary constraints on RNA molecules are very different from those of proteins, necessitating development of a completely new suite of informatic tools to address these challenges. In RNA Sequence, Structure, Function: Computational and Bioinformatic Methods, expert researchers in the field describe a substantial and relevant fraction of these methodologies from both practical and computational/algorithmic perspectives. Focusing on both of these directions addresses both the biologist interested in knowing more about RNA bioinformatics as well as the bioinformaticist interested in more detailed aspects of the algorithms. Written in the highly successful Methods in Molecular Biology series format, the chapters include the kind of detailed description and implementation advice that is crucial for getting optimal results. Thorough and intuitive, RNA Sequence, Structure, Function: Computational and Bioinformatic Methods aids scientists in continuing to study key methods and principles of RNA bioinformatics.
Download or read book RNA Sequence Structure and Function written by Jan Gorodkin and published by . This book was released on 2014 with total page 533 pages. Available in PDF, EPUB and Kindle. Book excerpt: The existence of genes for RNA molecules not coding for proteins (ncRNAs) has been recognized since the 1950's, but until recently, aside from the critically important ribosomal and transfer RNA genes, most focus has been on protein coding genes. However, a long series of striking discoveries, from RNA's ability to carry out catalytic function, to discovery of riboswitches, microRNAs and other ribo-regulators performing critical tasks in essentially all living organisms, has created a burgeoning interest in this primordial component of the biosphere. However, the structural characteristics and evolutionary constraints on RNA molecules are very different from those of proteins, necessitating development of a completely new suite of informatic tools to address these challenges. In RNA Sequence, Structure, Function: Computational and Bioinformatic Methods, expert researchers in the field describe a substantial and relevant fraction of these methodologies from both practical and computational/algorithmic perspectives. Focusing on both of these directions addresses both the biologist interested in knowing more about RNA bioinformatics as well as the bioinformaticist interested in more detailed aspects of the algorithms. Written in the highly successful Methods in Molecular Biology series format, the chapters include the kind of detailed description and implementation advice that is crucial for getting optimal results. Thorough and intuitive, RNA Sequence, Structure, Function: Computational and Bioinformatic Methods aids scientists in continuing to study key methods and principles of RNA bioinformatics.
Download or read book RNA Folding written by Ronny Lorenz and published by Springer Nature. This book was released on with total page 407 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Molecular Biology of The Cell written by Bruce Alberts and published by . This book was released on 2002 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book RNA 3D Structure Analysis and Prediction written by Neocles Leontis and published by Springer Science & Business Media. This book was released on 2012-06-05 with total page 402 pages. Available in PDF, EPUB and Kindle. Book excerpt: With the dramatic increase in RNA 3D structure determination in recent years, we now know that RNA molecules are highly structured. Moreover, knowledge of RNA 3D structures has proven crucial for understanding in atomic detail how they carry out their biological functions. Because of the huge number of potentially important RNA molecules in biology, many more than can be studied experimentally, we need theoretical approaches for predicting 3D structures on the basis of sequences alone. This volume provides a comprehensive overview of current progress in the field by leading practitioners employing a variety of methods to model RNA 3D structures by homology, by fragment assembly, and by de novo energy and knowledge-based approaches.
Download or read book RNA 3D Structure Analysis and Prediction written by Neocles Leontis and published by Springer Science & Business Media. This book was released on 2012-06-05 with total page 402 pages. Available in PDF, EPUB and Kindle. Book excerpt: With the dramatic increase in RNA 3D structure determination in recent years, we now know that RNA molecules are highly structured. Moreover, knowledge of RNA 3D structures has proven crucial for understanding in atomic detail how they carry out their biological functions. Because of the huge number of potentially important RNA molecules in biology, many more than can be studied experimentally, we need theoretical approaches for predicting 3D structures on the basis of sequences alone. This volume provides a comprehensive overview of current progress in the field by leading practitioners employing a variety of methods to model RNA 3D structures by homology, by fragment assembly, and by de novo energy and knowledge-based approaches.
Download or read book RNA Structure Determination written by Douglas H. Turner and published by Humana. This book was released on 2016-09-24 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: This volume provides protocols and procedures for determining and modeling RNA structure. Chapters guide the reader through protocols for RNA secondary structure prediction, single sequence modeling, Crumple, RNAstructure to model conserved secondary structures with multiple homologs, the prediction of bimolecular secondary structures with RNAstructure, STarMir, protocols for structure mapping, mapping data to constrain or restrain RNA secondary structure prediction with RNAstructure, unassigned NMR resonances, modeling protocols for Rosetta FARFAR, RNAComposer , ModeRNA, and MC-Fold. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and Practical, RNA Structure Determination: Methods and Protocols aims to ensure successful results in the further study of this vital field.
Download or read book Analysis of Non coding RNA Sequence Structure and Function Using Comparative Transcriptomics and Biophysics Approaches written by Alberto Lopez Ezquerra and published by . This book was released on 2020 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Biological Sequence Analysis written by Richard Durbin and published by Cambridge University Press. This book was released on 1998-04-23 with total page 372 pages. Available in PDF, EPUB and Kindle. Book excerpt: Probabilistic models are becoming increasingly important in analysing the huge amount of data being produced by large-scale DNA-sequencing efforts such as the Human Genome Project. For example, hidden Markov models are used for analysing biological sequences, linguistic-grammar-based probabilistic models for identifying RNA secondary structure, and probabilistic evolutionary models for inferring phylogenies of sequences from different organisms. This book gives a unified, up-to-date and self-contained account, with a Bayesian slant, of such methods, and more generally to probabilistic methods of sequence analysis. Written by an interdisciplinary team of authors, it aims to be accessible to molecular biologists, computer scientists, and mathematicians with no formal knowledge of the other fields, and at the same time present the state-of-the-art in this new and highly important field.
Download or read book Non Protein Coding RNAs written by Nils Walter and published by Springer Science & Business Media. This book was released on 2008-11-18 with total page 400 pages. Available in PDF, EPUB and Kindle. Book excerpt: The 2006 Nobel Prize in Physiology or Medicine was awarded to the discoverers of RNA interference, Andrew Fire and Craig Mello. This prize, which follows “RNA” Nobels for splicing and RNA catalysis, highlights just one class of recently discovered non-protein coding RNAs. Remarkably, non-coding RNAs are thought to outnumber protein coding genes in mammals by perhaps as much as four-fold. In fact, it appears that the complexity of an organism correlates with the fraction of its genome devoted to non-protein coding RNAs. Essential biological processes as diverse as cell differentiation, suppression of infecting viruses and parasitic tra- posons, higher-level organization of eukaryotic chromosomes, and gene expression are found to be largely directed by non-protein coding RNAs. Currently, bioinformatic, high-throughput sequencing, and biochemical approaches are identifying an increasing number of these RNAs. Unfortunately, our ability to characterize the molecular details of these RNAs is significantly lacking. The biophysical study of these RNAs is an emergent field that is unraveling the molecular underpinnings of how RNA fulfills its multitude of roles in sustaining cellular life. The resulting understanding of the physical and chemical processes at the molecular level is critical to our ability to harness RNA for use in biotechnology and human therapy, a prospect that has recently spawned a multi-billion dollar industry.
Download or read book Handbook of RNA Biochemistry written by Roland K. Hartmann and published by John Wiley & Sons. This book was released on 2015-06-22 with total page 1370 pages. Available in PDF, EPUB and Kindle. Book excerpt: The second edition of a highly acclaimed handbook and ready reference. Unmatched in its breadth and quality, around 100 specialists from all over the world share their up-to-date expertise and experiences, including hundreds of protocols, complete with explanations, and hitherto unpublished troubleshooting hints. They cover all modern techniques for the handling, analysis and modification of RNAs and their complexes with proteins. Throughout, they bear the practising bench scientist in mind, providing quick and reliable access to a plethora of solutions for practical questions of RNA research, ranging from simple to highly complex. This broad scope allows the treatment of specialized methods side by side with basic biochemical techniques, making the book a real treasure trove for every researcher experimenting with RNA.
Download or read book Computer Assisted Modeling written by National Research Council and published by National Academies Press. This book was released on 1987-02-01 with total page 186 pages. Available in PDF, EPUB and Kindle. Book excerpt: In much of biology, the search for understanding the relation between structure and function is now taking place at the macromolecular level. Proteins, nucleic acids, and polysaccharides are macromolecule--polymers formed from families of simpler subunits. Because of their size and complexity, the polymers are capable of both inter- and intramolecular interactions. These interactions confer upon the polymers distinctive three-dimensional shapes. These tertiary configurations, in turn, determine the function of the macromolecule. Computers have become so inextricably involved in empirical studies of three-dimensional macromolecular structure that mathematical modeling, or theory, and experimental approaches are interrelated aspects of a single enterprise.
Download or read book RNA Sequence Classification Using Secondary Structure Fingerprints Sequence Based Features and Deep Learning written by Kevin Sutanto and published by . This book was released on 2021 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: RNAs are involved in different facets of biological processes; including but not limited to controlling and inhibiting gene expressions, enabling transcription and translation from DNA to proteins, in processes involving diseases such as cancer, and virus-host interactions. As such, there are useful applications that may arise from studies and analyses involving RNAs, such as detecting cancer by measuring the abundance of specific RNAs, detecting and identifying infections involving RNA viruses, identifying the origins of and relationships between RNA viruses, and identifying potential targets when designing novel drugs. Extracting sequences from RNA samples is usually not a major limitation anymore thanks to sequencing technologies such as RNA-Seq. However, accurately identifying and analyzing the extracted sequences is often still the bottleneck when it comes to developing RNA-based applications. Like proteins, functional RNAs are able to fold into complex structures in order to perform specific functions throughout their lifecycle. This suggests that structural information can be used to identify or classify RNA sequences, in addition to the sequence information of the RNA itself. Furthermore, a strand of RNA may have more than one possible structural conformations it can fold into, and it is also possible for a strand to form different structures in vivo and in vitro. However, past studies that utilized secondary structure information for RNA identification purposes have relied on one predicted secondary structure for each RNA sequence, despite the possible one-to-many relationship between a strand of RNA and the possible secondary structures. Therefore, we hypothesized that using a representation that includes the multiple possible secondary structures of an RNA for classification purposes may improve the classification performance. We proposed and built a pipeline that produces secondary structure fingerprints given a sequence of RNA, that takes into account the aforementioned multiple possible secondary structures for a single RNA. Using this pipeline, we explored and developed different types of secondary structure fingerprints in our studies. A type of fingerprints serves as high-level topological representations of the RNA structure, while another type represents matches with common known RNA secondary structure motifs we have curated from databases and the literature. Next, to test our hypothesis, the different fingerprints are then used with deep learning and with different datasets, alone and together with various sequence-based features, to investigate how the secondary structure fingerprints affect the classification performance. Finally, by analyzing our findings, we also propose approaches that can be adopted by future studies to further improve our secondary structure fingerprints and classification performance.
Download or read book RNA Folding written by Christina Waldsich and published by Humana. This book was released on 2016-08-23 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: Focusing on in vitro and intracellular RNA structure formation, RNA Folding: Methods and Protocols provides a comprehensive collection of experimental protocols which are suitable to dissect RNA folding pathways and to characterize the structure of RNA folding intermediates at nucleotide or even atomic resolution. The presented techniques include powerful tools with a long tradition in RNA research as well as more advanced, novel methods, thus the methods span multiple disciplines, including molecular biology, biochemistry, biophysics, and computational biology. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Practical and authoritative, RNA Folding: Methods and Protocols serves as a vital reference for researchers attempting to gain insights into the secrets of this astounding macromolecule.
Download or read book Biophysics of RNA Folding written by Rick Russell and published by Springer Science & Business Media. This book was released on 2012-12-09 with total page 238 pages. Available in PDF, EPUB and Kindle. Book excerpt: This volume, written by experts in the field, discusses the current understanding of the biophysical principles that govern RNA folding, with featured RNAs including the ribosomal RNAs, viral RNAs, and self-splicing introns. In addition to the fundamental features of RNA folding, the central experimental and computational approaches in the field are presented with an emphasis on their individual strengths and limitations, and how they can be combined to be more powerful than any method alone; these approaches include NMR, single molecule fluorescence, site-directed spin labeling, structure mapping, comparative sequence analysis, graph theory, course-grained 3D modeling, and more. This volume will be of interest to professional researchers and advanced students entering the field of RNA folding.
Download or read book RNA Structure and Function written by Jan Barciszewski and published by Springer Nature. This book was released on 2023-12-05 with total page 662 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book focuses on the current status of our understanding of RNA, a key biological molecule. The various RNAs covered are messenger RNA, ribosomal RNA, transfer RNA, noncoding RNAs, modified nucleosides, and RNA enzymes. The different chapters detail methods to investigate RNA structure and function, the chemistry of modified RNAs, and the latest advances in our understanding of the vast array of biological processes in which RNA is involved. RNA, in one form or another, touches almost everything in a cell. RNA has both structural and catalytic properties. RNA fulfills a broad range of functions. These molecules are no longer seen as passive elements transferring the genetic information from DNA into proteins but regulate the activity of genes during development, cellular differentiation, and changing environments. RNAs are involved in various aspects of cell physiology and disease development. Discoveries of RNA with unexpected diverse functions in healthy and diseased cells, such as the role of RNA as both the source and countermeasure to cancer or severe viral infection, stimulate new trends, passion, and solutions for molecular medicine. In this book, fundamental questions about the biochemical and genetic importance of RNA, how mRNAs are generated and used to produce proteins, how noncoding and catalytic RNAs mediate key cellular processes, how to determine RNA structure and how to apply RNA in treatment of diseases. This book is an essential resource for researches in academia and industry contributing to the development of new RNA therapeutics. The book is geared toward scientists from the graduate level on up and particularly appeals to active investigators in RNA biology, molecular biology, and biochemistry.
Download or read book The Importance of Rna Sequence and Structure in the Assembly and Function of Signal Recognition Particle written by David Alan Selinger and published by . This book was released on 1993 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt:
