Protein Homology Detection Through Alignment Of Markov Random Fields

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Protein Homology Detection Through Alignment of Markov Random Fields

Author : Jinbo Xu
Publisher : Springer
ISBN 13 : 3319149148
Total Pages : 51 pages
Book Rating : 4.3/5 (191 download)

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Book Synopsis Protein Homology Detection Through Alignment of Markov Random Fields by : Jinbo Xu

Download or read book Protein Homology Detection Through Alignment of Markov Random Fields written by Jinbo Xu and published by Springer. This book was released on 2015-01-22 with total page 51 pages. Available in PDF, EPUB and Kindle. Book excerpt: This work covers sequence-based protein homology detection, a fundamental and challenging bioinformatics problem with a variety of real-world applications. The text first surveys a few popular homology detection methods, such as Position-Specific Scoring Matrix (PSSM) and Hidden Markov Model (HMM) based methods, and then describes a novel Markov Random Fields (MRF) based method developed by the authors. MRF-based methods are much more sensitive than HMM- and PSSM-based methods for remote homolog detection and fold recognition, as MRFs can model long-range residue-residue interaction. The text also describes the installation, usage and result interpretation of programs implementing the MRF-based method.

50 years of Statistical Physics in Mexico: Development, State of the Art and Perspectives

Author : Ramon Castañeda-Priego
Publisher : Frontiers Media SA
ISBN 13 : 2889712958
Total Pages : 213 pages
Book Rating : 4.8/5 (897 download)

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Book Synopsis 50 years of Statistical Physics in Mexico: Development, State of the Art and Perspectives by : Ramon Castañeda-Priego

Download or read book 50 years of Statistical Physics in Mexico: Development, State of the Art and Perspectives written by Ramon Castañeda-Priego and published by Frontiers Media SA. This book was released on 2021-09-13 with total page 213 pages. Available in PDF, EPUB and Kindle. Book excerpt:

Research in Computational Molecular Biology

Author : Roded Sharan
Publisher : Springer
ISBN 13 : 3319052691
Total Pages : 480 pages
Book Rating : 4.3/5 (19 download)

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Book Synopsis Research in Computational Molecular Biology by : Roded Sharan

Download or read book Research in Computational Molecular Biology written by Roded Sharan and published by Springer. This book was released on 2014-02-28 with total page 480 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book constitutes the refereed proceedings of the 18th Annual International Conference on Research in Computational Molecular Biology, RECOMB 2014, held in Pittsburgh, PA, USA, in April 2014. The 35 extended abstracts were carefully reviewed and selected from 154 submissions. They report on original research in all areas of computational molecular biology and bioinformatics.

Homology Modeling

Author : Sławomir Filipek
Publisher : Springer Nature
ISBN 13 : 1071629743
Total Pages : 379 pages
Book Rating : 4.0/5 (716 download)

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Book Synopsis Homology Modeling by : Sławomir Filipek

Download or read book Homology Modeling written by Sławomir Filipek and published by Springer Nature. This book was released on 2023-03-23 with total page 379 pages. Available in PDF, EPUB and Kindle. Book excerpt: This detailed volume provides state-of-the-art methodologies and reviews of important topics in the field of homology modeling. From homology modeling in the twilight zone and improving accuracy through sequence space analysis to approaches to construct multi-protein complex models, the book explores a wide variety of uses and applications of this valuable technique. Written for the highly successful Methods in Molecular Biology series, the chapters include introductions to their respective topics, lists of the necessary programs, webservers, and databases, step-by-step and readily reproducible protocols, as well as tips on troubleshooting and avoiding known pitfalls. Authoritative and practical, Homology Modeling: Methods and Protocols serves as an ideal guide to recent homology modeling procedures, assumptions made, and model quality assessment that will illuminate the black box of homology modeling for novice readers and broaden the knowledge of this methodology for professionals.

Research and Applications in Global Supercomputing

Author : Segall, Richard S.
Publisher : IGI Global
ISBN 13 : 1466674628
Total Pages : 696 pages
Book Rating : 4.4/5 (666 download)

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Book Synopsis Research and Applications in Global Supercomputing by : Segall, Richard S.

Download or read book Research and Applications in Global Supercomputing written by Segall, Richard S. and published by IGI Global. This book was released on 2015-01-31 with total page 696 pages. Available in PDF, EPUB and Kindle. Book excerpt: Rapidly generating and processing large amounts of data, supercomputers are currently at the leading edge of computing technologies. Supercomputers are employed in many different fields, establishing them as an integral part of the computational sciences. Research and Applications in Global Supercomputing investigates current and emerging research in the field, as well as the application of this technology to a variety of areas. Highlighting a broad range of concepts, this publication is a comprehensive reference source for professionals, researchers, students, and practitioners interested in the various topics pertaining to supercomputing and how this technology can be applied to solve problems in a multitude of disciplines.

Biotechnology: Concepts, Methodologies, Tools, and Applications

Author : Management Association, Information Resources
Publisher : IGI Global
ISBN 13 : 152258904X
Total Pages : 2183 pages
Book Rating : 4.5/5 (225 download)

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Book Synopsis Biotechnology: Concepts, Methodologies, Tools, and Applications by : Management Association, Information Resources

Download or read book Biotechnology: Concepts, Methodologies, Tools, and Applications written by Management Association, Information Resources and published by IGI Global. This book was released on 2019-06-07 with total page 2183 pages. Available in PDF, EPUB and Kindle. Book excerpt: Biotechnology can be defined as the manipulation of biological process, systems, and organisms in the production of various products. With applications in a number of fields such as biomedical, chemical, mechanical, and civil engineering, research on the development of biologically inspired materials is essential to further advancement. Biotechnology: Concepts, Methodologies, Tools, and Applications is a vital reference source for the latest research findings on the application of biotechnology in medicine, engineering, agriculture, food production, and other areas. It also examines the economic impacts of biotechnology use. Highlighting a range of topics such as pharmacogenomics, biomedical engineering, and bioinformatics, this multi-volume book is ideally designed for engineers, pharmacists, medical professionals, practitioners, academicians, and researchers interested in the applications of biotechnology.

Machine Learning and Knowledge Discovery in Databases

Author : Paolo Frasconi
Publisher : Springer
ISBN 13 : 331946227X
Total Pages : 825 pages
Book Rating : 4.3/5 (194 download)

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Book Synopsis Machine Learning and Knowledge Discovery in Databases by : Paolo Frasconi

Download or read book Machine Learning and Knowledge Discovery in Databases written by Paolo Frasconi and published by Springer. This book was released on 2016-09-03 with total page 825 pages. Available in PDF, EPUB and Kindle. Book excerpt: The three volume set LNAI 9851, LNAI 9852, and LNAI 9853 constitutes the refereed proceedings of the European Conference on Machine Learning and Knowledge Discovery in Databases, ECML PKDD 2016, held in Riva del Garda, Italy, in September 2016. The 123 full papers and 16 short papers presented were carefully reviewed and selected from a total of 460 submissions. The papers presented focus on practical and real-world studies of machine learning, knowledge discovery, data mining; innovative prototype implementations or mature systems that use machine learning techniques and knowledge discovery processes in a real setting; recent advances at the frontier of machine learning and data mining with other disciplines. Part I and Part II of the proceedings contain the full papers of the contributions presented in the scientific track and abstracts of the scientific plenary talks. Part III contains the full papers of the contributions presented in the industrial track, short papers describing demonstration, the nectar papers, and the abstracts of the industrial plenary talks.

Computational Phylogenetics

Author : Tandy Warnow
Publisher : Cambridge University Press
ISBN 13 : 1107184711
Total Pages : 399 pages
Book Rating : 4.1/5 (71 download)

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Book Synopsis Computational Phylogenetics by : Tandy Warnow

Download or read book Computational Phylogenetics written by Tandy Warnow and published by Cambridge University Press. This book was released on 2017-11-02 with total page 399 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book presents the foundations of phylogeny estimation and technical material enabling researchers to develop improved computational methods.

A Journey Through 50 Years of Structural Bioinformatics in Memoriam of Cyrus Chothia

Author : Alfredo Iacoangeli
Publisher : Frontiers Media SA
ISBN 13 : 2889747050
Total Pages : 131 pages
Book Rating : 4.8/5 (897 download)

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Book Synopsis A Journey Through 50 Years of Structural Bioinformatics in Memoriam of Cyrus Chothia by : Alfredo Iacoangeli

Download or read book A Journey Through 50 Years of Structural Bioinformatics in Memoriam of Cyrus Chothia written by Alfredo Iacoangeli and published by Frontiers Media SA. This book was released on 2022-08-16 with total page 131 pages. Available in PDF, EPUB and Kindle. Book excerpt: The cover image for this Research Topic was designed by Claire Marks.

Multiple Alignments, Hidden Markov Models and Svms

Author : Mohamad Firdaus Abdullah
Publisher : LAP Lambert Academic Publishing
ISBN 13 : 9783847331711
Total Pages : 164 pages
Book Rating : 4.3/5 (317 download)

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Book Synopsis Multiple Alignments, Hidden Markov Models and Svms by : Mohamad Firdaus Abdullah

Download or read book Multiple Alignments, Hidden Markov Models and Svms written by Mohamad Firdaus Abdullah and published by LAP Lambert Academic Publishing. This book was released on 2012 with total page 164 pages. Available in PDF, EPUB and Kindle. Book excerpt: Remote protein homology detection is a problem of detecting evolutionary relationship between proteins at low sequence similarity level. Among several problems in remote protein homology detection include the questions of determining which combination of multiple alignment and classification techniques is the best as well as the misalignment of protein sequences during the alignment process. Therefore, this study deals with remote protein homology detection via assessing the impact of using structural information on protein multiple alignments over sequence information. This study further presents the best combinations of multiple alignment and classification programs to be chosen. This study also improves the quality of the multiple alignments via integration of a refinement algorithm.

Theoretical and Computational Methods in Genome Research

Author : Sándor Suhai
Publisher : Springer Science & Business Media
ISBN 13 : 1461559030
Total Pages : 332 pages
Book Rating : 4.4/5 (615 download)

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Book Synopsis Theoretical and Computational Methods in Genome Research by : Sándor Suhai

Download or read book Theoretical and Computational Methods in Genome Research written by Sándor Suhai and published by Springer Science & Business Media. This book was released on 2012-12-06 with total page 332 pages. Available in PDF, EPUB and Kindle. Book excerpt: The application ofcomputational methods to solve scientific and practical problems in genome research created a new interdisciplinary area that transcends boundaries tradi tionally separating genetics, biology, mathematics, physics, and computer science. Com puters have, of course, been intensively used in the field of life sciences for many years, even before genome research started, to store and analyze DNA or protein sequences; to explore and model the three-dimensional structure, the dynamics, and the function of biopolymers; to compute genetic linkage or evolutionary processes; and more. The rapid development of new molecular and genetic technologies, combined with ambitious goals to explore the structure and function ofgenomes ofhigher organisms, has generated, how ever, not only a huge and exponentially increasing body of data but also a new class of scientific questions. The nature and complexity of these questions will also require, be yond establishing a new kind ofalliance between experimental and theoretical disciplines, the development of new generations both in computer software and hardware technolo gies. New theoretical procedures, combined with powerful computational facilities, will substantially extend the horizon of problems that genome research can attack with suc cess. Many of us still feel that computational models rationalizing experimental findings in genome research fulfill their promises more slowly than desired. There is also an uncer tainty concerning the real position of a "theoretical genome research" in the network of established disciplines integrating their efforts in this field.

Introduction to Data Mining for the Life Sciences

Author : Rob Sullivan
Publisher : Springer Science & Business Media
ISBN 13 : 1597452904
Total Pages : 644 pages
Book Rating : 4.5/5 (974 download)

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Book Synopsis Introduction to Data Mining for the Life Sciences by : Rob Sullivan

Download or read book Introduction to Data Mining for the Life Sciences written by Rob Sullivan and published by Springer Science & Business Media. This book was released on 2012-01-07 with total page 644 pages. Available in PDF, EPUB and Kindle. Book excerpt: Data mining provides a set of new techniques to integrate, synthesize, and analyze tdata, uncovering the hidden patterns that exist within. Traditionally, techniques such as kernel learning methods, pattern recognition, and data mining, have been the domain of researchers in areas such as artificial intelligence, but leveraging these tools, techniques, and concepts against your data asset to identify problems early, understand interactions that exist and highlight previously unrealized relationships through the combination of these different disciplines can provide significant value for the investigator and her organization.

Big Data Analytics in Genomics

Author : Ka-Chun Wong
Publisher : Springer
ISBN 13 : 3319412795
Total Pages : 428 pages
Book Rating : 4.3/5 (194 download)

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Book Synopsis Big Data Analytics in Genomics by : Ka-Chun Wong

Download or read book Big Data Analytics in Genomics written by Ka-Chun Wong and published by Springer. This book was released on 2016-10-24 with total page 428 pages. Available in PDF, EPUB and Kindle. Book excerpt: This contributed volume explores the emerging intersection between big data analytics and genomics. Recent sequencing technologies have enabled high-throughput sequencing data generation for genomics resulting in several international projects which have led to massive genomic data accumulation at an unprecedented pace. To reveal novel genomic insights from this data within a reasonable time frame, traditional data analysis methods may not be sufficient or scalable, forcing the need for big data analytics to be developed for genomics. The computational methods addressed in the book are intended to tackle crucial biological questions using big data, and are appropriate for either newcomers or veterans in the field.This volume offers thirteen peer-reviewed contributions, written by international leading experts from different regions, representing Argentina, Brazil, China, France, Germany, Hong Kong, India, Japan, Spain, and the USA. In particular, the book surveys three main areas: statistical analytics, computational analytics, and cancer genome analytics. Sample topics covered include: statistical methods for integrative analysis of genomic data, computation methods for protein function prediction, and perspectives on machine learning techniques in big data mining of cancer. Self-contained and suitable for graduate students, this book is also designed for bioinformaticians, computational biologists, and researchers in communities ranging from genomics, big data, molecular genetics, data mining, biostatistics, biomedical science, cancer research, medical research, and biology to machine learning and computer science. Readers will find this volume to be an essential read for appreciating the role of big data in genomics, making this an invaluable resource for stimulating further research on the topic.

Biological Sequence Analysis

Author : Richard Durbin
Publisher : Cambridge University Press
ISBN 13 : 113945739X
Total Pages : 372 pages
Book Rating : 4.1/5 (394 download)

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Book Synopsis Biological Sequence Analysis by : Richard Durbin

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.

Protein Structure Prediction

Author : Mohammed Zaki
Publisher : Springer Science & Business Media
ISBN 13 : 1588297527
Total Pages : 338 pages
Book Rating : 4.5/5 (882 download)

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Book Synopsis Protein Structure Prediction by : Mohammed Zaki

Download or read book Protein Structure Prediction written by Mohammed Zaki and published by Springer Science & Business Media. This book was released on 2007-09-12 with total page 338 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book covers elements of both the data-driven comparative modeling approach to structure prediction and also recent attempts to simulate folding using explicit or simplified models. Despite the unsolved mystery of how a protein folds, advances are being made in predicting the interactions of proteins with other molecules. Also rapidly advancing are the methods for solving the inverse folding problem, the problem of finding a sequence to fit a structure. This book focuses on the various computational methods for prediction, their successes and their limitations, from the perspective of their most well known practitioners.

SHsearch. A Method for Fast Remote Homology Detection

Author : Mohamed Baddar
Publisher : GRIN Verlag
ISBN 13 : 3668534489
Total Pages : 23 pages
Book Rating : 4.6/5 (685 download)

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Book Synopsis SHsearch. A Method for Fast Remote Homology Detection by : Mohamed Baddar

Download or read book SHsearch. A Method for Fast Remote Homology Detection written by Mohamed Baddar and published by GRIN Verlag. This book was released on 2017-09-26 with total page 23 pages. Available in PDF, EPUB and Kindle. Book excerpt: Master's Thesis from the year 2014 in the subject Statistics, grade: 3.8, , language: English, abstract: Remote homology detection is the problem of detecting homology in cases of low sequence similarity. It is a hard computational problem with no approach that works well in all cases. Methods based on profile hidden Markov models (HMM) often exhibit relatively higher sensitivity for detecting remote homologies than commonly used approaches. However, calculating similarity scores in profile HMM methods is computationally intensive as they use dynamic programming algorithms. In this paper, we introduce SHsearch: a new method for remote protein homology detection. Our method is implemented as a modification of HHsearch: a remote protein homology detection method based on comparing two profile HMMs. The motivation for modification was to reduce the run time of HHsearch significantly with minimal sensitivity loss. SHsearch focuses on comparing the important submodels of the query and database HMMs instead of comparing the complete models. Hence, SHsearch achieves a significant speedup over HHsearch with minimal loss in sensitivity. On S C O P 1.63, SHsearch achieved 88x speedup with 8.2% loss in sensitivity with respect to HHsearch at an error rate of 10%, which is deemed to be an acceptable tradeoff.

Introduction to Protein Structure Prediction

Author : Huzefa Rangwala
Publisher : John Wiley & Sons
ISBN 13 : 111809946X
Total Pages : 611 pages
Book Rating : 4.1/5 (18 download)

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Book Synopsis Introduction to Protein Structure Prediction by : Huzefa Rangwala

Download or read book Introduction to Protein Structure Prediction written by Huzefa Rangwala and published by John Wiley & Sons. This book was released on 2011-03-16 with total page 611 pages. Available in PDF, EPUB and Kindle. Book excerpt: A look at the methods and algorithms used to predict protein structure A thorough knowledge of the function and structure of proteins is critical for the advancement of biology and the life sciences as well as the development of better drugs, higher-yield crops, and even synthetic bio-fuels. To that end, this reference sheds light on the methods used for protein structure prediction and reveals the key applications of modeled structures. This indispensable book covers the applications of modeled protein structures and unravels the relationship between pure sequence information and three-dimensional structure, which continues to be one of the greatest challenges in molecular biology. With this resource, readers will find an all-encompassing examination of the problems, methods, tools, servers, databases, and applications of protein structure prediction and they will acquire unique insight into the future applications of the modeled protein structures. The book begins with a thorough introduction to the protein structure prediction problem and is divided into four themes: a background on structure prediction, the prediction of structural elements, tertiary structure prediction, and functional insights. Within those four sections, the following topics are covered: Databases and resources that are commonly used for protein structure prediction The structure prediction flagship assessment (CASP) and the protein structure initiative (PSI) Definitions of recurring substructures and the computational approaches used for solving sequence problems Difficulties with contact map prediction and how sophisticated machine learning methods can solve those problems Structure prediction methods that rely on homology modeling, threading, and fragment assembly Hybrid methods that achieve high-resolution protein structures Parts of the protein structure that may be conserved and used to interact with other biomolecules How the loop prediction problem can be used for refinement of the modeled structures The computational model that detects the differences between protein structure and its modeled mutant Whether working in the field of bioinformatics or molecular biology research or taking courses in protein modeling, readers will find the content in this book invaluable.