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 : 59 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 59 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.

Modeling Protein Structure Alignment Based on Markov Random Field Theory

Author : Xin Sheng
Publisher :
ISBN 13 :
Total Pages : 101 pages
Book Rating : 4.:/5 (688 download)

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Book Synopsis Modeling Protein Structure Alignment Based on Markov Random Field Theory by : Xin Sheng

Download or read book Modeling Protein Structure Alignment Based on Markov Random Field Theory written by Xin Sheng and published by . This book was released on 1999 with total page 101 pages. Available in PDF, EPUB and Kindle. Book excerpt:

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.

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.

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:

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.

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.

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.

Machine Learning and Knowledge Discovery in Databases

Author : Paolo Frasconi
Publisher : Springer
ISBN 13 : 331946227X
Total Pages : 850 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 850 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 2018 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.

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.

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.

SHsearch. A Method for Fast Remote Homology Detection

Author : Mohamed Baddar
Publisher : GRIN Verlag
ISBN 13 : 3668534489
Total Pages : 29 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 29 pages. Available in PDF, EPUB and Kindle. Book excerpt: Master's Thesis from the year 2014 in the subject Mathematics - 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.

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.

Kernels for Protein Homology Detection

Author : John Dylan Spalding
Publisher :
ISBN 13 :
Total Pages : pages
Book Rating : 4.:/5 (757 download)

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Book Synopsis Kernels for Protein Homology Detection by : John Dylan Spalding

Download or read book Kernels for Protein Homology Detection written by John Dylan Spalding and published by . This book was released on 2009 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: Determining protein sequence similarity is an important task for protein classification and homology detection, which is typically performed using sequence alignment algorithms. Fast and accurate alignment-free kernel based classifiers exist, that treat protein sequences as a 'bag of words'. Kernels implicitly map the sequences to a high dimensional feature space, and can be thought of as an inner product between two vectors in that space. This allows an algorithm that can be expressed purely in terms of inner products to be 'kernelised', where the algorithm implicitly operates in the kernel's feature space. A weighted string kernel, where the weighting is derived using probabilistic methods, is implemented using a binary data representation, and the results reported. Alternative forms of data representation, such as Ising and frequency forms, are implemented and the results discussed. These results are then used to inform the development of a variety of novel kernels for protein sequence comparison. Alternative forms of classifier are investigated, such as nearest neighbour, support vector machines, and multiple kernel learning. A kernelized Gaussian classifier is derived and tested, which is informative as it returns a score related to the probability of a sequence belonging to a particular classification. Support vector machines are tested with the introduced kernels, and the results compared to alternate classifiers. As similarity can be thought of as having different components, such as composition and position, multiple kernel learning is investigated with the novel kernels developed here. The results show that a support vector machine, using either single or multiple kernels, is the best classifier for remote protein homology detection out of all the classifiers tested in this thesis.

Remote Protein Homology Detection Using Hidden Markov Models

Author : Steven Johnson
Publisher :
ISBN 13 : 9781109887518
Total Pages : 92 pages
Book Rating : 4.8/5 (875 download)

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Book Synopsis Remote Protein Homology Detection Using Hidden Markov Models by : Steven Johnson

Download or read book Remote Protein Homology Detection Using Hidden Markov Models written by Steven Johnson and published by . This book was released on 2006 with total page 92 pages. Available in PDF, EPUB and Kindle. Book excerpt: The first sequence comparison algorithms were introduced over 30 years ago. The motivation behind that work still exists today, to connect the vast reservoir of existing protein knowledge to lesser known sequences. If two proteins are deemed homologous, then information regarding function and structure may be common between them. At the least, it provides a basis for hypotheses and experimentation. Sequence comparison methods, and the data access that they rely on, have grown considerably over the decades. This growth has primarily come from a constant cycle of incorporating biological sources of information into search algorithms; the identification of more distant homologies, and the further refinement of information gained from the new homologies into the next generation of algorithms and search strategies. The focus of this research has been in the use of Hidden Markov Models (HMMs) for remote protein homology detection. We have implemented information content sequence weighting to improve local alignment searches. We identified that the Forward null score distribution can be approximated by the exponential distribution and utilized this to calculate accurate and robust P-values for HHM Forward scores. In addition, we have developed an HMM search heuristic to decrease the time required to search large databases. Further, we have incorporated this heuristic into an iterative HMM search method that significantly increases search sensitivity.