Sequence Analysis in a Nutshell A Guide to Tools

Sequence Analysis in a Nutshell  A Guide to Tools

Author: Scott Markel

Publisher: "O'Reilly Media, Inc."

ISBN: 059600494X

Category: Computers

Page: 286

View: 181

This work pulls together all of the vital information about the most commonly used databases, analytical tools, and tables used in sequence analysis.
Categories: Computers

Advances in Sequence Analysis Theory Method Applications

Advances in Sequence Analysis  Theory  Method  Applications

The research trend in sequence analysis was structured in the 1990s and 2000s
around a core program with a limited number of ... Sequence Analysis in 2014 5
The Core Program of Sequence Analysis Sequence Comparison in a Nutshell.

Author: Philippe Blanchard

Publisher: Springer

ISBN: 9783319049694

Category: Social Science

Page: 304

View: 345

This book gives a general view of sequence analysis, the statistical study of successions of states or events. It includes innovative contributions on life course studies, transitions into and out of employment, contemporaneous and historical careers, and political trajectories. The approach presented in this book is now central to the life-course perspective and the study of social processes more generally. This volume promotes the dialogue between approaches to sequence analysis that developed separately, within traditions contrasted in space and disciplines. It includes the latest developments in sequential concepts, coding, atypical datasets and time patterns, optimal matching and alternative algorithms, survey optimization, and visualization. Field studies include original sequential material related to parenting in 19th-century Belgium, higher education and work in Finland and Italy, family formation before and after German reunification, French Jews persecuted in occupied France, long-term trends in electoral participation, and regime democratization. Overall the book reassesses the classical uses of sequences and it promotes new ways of collecting, formatting, representing and processing them. The introduction provides basic sequential concepts and tools, as well as a history of the method. Chapters are presented in a way that is both accessible to the beginner and informative to the expert.
Categories: Social Science

In Silico Technologies in Drug Target Identification and Validation

In Silico Technologies in Drug Target Identification and Validation

He is a co-author, with Scott Markel, of Sequence Analysis in a Nutshell: A Guide
to Common Tools and Databases. He has also taught at the University of
California Santa Cruz Extension and at other colleges in northern California. Dr.
Leon ...

Author: Darryl Leon

Publisher: CRC Press

ISBN: 9781420015737

Category: Medical

Page: 504

View: 713

The pharmaceutical industry relies on numerous well-designed experiments involving high-throughput techniques and in silico approaches to analyze potential drug targets. These in silico methods are often predictive, yielding faster and less expensive analyses than traditional in vivo or in vitro procedures. In Silico Technologies in Drug Target Identification and Validation addresses the challenge of testing a growing number of new potential targets and reviews currently available in silico approaches for identifying and validating these targets. The book emphasizes computational tools, public and commercial databases, mathematical methods, and software for interpreting complex experimental data. The book describes how these tools are used to visualize a target structure, identify binding sites, and predict behavior. World-renowned researchers cover many topics not typically found in most informatics books, including functional annotation, siRNA design, pathways, text mining, ontologies, systems biology, database management, data pipelining, and pharmacogenomics. Covering issues that range from prescreening target selection to genetic modeling and valuable data integration, In Silico Technologies in Drug Target Identification and Validation is a self-contained and practical guide to the various computational tools that can accelerate the identification and validation stages of drug target discovery and determine the biological functionality of potential targets more effectively. Daniel E. Levy, editor of the Drug Discovery Series, is the founder of DEL BioPharma, a consulting service for drug discovery programs. He also maintains a blog that explores organic chemistry.
Categories: Medical

Time Sequence Analysis in Geophysics Third Edition

Time Sequence Analysis in Geophysics  Third Edition

IN GEOPHYSICS Third Edition E . R . Kanasewich The Third Edition published
since the original text in 1973 , this completely reset and revised version of Time
Sequence Analysis in Geophysics will be welcomed by the geophysical industry
 ...

Author: E. R. Kanasewich

Publisher: University of Alberta

ISBN: 0888640749

Category: Science

Page: 480

View: 839

Time sequence analysis is the study of relations between a sequence of data points or sequence of signals in order to determine the physical properties of the earth. Providing an up-to-date treatment on time series and time sequence, this book is intended for senior or graduate students in seismology, geomagnetism and exploratory geophysics.
Categories: Science

Sequence Analysis Primer

Sequence Analysis Primer

In the analysis of prokaryotic DN A sequences, these features include signals for
the initiation of transcription and translation, the ribosome binding site (RBS), and
transcriptional and translational termination signals. The analysis of eukaryotic ...

Author: Michael Gribskov

Publisher: Oxford University Press

ISBN: 9780195356830

Category: Science

Page:

View: 621

Computerized sequence analysis is an integral part of biotechnological research, yet many biologists have received no formal training in this important technology. Sequence Analysis Primer offers the beginner the necessary background to enter this vital field and helps more seasoned researchers to fine-tune their approach. It covers basic data manipulation such as homology searches, stem-loop identification, and protein secondary structure prediction, and is compatible with most sequence analysis programs. A detailed example giving steps for characterizing a new gene sequence provides users with hands-on experience when combined with their current software. The book will be invaluable to researchers and students in molecular biology, genetics, biochemistry, microbiology, and biotechnology.
Categories: Science

Problems and Solutions in Biological Sequence Analysis

Problems and Solutions in Biological Sequence Analysis

PROBLEMS AND SOLUTIONS IN BIOLOGICAL SEQUENCE ANALYSIS This
book is the first of its kind to provide a large collection of bioinformatics problems
with accompanying solutions. Notably, the problem set includes all of the
problems ...

Author: Mark Borodovsky

Publisher: Cambridge University Press

ISBN: 9781139458122

Category: Science

Page:

View: 810

This book is the first of its kind to provide a large collection of bioinformatics problems with accompanying solutions. Notably, the problem set includes all of the problems offered in Biological Sequence Analysis (BSA), by Durbin et al., widely adopted as a required text for bioinformatics courses at leading universities worldwide. Although many of the problems included in BSA as exercises for its readers have been repeatedly used for homework and tests, no detailed solutions for the problems were available. Bioinformatics instructors had therefore frequently expressed a need for fully worked solutions and a larger set of problems for use on courses. This book provides just that: following the same structure as BSA and significantly extending the set of workable problems, it will facilitate a better understanding of the contents of the chapters in BSA and will help its readers develop problem-solving skills that are vitally important for conducting successful research in the growing field of bioinformatics. All of the material has been class-tested by the authors at Georgia Tech, where the first ever M.Sc. degree program in Bioinformatics was held.
Categories: Science

Exome Sequence Analysis and Interpretation

Exome Sequence Analysis and Interpretation

Genomic analysis Analysis of DNA RNA including but not limited to whole
genome sequencing and other biochemical analysis will be performed on tissue
samples collected from the individual. The nature and extent of analysis will be ...

Author: Vinod Scaria

Publisher: Research in Genomics

ISBN:

Category: Computers

Page: 124

View: 880

A concise handbook on exome sequencing for clinicians and clinical geneticists.
Categories: Computers

Sequence Analysis in Molecular Biology

Sequence Analysis in Molecular Biology

... and if current proposals to sequence “the” human genome (as if this were a
well-defined entity) are put into practice, automated data handling and, above all,
data analysis must be given a very high priority. If this book has done nothing
else, ...

Author: Gunnar Von Heijne

Publisher: Elsevier

ISBN: 9780323160285

Category: Science

Page: 202

View: 524

Sequence Analysis in Molecular Biology: Treasure Trove or Trivial Pursuit presents the methods for sequence analysis of DNA and proteins. This book contains eight chapters that consider the sequence analysis either directly on a microcomputer or using one of the main sequence/programs data banks. This book starts with a description of the main nucleic acid and protein sequence data banks, followed by a short section on the ""housekeeping aids"" that the computer can provide during a sequencing project. Chapters 4 and 5 deal with nucleic acid and protein sequence analysis. Chapter 6 treats algorithms for homology searching and sequence alignments. Chapter 7 presents some selected examples of how computer modeling can help decide whether an observed sequence pattern is significant or not, and how computer simulation is sometimes used to get a feeling for the behavior of intrinsically complex sequence-dependent processes. Chapter 8 contains some comments on the role of theoretical sequence analysis in molecular biology. This book is directed toward molecular biologists.
Categories: Science

Mathematical Approaches to Polymer Sequence Analysis and Related Problems

Mathematical Approaches to Polymer Sequence Analysis and Related Problems

Ettore Mosca and Luciano Milanesi Abstract Sequence analysis methods predict
macromolecule properties and intermolecular interactions. These data can be
used to reconstruct molecular networks, which are complex systems that regulate
 ...

Author: Renato Bruni

Publisher: Springer Science & Business Media

ISBN: 1441968008

Category: Science

Page: 248

View: 532

An edited volume describing the latest developments in approaching the problem of polymer sequence analysis, with special emphasis on the most relevant biopolymers (peptides and DNA) but not limited to them. The chapters will include peptide sequence analysis, DNA sequence analysis, analysis of biopolymers and nonpolymers, sequence alignment problems, and more.
Categories: Science

Biological Sequence Analysis Using the SeqAn C Library

Biological Sequence Analysis Using the SeqAn C   Library

The sequence of nucleotides in the DNA therefore defines the order of amino
acids in the protein, which further specifies the three-dimensional shape the
protein folds into. RNA may also fold into a structure that is crucial to fulfill its
purposes in ...

Author: Andreas Gogol-Döring

Publisher: CRC Press

ISBN: 1420076248

Category: Science

Page: 329

View: 983

An Easy-to-Use Research Tool for Algorithm Testing and Development Before the SeqAn project, there was clearly a lack of available implementations in sequence analysis, even for standard tasks. Implementations of needed algorithmic components were either unavailable or hard to access in third-party monolithic software products. Addressing these concerns, the developers of SeqAn created a comprehensive, easy-to-use, open source C++ library of efficient algorithms and data structures for the analysis of biological sequences. Written by the founders of this project, Biological Sequence Analysis Using the SeqAn C++ Library covers the SeqAn library, its documentation, and the supporting infrastructure. The first part of the book describes the general library design. It introduces biological sequence analysis problems, discusses the benefit of using software libraries, summarizes the design principles and goals of SeqAn, details the main programming techniques used in SeqAn, and demonstrates the application of these techniques in various examples. Focusing on the components provided by SeqAn, the second part explores basic functionality, sequence data structures, alignments, pattern and motif searching, string indices, and graphs. The last part illustrates applications of SeqAn to genome alignment, consensus sequence in assembly projects, suffix array construction, and more. This handy book describes a user-friendly library of efficient data types and algorithms for sequence analysis in computational biology. SeqAn enables not only the implementation of new algorithms, but also the sound analysis and comparison of existing algorithms. Visit SeqAn for more information.
Categories: Science

Advances in Genomic Sequence Analysis and Pattern Discovery

Advances in Genomic Sequence Analysis and Pattern Discovery

By clicking the “sequence hits” number from the column “Unique sequence
occurrences” (Fig. 1(b)), AGRIS provides detailed location information of the
queried word (Fig. 2). Besides including the locations of the selected word in the
chosen ...

Author: Laura Elnitski

Publisher: World Scientific

ISBN: 9789814327725

Category: Science

Page: 223

View: 747

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.
Categories: Science

MacHine Learning Based Sequence Analysis Bioinformatics and Nanopore Transduction Detection

MacHine Learning Based Sequence Analysis  Bioinformatics and Nanopore Transduction Detection

In this book you will find a unified method for signal analysis, pattern recognition,
and computational science that is based on machine learning. Examples in the
context of nanopore transduction detector (NTD) applications and gene structure
 ...

Author: Stephen Winters-Hilt

Publisher: Lulu.com

ISBN: 9781257645251

Category: Bioinformatics

Page: 434

View: 755

This is intended to be a simple and accessible book on machine learning methods and their application in computational genomics and nanopore transduction detection. This book has arisen from eight years of teaching one-semester courses on various machine-learning, cheminformatics, and bioinformatics topics. The book begins with a description of ad hoc signal acquisition methods and how to orient on signal processing problems with the standard tools from information theory and signal analysis. A general stochastic sequential analysis (SSA) signal processing architecture is then described that implements Hidden Markov Model (HMM) methods. Methods are then shown for classification and clustering using generalized Support Vector Machines, for use with the SSA Protocol, or independent of that approach. Optimization metaheuristics are used for tuning over algorithmic parameters throughout. Hardware implementations and short code examples of the various methods are also described.
Categories: Bioinformatics

Classical Electromagnetism in a Nutshell

Classical Electromagnetism in a Nutshell

Obviously, there are many sequences that we can choose, and δ(x) is associated
with the entire class of sequences ... The definition of generalized functions in
terms of sequences allows one to perform most operations of analysis in the
usual ...

Author: Anupam Garg

Publisher: Princeton University Press

ISBN: 9781400842759

Category: Science

Page: 712

View: 720

This graduate-level physics textbook provides a comprehensive treatment of the basic principles and phenomena of classical electromagnetism. While many electromagnetism texts use the subject to teach mathematical methods of physics, here the emphasis is on the physical ideas themselves. Anupam Garg distinguishes between electromagnetism in vacuum and that in material media, stressing that the core physical questions are different for each. In vacuum, the focus is on the fundamental content of electromagnetic laws, symmetries, conservation laws, and the implications for phenomena such as radiation and light. In material media, the focus is on understanding the response of the media to imposed fields, the attendant constitutive relations, and the phenomena encountered in different types of media such as dielectrics, ferromagnets, and conductors. The text includes applications to many topical subjects, such as magnetic levitation, plasmas, laser beams, and synchrotrons. Classical Electromagnetism in a Nutshell is ideal for a yearlong graduate course and features more than 300 problems, with solutions to many of the advanced ones. Key formulas are given in both SI and Gaussian units; the book includes a discussion of how to convert between them, making it accessible to adherents of both systems. Offers a complete treatment of classical electromagnetism Emphasizes physical ideas Separates the treatment of electromagnetism in vacuum and material media Presents key formulas in both SI and Gaussian units Covers applications to other areas of physics Includes more than 300 problems
Categories: Science

Computer Analysis of Sequence Data

Computer Analysis of Sequence Data

Introduction Profile analysis uses information from a group of aligned sequences
to create a generalized probe, the profile, for sequence or structural motifs. The
profile contains information about the location and type of sequence conservation
 ...

Author: Annette M. Griffin

Publisher: Springer Science & Business Media

ISBN: 9780896032767

Category: Science

Page: 433

View: 231

DNA sequencing has become increasingly efficient over the years, resulting in an enormous increase in the amount of data gener ated. In recent years, the focus of sequencing has shifted, from being the endpoint of a project, to being a starting point. This is especially true for such major initiatives as the human genome project, where vast tracts of DNA of unknown function are sequenced. This sheer volume of available data makes advanced computer methods essen tial to analysis, and a familiarity with computers and sequence analy sis software a vital requirement for the researcher involved with DNA sequencing. Even for nonsequencers, a familiarity with sequence analysis software can be important. For instance, gene sequences already present in the databases can be extremely useful in the design of cloning and genetic manipulation experiments. This two-part work on Computer Analysis of Sequence Data is designed to be a practical aid to the researcher who uses computers for the acquisition, storage, or analysis of nucleic acid (and/or pro tein) sequences. Each chapter is written such that a competent scien tist with basic computer literacy can carry out the procedure successfully at the first attempt by simply following the detailed prac tical instructions that have been described by the author. A Notes section, which is included at the end of each chapter, provides advice on overcoming the common problems and pitfalls sometimes encoun tered by users of the sequence analysis software.
Categories: Science

Automated DNA Sequencing and Analysis

Automated DNA Sequencing and Analysis

This book reviews and assesses the state of the art of automated DNA sequence
analysis, from the construction of clone libraries to the development of laboratory
and community databases. The book is targeted at both small laboratories that ...

Author: Mark D. Adams

Publisher: Elsevier

ISBN: 9780080926391

Category: Science

Page: 368

View: 427

A timely book for DNA researchers, Automated DNA Sequencing and Analysis reviews and assesses the state of the art of automated DNA sequence analysis-from the construction of clone libraries to the developmentof laboratory and community databases. It presents the methodologies and strategies of automated DNA sequence analysis in a way that allows them to be compared and contrasted. By taking a broad view of the process of automated sequence analysis, the present volume bridges the gap between the protocols supplied with instrument and reaction kits and the finalized data presented in the research literature. It will be an invaluable aid to both small laboratories that are interested in taking maximum advantageof automated sequence resources and to groups pursuing large-scale cDNA and genomic sequencing projects. * The field of automation in DAN sequencing and analysis is rapidly moving. Hovever, as the technology becomes commonplace, those applying the techniques involved to their research fields need a text which both expands on the protocols supplied by manufacturers with their instruments and explains how to utilise the data produced. This book fulfils those needs, reviews the history of the art and provides pointers to future development.
Categories: Science

Phylogenetic Analysis of DNA Sequences

Phylogenetic Analysis of DNA Sequences

5 Aligning DNA Sequences: Homology and Phylogenetic Weighting DAVID P.
MINDELL Ever since the term homology was ... Phylogenetic analysis of DNA
sequences involves their alignment in such a way that homologous nucleotide
base ...

Author: Michael M. Miyamoto

Publisher: Oxford University Press

ISBN: 0195361970

Category: Science

Page: 368

View: 235

With increasing frequency, systematic and evolutionary biologists have turned to the techniques of molecular biology to complement their traditional morphological and anatomical approaches to questions of the historical relationship and descent among groups of animals and plants. In particular, the comparative analysis of DNA sequences is becoming a common and important focus of research attention today. The objective of this volume is to survey the emerging field of molecular systematics of DNA sequences, and to appraise the strengths and limitations of the different approaches yielded by these techniques. The contributors are an internationally recognized group of investigators from different schools and disciplines who critically address a diversity of crucial questions about DNA systematics, including DNA sequence data acquisition, phylogenetic inference, congruence and consensus problems, limitations of molecular data, and the integration of molecular and morphological data sets. The work will interest all botanists and zoologists involved in systematics, taxonomy, and evolution.
Categories: Science

Analysis of Amino Acid Sequences

Analysis of Amino Acid Sequences

(2) Protein sequence termini can be used to limit the extent of domains, as a
domain cannot extend beyond a protein terminus. (3) Repeats in ... Another
difficult case for sequence analysis of domains are discontinuous domains. In
some ...

Author:

Publisher: Elsevier

ISBN: 9780080493367

Category: Science

Page: 514

View: 696

Amino acid sequence analysis is useful for the study of problems ranging from modifications of single molecules to complex networks and interactions of species. Many available amino acid sequences are providing the basis for various studies at the proteome level. The dynamics of protein expression and the simulation of complex biological systems in which proteins interact with certain kinetics and in their respective compartments are just about to be tackled. Amino acid sequences will be crucial reference points for such studies. Mass spectrometric analysis of proteins Protein sequence databases Amino acid substitution matrices Amino acid-based phylogeny and alignment Individual variation in protein-coding sequences of the human genome Identifying nature's protein Lego® set
Categories: Science

Mathematical Methods of Analysis of Biopolymer Sequences

Mathematical Methods of Analysis of Biopolymer Sequences

One of the most important problems of the biological sequence analysis is the
search for similar sequences or sequence fragments and measuring the
observed similarity. One of the most widespread and theoretically substantiated
definitions ...

Author: Semen Grigorʹevich Gindikin

Publisher: American Mathematical Soc.

ISBN: 0821871153

Category: Science

Page: 150

View: 911

This collection contains papers by participants in the seminar on mathematical methods in molecular biology who worked for several years at the Laboratory of Molecular Biology and Bioorganic Chemistry (now the Institute of Physical and Chemical Problems in Biology) at Moscow State University. The seminar united mathematicians and biologists around the problems of biological sequences. The collection includes original results as well as expository material and spans a range of perspectives, from purely mathematical problems to algorithms and their computer realizations. For this reason, the book is of interest to mathematicians, statisticians, biologists, and computational scientists who work with biopolymer sequences.
Categories: Science

Affine Analysis of Image Sequences

Affine Analysis of Image Sequences

Chapter 2 Corner extraction and tracking 2.1 Introduction The first competence
required of a motion analysis system is the ... 2.2 Feature—based
correspondence Image sequence analysis begins with an attempt to find a vector
field describing ...

Author: Larry S. Shapiro

Publisher: Cambridge University Press

ISBN: 0521019788

Category: Computers

Page: 228

View: 794

Computer vision is a rapidly growing field which aims to make computers 'see' as effectively as humans. In this book, based on his award-winning thesis, Dr Shapiro presents a new computer vision framework for interpreting time-varying imagery.
Categories: Computers

Sequence Evolution Function

Sequence     Evolution     Function

Principles And Methods Of Sequence Analysis We aligned sequences by eye .
Troy CS , MacHugh DE , Bailey JF , Magee DA , Loftus RT , Cunningham P ,
Chamberlain AT , Sykes BC , Bradley DG . Genetic evidence for Near - Eastern
origins ...

Author: Eugene Koonin

Publisher: Springer Science & Business Media

ISBN: 1402072740

Category: Science

Page: 462

View: 867

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.
Categories: Science