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Author: Shaojie Zhang Publisher: ISBN: Category : Languages : en Pages : 108
Book Description
The discovery of novel non-coding RNAs has been among the most exciting recent developments in Biology, yet, many more remain undiscovered. It has been hypothesized that there is in fact an abundance of functional non-coding RNAs (ncRNAs) with various catalytic and regulatory functions. Computational methods tailored specifically for ncRNA discovery are being actively developed. As the inherent signal for ncRNA is weaker than that for protein coding genes, comparative methods offer the most promising approach. In this dissertation, we address several open issues and problems on computational methods for genome wide non-coding RNA discovery and analysis: (1) We first consider the following problem: Given an RNA sequence with a known secondary structure, efficiently detect all structural homologs in a genomic database by computing the sequence and structure similarity to the query. Our approach, based on structural filters that eliminate a large portion of the database, while retaining the true homologs, allows us to search a typical bacterial genome in minutes on a standard PC. This results is two orders of magnitude better than currently available software for the problem. (2) We formalize the concept of a filter and provide figures of merit that allow comparison between filters. We design efficient sequence based filters that dominate the current state-of-the-art HMM filters. We provide a new formulation of the covariance model that allows speeding up RNA alignment. We demonstrate the power of our approach on both synthetic data and real bacterial genomes. We then apply our algorithm to the detection of novel riboswitch elements from the whole bacterial and archaeal genomes and environmental sequence data. Our results point to a number of novel riboswitch candidates, and include genomes that were not previously known to contain riboswitches. (3) We propose a novel framework to predict the common secondary structure for unaligned RNA sequences. By matching putative stacks in RNA sequences, we make use of both primary sequence information and thermodynamic stability for prediction at the same time. We show that our method can predict the correct common RNA secondary structures even when we are only given a limited number of unaligned RNA sequences, and it outperforms current algorithms in sensitivity and accuracy. Together these contributions made efforts toward genome wide ncRNA discovery for exploring the modern RNA world.
Author: Shaojie Zhang Publisher: ISBN: Category : Languages : en Pages : 108
Book Description
The discovery of novel non-coding RNAs has been among the most exciting recent developments in Biology, yet, many more remain undiscovered. It has been hypothesized that there is in fact an abundance of functional non-coding RNAs (ncRNAs) with various catalytic and regulatory functions. Computational methods tailored specifically for ncRNA discovery are being actively developed. As the inherent signal for ncRNA is weaker than that for protein coding genes, comparative methods offer the most promising approach. In this dissertation, we address several open issues and problems on computational methods for genome wide non-coding RNA discovery and analysis: (1) We first consider the following problem: Given an RNA sequence with a known secondary structure, efficiently detect all structural homologs in a genomic database by computing the sequence and structure similarity to the query. Our approach, based on structural filters that eliminate a large portion of the database, while retaining the true homologs, allows us to search a typical bacterial genome in minutes on a standard PC. This results is two orders of magnitude better than currently available software for the problem. (2) We formalize the concept of a filter and provide figures of merit that allow comparison between filters. We design efficient sequence based filters that dominate the current state-of-the-art HMM filters. We provide a new formulation of the covariance model that allows speeding up RNA alignment. We demonstrate the power of our approach on both synthetic data and real bacterial genomes. We then apply our algorithm to the detection of novel riboswitch elements from the whole bacterial and archaeal genomes and environmental sequence data. Our results point to a number of novel riboswitch candidates, and include genomes that were not previously known to contain riboswitches. (3) We propose a novel framework to predict the common secondary structure for unaligned RNA sequences. By matching putative stacks in RNA sequences, we make use of both primary sequence information and thermodynamic stability for prediction at the same time. We show that our method can predict the correct common RNA secondary structures even when we are only given a limited number of unaligned RNA sequences, and it outperforms current algorithms in sensitivity and accuracy. Together these contributions made efforts toward genome wide ncRNA discovery for exploring the modern RNA world.
Author: Cuncong Zhong Publisher: ISBN: Category : Languages : en Pages : 181
Book Description
These novel algorithms have led to the discovery of many novel RNA structural motif instances, which have significantly deepened our understanding to the RNA molecular functions. The genome-wide clustering of ncRNA elements in fly 3'-UTR has predicted a cluster of genes that are responsible for the spermatogenesis process. More importantly, these genes are very likely to be co-regulated by their common 3'-UTR elements. We anticipate that these algorithms and the corresponding software tools will significantly promote the comparative ncRNA research in the future.
Author: Yun Zheng Publisher: Academic Press ISBN: 0128143665 Category : Science Languages : en Pages : 320
Book Description
Computational Non-coding RNA Biology is a resource for the computation of non-coding RNAs. The book covers computational methods for the identification and quantification of non-coding RNAs, including miRNAs, tasiRNAs, phasiRNAs, lariat originated circRNAs and back-spliced circRNAs, the identification of miRNA/siRNA targets, and the identification of mutations and editing sites in miRNAs. The book introduces basic ideas of computational methods, along with their detailed computational steps, a critical component in the development of high throughput sequencing technologies for identifying different classes of non-coding RNAs and predicting the possible functions of these molecules. Finding, quantifying, and visualizing non-coding RNAs from high throughput sequencing datasets at high volume is complex. Therefore, it is usually possible for biologists to complete all of the necessary steps for analysis. Presents a comprehensive resource of computational methods for the identification and quantification of non-coding RNAs Introduces 23 practical computational pipelines for various topics of non-coding RNAs Provides a guide to assist biologists and other researchers dealing with complex datasets Introduces basic computational methods and provides guidelines for their replication by researchers Offers a solution to researchers approaching large and complex sequencing datasets
Author: Ping Ge Publisher: ISBN: Category : Languages : en Pages : 116
Book Description
This approach can avoid the time-consuming base pair matching in the secondary structure alignment. The application of ProbeAlign to the FragSeq datasets shows its capability of genome-wide ncRNAs analysis. For RNA tertiary structure analysis, we rst developed a computational tool, named STAR3D, to nd the global conservation in RNA 3D structures. STAR3D aims at nding the consensus of stacks by using 2D topology and 3D geometry together. Then, the loop regions can be ordered and aligned according to their relative positions in the consensus. This stackguided alignment method adopts the divide-and-conquer strategy into RNA 3D structural alignment, which has improved its e ciency dramatically. Furthermore, we also have clustered all loop regions in non-redundant RNA 3D structures to de novo detect plausible RNA structural motifs. The computational pipeline, named RNAMSC, was extended to handle large-scale PDB datasets, and solid downstream analysis was performed to ensure the clustering results are valid and easily to be applied to further research. The nal results contain many interesting variations of known motifs, such as GNAA tetraloop, kink-turn, sarcinricin and t-loops. We also discovered novel functional motifs that conserved in a wide range of ncRNAs, including ribosomal RNA, sgRNA, SRP RNA, GlmS riboswitch and twister ribozyme.
Author: Francisco A. Gómez Vela Publisher: MDPI ISBN: 3039437712 Category : Medical Languages : en Pages : 222
Book Description
In recent decades, new technologies have made remarkable progress in helping to understand biological systems. Rapid advances in genomic profiling techniques such as microarrays or high-performance sequencing have brought new opportunities and challenges in the fields of computational biology and bioinformatics. Such genetic sequencing techniques allow large amounts of data to be produced, whose analysis and cross-integration could provide a complete view of organisms. As a result, it is necessary to develop new techniques and algorithms that carry out an analysis of these data with reliability and efficiency. This Special Issue collected the latest advances in the field of computational methods for the analysis of gene expression data, and, in particular, the modeling of biological processes. Here we present eleven works selected to be published in this Special Issue due to their interest, quality, and originality.
Author: Xin Lai Publisher: Humana Press ISBN: 9781493989812 Category : Science Languages : en Pages : 390
Book Description
This volume details a collection of state-of-art methods including identification of novel ncRNAs and their targets, functional annotation and disease association in different biological contexts. Chapters guide readers through an overview of disease-specific ncRNAs, computational methods and workflows for ncRNA discovery, annotation based on high-throughput sequencing data, bioinformatics tools and databases for ncRNA analyses, network-based methods, and kinetic modelling of ncRNA-mediated gene regulation. 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 cutting-edge, Computational Biology of Non-Coding RNA: Methods and Protocols aims to provide a state-of-the-art collection of computational methods and approaches that will be of value to researchers interested in ncRNA field.
Author: Cyriac Kandoth Publisher: ISBN: Category : DNA Languages : en Pages : 126
Book Description
"The need for automating genome analysis is a result of the tremendous amount of genomic data. As of today, a high-throughput DNA sequencing machine can run millions of sequencing reactions in parallel, and it is becoming faster and cheaper to sequence the entire genome of an organism. Public databases containing genomic data are growing exponentially, and hence the rise in demand for intuitive automated methods of DNA analysis and subsequent gene identification. However, the complexity of gene organization makes automation a challenging task, and smart algorithm design and parallelization are necessary to perform accurate analyses in reasonable amounts of time. This work describes two such automated methods for the identification of novel genes within given DNA sequences. The first method utilizes negative selection patterns as an evolutionary rationale for the identification of additional members of a gene family. As input it requires a known protein coding gene in that family. The second method is a massively parallel data mining algorithm that searches a whole genome for inverted repeats (palindromic sequences) and identifies potential precursors of non-coding RNA genes. Both methods were validated successfully on the fully sequenced and well studied plant species, Arabidopsis thaliana"--Abstract, leaf iv.
Author: Ning Yu Publisher: ISBN: Category : Languages : en Pages : 52
Book Description
The purpose of researching bacterial gene expression is to control and prevent the diseases which are caused by bacteria. Recently researchers discovered small non-coding RNAs (ncRNA/sRNA) perform a variety of critical regulatory functions in bacteria. The genome-wide searching for sRNAs, especially the computational method, has become an effective way to predict the small non-coding RNAs because sRNAs have the consistent sequence characteristics. This article proposes a hybrid computational approach, HybridRNA, for the prediction of small non-coding RNAs, which integrates three critical techniques, including secondary structural algorithm, thermo-dynamic stability analysis and sequence conservation prediction. Relying on these computational techniques, our approach was used to search for sRNAs in Streptococcus pyogenes which is one of the most important bacteria for human health. This search led five strongest candidates of sRNA to be predicted as the key components of known regulatory pathways in S. pyogens.
Author: Julia A. Chekanova Publisher: Humana Press ISBN: 9781493990443 Category : Science Languages : en Pages : 480
Book Description
This volume focuses on various approaches to studying long non-coding RNAs (lncRNAs), including techniques for finding lncRNAs, localization, and observing their functions. The chapters in this book cover how to catalog lncRNAs in various plant species; determining subcellular localization; protein interactions; structures; and RNA modifications. 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. Cutting-edge and innovative, Plant Long Non-Coding RNAs: Methods and Protocols is a valuable resource that aids researchers in understanding the functions of lncRNAs in different plant species, and helps them explore currently uncharted facets of plant biology.
Author: Santosh Kumar Upadhyay Publisher: Academic Press ISBN: 0128214635 Category : Science Languages : en Pages : 390
Book Description
The growth of human population has increased the demand for improved yield and quality of crops and horticultural plants. However, plant productivity continues to be threatened by stresses such as heat, cold, drought, heavy metals, UV radiations, bacterial and fungal pathogens, and insect pests. Long noncoding RNAs are associated with various developmental pathways, regulatory systems, abiotic and biotic stress responses and signaling, and can provide an alternative strategy for stress management in plants. Long Noncoding RNAs in Plants: Roles in development and stress provides the most recent advances in LncRNAs, including identification, characterization, and their potential applications and uses. Introductory chapters include the basic features and brief history of development of lncRNAs studies in plants. The book then provides the knowledge about the lncRNAs in various important agricultural and horticultural crops such as cereals, legumes, fruits, vegetables, and fiber crop cotton, and their roles and applications in abiotic and biotic stress management. Includes the latest advances and research in long noncoding RNAs in plants Provides alternative strategies for abiotic and biotic stress management in horticultural plants and agricultural crops Focuses on the application and uses of long noncoding RNAs