Download or read book Finding Conserved Patterns in Biological Sequences Networks and Genomes written by Qingwu Yang and published by . This book was released on 2010 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: Biological patterns are widely used for identifying biologically interesting regions within macromolecules, classifying biological objects, predicting functions and studying evolution. Good pattern finding algorithms will help biologists to formulate and validate hypotheses in an attempt to obtain important insights into the complex mechanisms of living things. In this dissertation, we aim to improve and develop algorithms for five biological pattern finding problems. For the multiple sequence alignment problem, we propose an alternative formulation in which a final alignment is obtained by preserving pairwise alignments specified by edges of a given tree. In contrast with traditional NPhard formulations, our preserving alignment formulation can be solved in polynomial time without using a heuristic, while having very good accuracy. For the path matching problem, we take advantage of the linearity of the query path to reduce the problem to finding a longest weighted path in a directed acyclic graph. We can find k paths with top scores in a network from the query path in polynomial time. As many biological pathways are not linear, our graph matching approach allows a non-linear graph query to be given. Our graph matching formulation overcomes the common weakness of previous approaches that there is no guarantee on the quality of the results. For the gene cluster finding problem, we investigate a formulation based on constraining the overall size of a cluster and develop statistical significance estimates that allow direct comparisons of clusters of different sizes. We explore both a restricted version which requires that orthologous genes are strictly ordered within each cluster, and the unrestricted problem that allows paralogous genes within a genome and clusters that may not appear in every genome. We solve the first problem in polynomial time and develop practical exact algorithms for the second one. In the gene cluster querying problem, based on a querying strategy, we propose an efficient approach for investigating clustering of related genes across multiple genomes for a given gene cluster. By analyzing gene clustering in 400 bacterial genomes, we show that our algorithm is efficient enough to study gene clusters across hundreds of genomes.
Download or read book Advances in Genomic Sequence Analysis and Pattern Discovery written by Laura Elnitski and published by World Scientific. This book was released on 2011 with total page 236 pages. Available in PDF, EPUB and Kindle. Book excerpt: Mapping the genomic landscapes is one of the most exciting frontiers of science. We have the opportunity to reverse engineer the blueprints and the control systems of living organisms. Computational tools are key enablers in the deciphering process. This book provides an in-depth presentation of some of the important computational biology approaches to genomic sequence analysis. The first section of the book discusses methods for discovering patterns in DNA and RNA. This is followed by the second section that reflects on methods in various ways, including performance, usage and paradigms.
Download or read book Discriminative Pattern Discovery on Biological Networks written by Fabio Fassetti and published by Springer. This book was released on 2017-09-01 with total page 51 pages. Available in PDF, EPUB and Kindle. Book excerpt: This work provides a review of biological networks as a model for analysis, presenting and discussing a number of illuminating analyses. Biological networks are an effective model for providing insights about biological mechanisms. Networks with different characteristics are employed for representing different scenarios. This powerful model allows analysts to perform many kinds of analyses which can be mined to provide interesting information about underlying biological behaviors. The text also covers techniques for discovering exceptional patterns, such as a pattern accounting for local similarities and also collaborative effects involving interactions between multiple actors (for example genes). Among these exceptional patterns, of particular interest are discriminative patterns, namely those which are able to discriminate between two input populations (for example healthy/unhealthy samples). In addition, the work includes a discussion on the most recent proposal on discovering discriminative patterns, in which there is a labeled network for each sample, resulting in a database of networks representing a sample set. This enables the analyst to achieve a much finer analysis than with traditional techniques, which are only able to consider an aggregated network of each population.
Download or read book Introduction to Evolutionary Genomics written by Naruya Saitou and published by Springer Science & Business Media. This book was released on 2014-01-22 with total page 476 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book is the first of its kind to explain the fundamentals of evolutionary genomics. The comprehensive coverage includes concise descriptions of a variety of genome organizations, a thorough discussion of the methods used, and a detailed review of genome sequence processing procedures. The opening chapters also provide the necessary basics for readers unfamiliar with evolutionary studies. Features: introduces the basics of molecular biology, DNA replication, mutation, phylogeny, neutral evolution, and natural selection; presents a brief evolutionary history of life from the primordial seas to the emergence of humans; describes the genomes of prokaryotes, eukaryotes, vertebrates, and humans; reviews methods for genome sequencing, phenotype data collection, homology searches and analysis, and phylogenetic tree and network building; discusses databases of genome sequences and related information, evolutionary distances, and population genomics; provides supplementary material at an associated website.
Download or read book Selected Topics In Post genome Knowledge Discovery written by Limsoon Wong and published by World Scientific. This book was released on 2004-06-11 with total page 176 pages. Available in PDF, EPUB and Kindle. Book excerpt: The Institute for Mathematical Sciences at the National University of Singapore organized a program on “Post-Genome Knowledge Discovery” from January to June 2002. The program focused on the computational and statistical analysis of sequences and genetics, and the mathematical modeling of complex biological interactions, which are critical to the accurate annotation of genomic sequences, the study of the interplay between genes and proteins, and the study of the genetic variability of species. As part of the program, tutorials for graduate students and newcomers to this transdisciplinary area of research were given by experts in these fields.This important volume collects the expanded notes of some of the tutorials that were given during the program. The topics include comparison and alignment of biological sequences, modeling and analysis of biological pathways, data mining and knowledge discovery from biological and clinical data.
Download or read book Algorithms in Computational Molecular Biology written by Mourad Elloumi and published by John Wiley & Sons. This book was released on 2011-04-04 with total page 1027 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book represents the most comprehensive and up-to-date collection of information on the topic of computational molecular biology. Bringing the most recent research into the forefront of discussion, Algorithms in Computational Molecular Biology studies the most important and useful algorithms currently being used in the field, and provides related problems. It also succeeds where other titles have failed, in offering a wide range of information from the introductory fundamentals right up to the latest, most advanced levels of study.
Download or read book Evolutionary Computing Strategies for the Detection of Conserved Patterns in Genomic DNA written by Robert G. Beiko and published by . This book was released on 2003 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: The detection of regulatory sequences in DNA is a challenging problem, especially when considered in the context of whole genomes. The degree of sequence conservation of regulatory protein binding sites is often weak, and the sites are obscured by surrounding intergenic sequence. Since structural interactions are vital for protein-DNA interactions, structural representations of regulatory sites can yield a more accurate model and a better understanding of within-site variability. However, the use of multiple alternative representations of DNA introduces a requirement for novel algorithms that can create and test different combinations of DNA features. The Genetic Algorithm Neural Network (GANN) was designed to identify combinations of patterns that can be used to distinguish between different classes of training sequence. GANN trains a set of artificial neural networks to classify sets of sequence using either backpropagation or a genetic algorithm, and uses an 'outer genetic algorithm' to choose the best inputs from a pool of DNA features that can include sequence, structure, and weight matrix representations. When trained with a subset of upstream sequences from a whole genome, GANN was able to detect patterns such as the Shine-Dalgarno sequence in Escherichia coli K12, and sequences consistent with archaeal promoters in the archaeon Sulfolobus solfataricus P2. The Motif Genetic Algorithm (MGA) constructs motif representations by concatenating minimal units of DNA sequence and structure. This algorithm was used to model conserved patterns in DNA, including the binding sites for E. coli cyclic AMP activated protein (CAP), integration host factor (IHF), and two different promoter types recognized by alternative bacterial sigma factors. The CAP models were used to detect other putative binding sites in upstream regions of the E. coli K12 genome, while attempts to train an accurate model of IHF binding sites revealed an important role for structural representations in motif modeling.
Download or read book Regulatory Genomics Proceedings Of The 3rd Annual Recomb Workshop written by Hon Wai Leong and published by World Scientific. This book was released on 2008-07-07 with total page 145 pages. Available in PDF, EPUB and Kindle. Book excerpt: Research in the field of gene regulation is evolving rapidly in the ever-changing scientific environment. Advances in microarray techniques and comparative genomics have enabled more comprehensive studies of regulatory genomics. The study of genomic binding locations of transcription factors has enabled a more comprehensive modeling of regulatory networks. In addition, complete genomic sequences and comparison of numerous related species have demonstrated the conservation of non-coding DNA sequences, which often provide evidence for cis-regulatory binding sites. Systematic methods to decipher the regulatory mechanism are also crucial for corroborating these regulatory networks; key to these methods are motif discovery algorithms that can help predict cis-regulatory elements. These DNA-motif discovery programs are becoming more sophisticated and are beginning to leverage evidence from comparative genomics. These topics and more were discussed at the 3rd Annual RECOMB Workshop on Regulatory Genomics, which brought together more than 90 attendees and included about 22 excellent talks from leading researchers in the field. This proceedings volume contains ten selected, original manuscripts that were presented during the workshop./a
Download or read book Sequence Evolution Function written by Eugene V. Koonin and published by Springer Science & Business Media. This book was released on 2013-06-29 with total page 482 pages. Available in PDF, EPUB and Kindle. Book excerpt: Sequence - Evolution - Function is an introduction to the computational approaches that play a critical role in the emerging new branch of biology known as functional genomics. The book provides the reader with an understanding of the principles and approaches of functional genomics and of the potential and limitations of computational and experimental approaches to genome analysis. Sequence - Evolution - Function should help bridge the "digital divide" between biologists and computer scientists, allowing biologists to better grasp the peculiarities of the emerging field of Genome Biology and to learn how to benefit from the enormous amount of sequence data available in the public databases. The book is non-technical with respect to the computer methods for genome analysis and discusses these methods from the user's viewpoint, without addressing mathematical and algorithmic details. Prior practical familiarity with the basic methods for sequence analysis is a major advantage, but a reader without such experience will be able to use the book as an introduction to these methods. This book is perfect for introductory level courses in computational methods for comparative and functional genomics.
Download or read book Repetitive Structures in Biological Sequences Algorithms and Applications written by Marco Pellegrini and published by Frontiers Media SA. This book was released on 2016-10-27 with total page 95 pages. Available in PDF, EPUB and Kindle. Book excerpt: Repetitive structures in biological sequences are emerging as an active focus of research and the unifying concept of "repeatome" (the ensemble of knowledge associated with repeating structures in genomic/proteomic sequences) has been recently proposed in order to highlight several converging trends. One main trend is the ongoing discovery that genomic repetitions are linked to many biological significant events and functions. Diseases (e.g. Huntington's disease) have been causally linked with abnormal expansion of certain repeating sequences in the human genome. Deletions or multiple copy duplications of genes (Copy Number Variations) are important in the aetiology of cancer, Alzheimer, and Parkinson diseases. A second converging trend has been the emergence of many different models and algorithms for detecting non-obvious repeating patterns in strings with applications to in genomic data. Borrowing methodologies from combinatorial pattern, matching, string algorithms, data structures, data mining and machine learning these new approaches break the limitations of the current approaches and offer a new way to design better trans-disciplinary research. The articles collected in this book provides a glance into the rich emerging area of repeatome research, addressing some of its pressing challenges. We believe that these contributions are valuable resources for repeatome research and will stimulate further research from bioinformatic, statistical, and biological points of view.
Download or read book Probabilistic Approaches in Comparative Analysis of Biological Networks and Sequences written by Sayed Sahraeian and published by . This book was released on 2013 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: Comparative analysis of genomic data investigates the relationship of genome structure and function across different biological species to shed light on their similarities and differences. In this dissertation, we study two important problems in comparative genomics, namely comparative sequence analysis and comparative network analysis. In the comparative sequence analysis, we study the multiple sequence alignment of protein and DNA sequences as well as the structural alignment of multiple RNA sequences. For closely related sequences, multiple sequence alignment can be efficiently performed through progressive techniques. However, for divergent sequences it is very challenging to predict an accurate alignment. Here, we introduce PicXAA, an efficient non-progressive technique for multiple protein and DNA sequence alignment. We also further extend PicXAA to PicXAA-R for structural alignment of RNA sequences. PicXAA and PicXAA-R greedily build up the alignment from sequence regions with high local similarity, thereby yielding an accurate global alignment that effectively captures local similarities among sequences. As another important research area in comparative genomics, we also investigate the comparative network analysis problem. Translation of increasing number of large-scale biological networks into meaningful biological insights requires efficient computational techniques. One such example is network querying, which aims to identify subnetwork regions in a large target network that are similar to a given query network. Here, we introduce an efficient algorithm for querying large-scale biological networks, called RESQUE. RESQUE adopts a semi-Markov random walk model to probabilistically estimate the correspondence scores between nodes that belong to different networks. The target network is iteratively reduced based on the estimated correspondence scores until the best matching subnetwork emerges. The proposed network querying scheme is computationally efficient, can handle any network query with an arbitrary topology, and yields accurate querying results. We also extend the idea used in RESQUE to develop an efficient algorithm for alignment of multiple large-scale biological networks, called SMETANA. SMETANA outperforms state-of- the-art network alignment techniques, in terms of both computational efficiency and alignment accuracy. The accomplished studies have enabled us to provide a coherent framework for probabilistic approach to comparative analysis of biological sequences and networks. Such a probabilistic framework helps us employ rigorous mathematical schemes to find accurate and efficient solutions to these problems. The electronic version of this dissertation is accessible from http://hdl.handle.net/1969.1/149225
Download or read book Dissertation Abstracts International written by and published by . This book was released on 2009 with total page 840 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Pattern Recognition in Bioinformatics written by Jagath C. Rajapakse and published by Springer. This book was released on 2006-09-30 with total page 197 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book constitutes the refereed proceedings of the International Workshop on Pattern Recognition in Bioinformatics, PRIB 2006, held in Hong Kong, within the scope of the 18th International Conference on Pattern Recognition, ICPR 2006. The book presents 19 revised full papers, covering all topics of the creation and maintenance of biological databases, and the discovery of knowledge from life sciences data. Includes an introduction to Pattern Recognition in Bioinformatics.
Download or read book Bioinformatics of Genome Regulation and Structure written by Nikolay Kolchanov and published by Springer Science & Business Media. This book was released on 2013-06-05 with total page 373 pages. Available in PDF, EPUB and Kindle. Book excerpt: - The data gathered can be used to solve a wide range of problems - for basic science and applied science
Download or read book Systems Biology for Signaling Networks written by Sangdun Choi and published by Springer Science & Business Media. This book was released on 2010-08-09 with total page 900 pages. Available in PDF, EPUB and Kindle. Book excerpt: System Biology encompasses the knowledge from diverse fields such as Molecular Biology, Immunology, Genetics, Computational Biology, Mathematical Biology, etc. not only to address key questions that are not answerable by individual fields alone, but also to help in our understanding of the complexities of biological systems. Whole genome expression studies have provided us the means of studying the expression of thousands of genes under a particular condition and this technique had been widely used to find out the role of key macromolecules that are involved in biological signaling pathways. However, making sense of the underlying complexity is only possible if we interconnect various signaling pathways into human and computer readable network maps. These maps can then be used to classify and study individual components involved in a particular phenomenon. Apart from transcriptomics, several individual gene studies have resulted in adding to our knowledge of key components that are involved in a signaling pathway. It therefore becomes imperative to take into account of these studies also, while constructing our network maps to highlight the interconnectedness of the entire signaling pathways and the role of that particular individual protein in the pathway. This collection of articles will contain a collection of pioneering work done by scientists working in regulatory signaling networks and the use of large scale gene expression and omics data. The distinctive features of this book would be: Act a single source of information to understand the various components of different signaling network (roadmap of biochemical pathways, the nature of a molecule of interest in a particular pathway, etc.), Serve as a platform to highlight the key findings in this highly volatile and evolving field, and Provide answers to various techniques both related to microarray and cell signaling to the readers.
Download or read book Analysis of Genomic and Proteomic Sequences Using DSP Techniques written by Raja Sekhar Kakumani and published by . This book was released on 2013 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Mapping and Sequencing the Human Genome written by National Research Council and published by National Academies Press. This book was released on 1988-01-01 with total page 128 pages. Available in PDF, EPUB and Kindle. Book excerpt: There is growing enthusiasm in the scientific community about the prospect of mapping and sequencing the human genome, a monumental project that will have far-reaching consequences for medicine, biology, technology, and other fields. But how will such an effort be organized and funded? How will we develop the new technologies that are needed? What new legal, social, and ethical questions will be raised? Mapping and Sequencing the Human Genome is a blueprint for this proposed project. The authors offer a highly readable explanation of the technical aspects of genetic mapping and sequencing, and they recommend specific interim and long-range research goals, organizational strategies, and funding levels. They also outline some of the legal and social questions that might arise and urge their early consideration by policymakers.
