Practical Protein Bioinformatics

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Practical Protein Bioinformatics

Florencio Pazos,Mónica Chagoyen
Practical Protein Bioinformatics Book PDF

Author : Florencio Pazos,Mónica Chagoyen
Publisher : Springer
Page : 111 pages
File Size : 46,8 Mb
Release : 2014-11-28
Category : Science
ISBN : 9783319127279

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Practical Protein Bioinformatics by Florencio Pazos,Mónica Chagoyen Pdf

This book describes more than 60 web-accessible computational tools for protein analysis and is totally practical, with detailed explanations on how to use these tools and interpret their results and minimal mentions to their theoretical basis (only when that is required for making a better use of them). It covers a wide range of tools for dealing with different aspects of proteins, from their sequences, to their three-dimensional structures, and the biological networks they are immersed in. The selection of tools is based on the experience of the authors that lead a protein bioinformatics facility in a large research centre, with the additional constraint that the tools should be accessible through standard web browsers without requiring the local installation of specific software, command-line tools, etc. The web tools covered include those aimed to retrieve protein information, look for similar proteins, generate pair-wise and multiple sequence alignments of protein sequences, work with protein domains and motifs, study the phylogeny of a family of proteins, retrieve, manipulate and visualize protein three-dimensional structures, predict protein structural features as well as whole three-dimensional structures, extract biological information from protein structures, summarize large protein sets, study protein interaction and metabolic networks, etc. The book is associated to a dynamic web site that will reflect changes in the web addresses of the tools, updates of these, etc. It also contains QR codes that can be scanned with any device to direct its browser to the tool web site. This monograph will be most valuable for researchers in experimental labs without specific knowledge on bioinformatics or computing.

Bioinformatics

Andreas D. Baxevanis,B. F. Francis Ouellette
Bioinformatics Book PDF

Author : Andreas D. Baxevanis,B. F. Francis Ouellette
Publisher : John Wiley & Sons
Page : 504 pages
File Size : 48,9 Mb
Release : 2004-03-24
Category : Computers
ISBN : 9780471461012

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Bioinformatics by Andreas D. Baxevanis,B. F. Francis Ouellette Pdf

"In this book, Andy Baxevanis and Francis Ouellette . . . haveundertaken the difficult task of organizing the knowledge in thisfield in a logical progression and presenting it in a digestibleform. And they have done an excellent job. This fine text will makea major impact on biological research and, in turn, on progress inbiomedicine. We are all in their debt." —Eric Lander from the Foreword Reviews from the First Edition "...provides a broad overview of the basic tools for sequenceanalysis ... For biologists approaching this subject for the firsttime, it will be a very useful handbook to keep on the shelf afterthe first reading, close to the computer." —Nature Structural Biology "...should be in the personal library of any biologist who usesthe Internet for the analysis of DNA and protein sequencedata." —Science "...a wonderful primer designed to navigate the novice throughthe intricacies of in scripto analysis ... The accomplished genesearcher will also find this book a useful addition to theirlibrary ... an excellent reference to the principles ofbioinformatics." —Trends in Biochemical Sciences This new edition of the highly successful Bioinformatics:A Practical Guide to the Analysis of Genes and Proteinsprovides a sound foundation of basic concepts, with practicaldiscussions and comparisons of both computational tools anddatabases relevant to biological research. Equipping biologists with the modern tools necessary to solvepractical problems in sequence data analysis, the Second Editioncovers the broad spectrum of topics in bioinformatics, ranging fromInternet concepts to predictive algorithms used on sequence,structure, and expression data. With chapters written by experts inthe field, this up-to-date reference thoroughly covers vitalconcepts and is appropriate for both the novice and the experiencedpractitioner. Written in clear, simple language, the book isaccessible to users without an advanced mathematical or computerscience background. This new edition includes: All new end-of-chapter Web resources, bibliographies, andproblem sets Accompanying Web site containing the answers to the problems,as well as links to relevant Web resources New coverage of comparative genomics, large-scale genomeanalysis, sequence assembly, and expressed sequence tags A glossary of commonly used terms in bioinformatics andgenomics Bioinformatics: A Practical Guide to the Analysis of Genesand Proteins, Second Edition is essential reading forresearchers, instructors, and students of all levels in molecularbiology and bioinformatics, as well as for investigators involvedin genomics, positional cloning, clinical research, andcomputational biology.

Practical Bioinformatics

Janusz M. Bujnicki
Practical Bioinformatics Book PDF

Author : Janusz M. Bujnicki
Publisher : Springer
Page : 265 pages
File Size : 43,8 Mb
Release : 2007-09-12
Category : Science
ISBN : 9783540742685

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Practical Bioinformatics by Janusz M. Bujnicki Pdf

This book presents applications of bioinformatics tools that experimental research scientists use in "daily practice." Its interdisciplinary approach combines computational and experimental methods to solve scientific problems. The book begins with reviews of computational methods for protein sequence-structure-function analysis, followed by methods that use experimental data obtained in the laboratory to improve functional predictions.

Practical Bioinformatics

Michael Agostino
Practical Bioinformatics Book PDF

Author : Michael Agostino
Publisher : Garland Science
Page : 392 pages
File Size : 43,7 Mb
Release : 2012-09-26
Category : Science
ISBN : 9781134063918

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Practical Bioinformatics by Michael Agostino Pdf

Practical Bioinformatics is specifically designed for biology majors, with a heavy emphasis on the steps required to perform bioinformatics analysis to answer biological questions. It is written for courses that have a practical, hands-on element and contains many exercises (for example, database searches, protein analysis, data interpretation) to

Bioinformatics

Hamid D. Ismail
Bioinformatics Book PDF

Author : Hamid D. Ismail
Publisher : CRC Press
Page : 466 pages
File Size : 43,8 Mb
Release : 2022-03-23
Category : Science
ISBN : 9781000519075

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Bioinformatics by Hamid D. Ismail Pdf

Bioinformatics: A Practical Guide to NCBI Databases and Sequence Alignments provides the basics of bioinformatics and in-depth coverage of NCBI databases, sequence alignment, and NCBI Sequence Local Alignment Search Tool (BLAST). As bioinformatics has become essential for life sciences, the book has been written specifically to address the need of a large audience including undergraduates, graduates, researchers, healthcare professionals, and bioinformatics professors who need to use the NCBI databases, retrieve data from them, and use BLAST to find evolutionarily related sequences, sequence annotation, construction of phylogenetic tree, and the conservative domain of a protein, to name just a few. Technical details of alignment algorithms are explained with a minimum use of mathematical formulas and with graphical illustrations. Key Features Provides readers with the most-used bioinformatics knowledge of bioinformatics databases and alignments including both theory and application via illustrations and worked examples. Discusses the use of Windows Command Prompt, Linux shell, R, and Python for both Entrez databases and BLAST. The companion website contains tutorials, R and Python codes, instructor materials including slides, exercises, and problems for students. This is the ideal textbook for bioinformatics courses taken by students of life sciences and for researchers wishing to develop their knowledge of bioinformatics to facilitate their own research.

The Practical Bioinformatician

Limsoon Wong
The Practical Bioinformatician Book PDF

Author : Limsoon Wong
Publisher : World Scientific
Page : 539 pages
File Size : 54,5 Mb
Release : 2004
Category : Medical
ISBN : 9789812388469

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The Practical Bioinformatician by Limsoon Wong Pdf

Computer scientists have increasingly been enlisted as "bioinformaticians" to assist molecular biologists in their research. This book is a practical introduction to bioinformatics for these computer scientists. The chapters are in-depth discussions by expert bioinformaticians on both general techniques and specific approaches to a range of selected bioinformatics problems. The book is organized into clusters of chapters on the following topics: - Overview of modern molecular biology and a broad spectrum of techniques from computer science -- data mining, machine learning, mathematical modeling, sequence alignment, data integration, workflow development, etc. - In-depth discussion of computational recognition of functional and regulatory sites in DNA sequences. - Incisive discussion of computational prediction of secondary structure of RNA sequences. - Overview of computational prediction of protein cellular localization, and selected discussions of inference of protein function. - Overview of methods for discovering protein-protein interactions. - Detailed discussion of approaches to gene expression analysis for the diagnosis of diseases, the treatment of diseases, and the understanding of gene functions. - Case studies on analysis of phylogenies, functional annotation of proteins, construction of purposebuilt integrated biological databases, and development of workflows underlying the large-scale-effort gene discovery. - Written in a practical, in-depth tutorial style - Covers a broad range of bioinformatics topics and of techniques used in bioinformatics - Comprehensive overviews of the development of various approaches in a number of selectedtopics - In-depth exposition of a number of important topics - Contributions by prominent researchers: Vladimir Bajic, Ming Li, Kenta Nakai, Limsoon Wong, Cathy Wu, etc. - Extensive, integrated references to background liter

Protein Bioinformatics

M. Michael Gromiha
Protein Bioinformatics Book PDF

Author : M. Michael Gromiha
Publisher : Academic Press
Page : 349 pages
File Size : 53,5 Mb
Release : 2011-04-21
Category : Science
ISBN : 9780123884244

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Protein Bioinformatics by M. Michael Gromiha Pdf

One of the most pressing tasks in biotechnology today is to unlock the function of each of the thousands of new genes identified every day. Scientists do this by analyzing and interpreting proteins, which are considered the task force of a gene. This single source reference covers all aspects of proteins, explaining fundamentals, synthesizing the latest literature, and demonstrating the most important bioinformatics tools available today for protein analysis, interpretation and prediction. Students and researchers of biotechnology, bioinformatics, proteomics, protein engineering, biophysics, computational biology, molecular modeling, and drug design will find this a ready reference for staying current and productive in this fast evolving interdisciplinary field. Explains all aspects of proteins including sequence and structure analysis, prediction of protein structures, protein folding, protein stability, and protein interactions Presents a cohesive and accessible overview of the field, using illustrations to explain key concepts and detailed exercises for students.

Protein Bioinformatics

Frédérique Lisacek
Protein Bioinformatics Book PDF

Author : Frédérique Lisacek
Publisher : Humana
Page : 0 pages
File Size : 53,8 Mb
Release : 2024-09-05
Category : Computers
ISBN : 1071640062

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Protein Bioinformatics by Frédérique Lisacek Pdf

This detailed volume explores techniques for protein bioinformatics research, including databases, software tools, and computational methods, in the context of protein science or proteomics and opening to other omics areas. Beginning with a section on proteogenomics, the book continues by covering posttranslational modifications, processing large-scale mass spectrometry data, protein structure and interactions, as well as protein feature inference. Written for the highly successful Methods in Molecular Biology series, chapters include the kind of detailed implementation advice to ensure efficacious results. Authoritative and practical, Protein Bioinformatics serves as an ideal guide for researchers in disciplines encompassing the biotechnological, pharmaceutical, biological, and medical sciences, as well as the computational and engineering sciences.

Bioinformatics

Andreas D. Baxevanis,B. F. Francis Ouellette
Bioinformatics Book PDF

Author : Andreas D. Baxevanis,B. F. Francis Ouellette
Publisher : Wiley-Interscience
Page : 572 pages
File Size : 44,8 Mb
Release : 2005
Category : Computers
ISBN : UOM:39015059591100

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Bioinformatics by Andreas D. Baxevanis,B. F. Francis Ouellette Pdf

Reviews of the Second Edition "In this book, Andy Baxevanis and Francis Ouellette . . . have undertaken the difficult task of organizing the knowledge in this field in a logical progression and presenting it in a digestible form. And they have done an excellent job. This fine text will make a major impact on biological research and, in turn, on progress in biomedicine. We are all in their debt." —Eric Lander, from the Foreword to the Second Edition "The editors and the chapter authors of this book are to be applauded for providing biologists with lucid and comprehensive descriptions of essential topics in bioinformatics. This book is easy to read, highly informative, and certainly timely. It is most highly recommended for students and for established investigators alike, for anyone who needs to know how to access and use the information derived in and from genomic sequencing projects." —Trends in Genetics "It is an excellent general bioinformatics text and reference, perhaps even the best currently available . . . Congratulations to the authors, editors, and publisher for producing a weighty, authoritative, readable, and attractive book." —Briefings in Bioinformatics "This book, written by the top scientists in the field of bioinformatics, is the perfect choice for every molecular biology laboratory." —The Quarterly Review of Biology This fully revised version of a world-renowned bestseller provides readers with a practical guide covering the full scope of key concepts in bioinformatics, from databases to predictive and comparative algorithms. Using relevant biological examples, the book provides background on and strategies for using many of the most powerful and commonly used computational approaches for biological discovery. This Third Edition reinforces key concepts that have stood the test of time while making the reader aware of new and important developments in this fast-moving field. With a new full-color and enlarged page design, Bioinformatics, Third Edition offers the most readable, up-to-date, and thorough introduction to the field for biologists. This new edition features: New chapters on genomic databases, predictive methods using RNA sequences, sequence polymorphisms, protein structure prediction, intermolecular interactions, and proteomic approaches for protein identification Detailed worked examples illustrating the strategic use of the concepts presented in each chapter, along with a collection of expanded, more rigorous problem sets suitable for classroom use Special topic boxes and appendices highlighting experimental strategies and advanced concepts Annotated reference lists, comprehensive lists of relevant Web resources, and an extensive glossary of commonly used terms in bioinformatics, genomics, and proteomics Bioinformatics, Third Edition is essential reading for researchers, instructors, and students of all levels in molecular biology and bioinformatics, as well as for investigators involved in genomics, clinical research, proteomics, and computational biology. www.wiley.com/bioinformatics

From Protein Structure to Function with Bioinformatics

Daniel John Rigden
From Protein Structure to Function with Bioinformatics Book PDF

Author : Daniel John Rigden
Publisher : Springer Science & Business Media
Page : 330 pages
File Size : 52,8 Mb
Release : 2008-12-11
Category : Science
ISBN : 9781402090585

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From Protein Structure to Function with Bioinformatics by Daniel John Rigden Pdf

Proteins lie at the heart of almost all biological processes and have an incredibly wide range of activities. Central to the function of all proteins is their ability to adopt, stably or sometimes transiently, structures that allow for interaction with other molecules. An understanding of the structure of a protein can therefore lead us to a much improved picture of its molecular function. This realisation has been a prime motivation of recent Structural Genomics projects, involving large-scale experimental determination of protein structures, often those of proteins about which little is known of function. These initiatives have, in turn, stimulated the massive development of novel methods for prediction of protein function from structure. Since model structures may also take advantage of new function prediction algorithms, the first part of the book deals with the various ways in which protein structures may be predicted or inferred, including specific treatment of membrane and intrinsically disordered proteins. A detailed consideration of current structure-based function prediction methodologies forms the second part of this book, which concludes with two chapters, focusing specifically on case studies, designed to illustrate the real-world application of these methods. With bang up-to-date texts from world experts, and abundant links to publicly available resources, this book will be invaluable to anyone who studies proteins and the endlessly fascinating relationship between their structure and function.

Bioinformatics

Shui Qing Ye
Bioinformatics Book PDF

Author : Shui Qing Ye
Publisher : CRC Press
Page : 646 pages
File Size : 50,9 Mb
Release : 2007-08-20
Category : Computers
ISBN : 9781584888116

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Bioinformatics by Shui Qing Ye Pdf

An emerging, ever-evolving branch of science, bioinformatics has paved the way for the explosive growth in the distribution of biological information to a variety of biological databases, including the National Center for Biotechnology Information. For growth to continue in this field, biologists must obtain basic computer skills while computer spe

BIOINFORMATICS: A PRACTICAL GUIDE TO THE ANALYSIS OF GENES AND PROTEINS, 3RD ED

Andreas D. Baxevanis,Francis B. F. Ouellette
BIOINFORMATICS A PRACTICAL GUIDE TO THE ANALYSIS OF GENES AND PROTEINS 3RD ED Book PDF

Author : Andreas D. Baxevanis,Francis B. F. Ouellette
Publisher : Unknown
Page : 560 pages
File Size : 43,5 Mb
Release : 2009-07-01
Category : Bioinformatics
ISBN : 8126521929

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BIOINFORMATICS: A PRACTICAL GUIDE TO THE ANALYSIS OF GENES AND PROTEINS, 3RD ED by Andreas D. Baxevanis,Francis B. F. Ouellette Pdf

Market_Desc: This new edition is aimed at advanced undergraduate and graduate school students taking an introductory bioinformatics courses, as well as professionals in genomics, molecular biology, biochemistry, biophysics, and computational biology. According to a Science review of a previous edition, this book should be in the personal library of any biologist who uses the Internet for the analysis of DNA and protein sequence data and is invaluable to beginners and seasoned researchers alike. Special Features: · Complete, expert coverage of key principles as well as the state-of-the-art in bioinformatics· All new chapters on: Genome Annotation, Genomic Databases, Predictive Methods Using RNA Sequences, Protein Structure Prediction, and Protein-Protein Interactions· Fully redesigned, appealing design with full color throughout and larger trim size· Reorganization of chapters into five main sections following a clear, logical sequence· Inclusion of greatly expanded and more rigorous problem sets· Special boxes highlighting experimental strategies and limitations· More diagrams and flowcharts to reinforce the main text· Enhanced use of real examples· written by the top scientists in the field of bioinformatics, [this book] is the perfect choice for every molecular biology laboratory --Quarterly Review of Biology (2/e)· No background in computer science or mathematics assumed About The Book: This fully revised third edition to an already classic resource provides readers with a practical guide covering the full scope of key concepts in bioinformatics, from databases to predictive and comparative algorithms. With a new full-color, enlarged page design, this edition offers the most readable, up-to-date, and thorough introduction to the field for biologists. All new features include special boxes, enhanced use of real examples, and expanded problem sets with answers provided on the book's dedicated website (www.wiley.com/bioinformatics). A glossary and appendix of sample file formats rounds out the book's reader-friendly, 'hands-on' treatment.The chapters have been reorganized into a more logical flow, with five main sections and a concluding section offering a primer on the use of Perl. Following the editors' introduction and perspective on why bioinformatics is important.

Structural Bioinformatics

Jenny Gu,Philip E. Bourne
Structural Bioinformatics Book PDF

Author : Jenny Gu,Philip E. Bourne
Publisher : John Wiley & Sons
Page : 1105 pages
File Size : 53,5 Mb
Release : 2011-09-20
Category : Science
ISBN : 9781118210567

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Structural Bioinformatics by Jenny Gu,Philip E. Bourne Pdf

Structural Bioinformatics was the first major effort to show the application of the principles and basic knowledge of the larger field of bioinformatics to questions focusing on macromolecular structure, such as the prediction of protein structure and how proteins carry out cellular functions, and how the application of bioinformatics to these life science issues can improve healthcare by accelerating drug discovery and development. Designed primarily as a reference, the first edition nevertheless saw widespread use as a textbook in graduate and undergraduate university courses dealing with the theories and associated algorithms, resources, and tools used in the analysis, prediction, and theoretical underpinnings of DNA, RNA, and proteins. This new edition contains not only thorough updates of the advances in structural bioinformatics since publication of the first edition, but also features eleven new chapters dealing with frontier areas of high scientific impact, including: sampling and search techniques; use of mass spectrometry; genome functional annotation; and much more. Offering detailed coverage for practitioners while remaining accessible to the novice, Structural Bioinformatics, Second Edition is a valuable resource and an excellent textbook for a range of readers in the bioinformatics and advanced biology fields. Praise for the previous edition: "This book is a gold mine of fundamental and practical information in an area not previously well represented in book form." —Biochemistry and Molecular Education "... destined to become a classic reference work for workers at all levels in structural bioinformatics...recommended with great enthusiasm for educators, researchers, and graduate students." —BAMBED "...a useful and timely summary of a rapidly expanding field." —Nature Structural Biology "...a terrific job in this timely creation of a compilation of articles that appropriately addresses this issue." —Briefings in Bioinformatics

Bioinformatics: Sequence, Structure and Databanks

Des Higgins,Willie Taylor
Bioinformatics Sequence Structure and Databanks Book PDF

Author : Des Higgins,Willie Taylor
Publisher : OUP Oxford
Page : 270 pages
File Size : 53,7 Mb
Release : 2000-09-14
Category : Science
ISBN : 9780191566011

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Bioinformatics: Sequence, Structure and Databanks by Des Higgins,Willie Taylor Pdf

Bioinformatics covers practical important topics in the analysis of protein sequences and structures. It includes comparing amino acid sequences to structures comparing structures to each other, searching information on entire protein families as well as searching with single sequences, how to use the Internet and how to set up and use the SRS molecular biology database management system. Finally, there are chapters on multiple sequence alignment and protein secondary structure prediction. Bioinformatics will be invaluable to occasional users of these techniques as well as experienced professionals or researchers.

Introduction to Bioinformatics

Stephen A. Krawetz,David D. Womble
Introduction to Bioinformatics Book PDF

Author : Stephen A. Krawetz,David D. Womble
Publisher : Springer Science & Business Media
Page : 776 pages
File Size : 46,6 Mb
Release : 2003-01-31
Category : Computers
ISBN : 1588290646

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Introduction to Bioinformatics by Stephen A. Krawetz,David D. Womble Pdf

CD-ROM contains: chapter illustrations -- full and trial versions of programs.