Sequence Analysis In A Nutshell

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

Sequence Analysis in a Nutshell: A Guide to Common Tools and Databases pulls together all of the vital information about the most commonly used databases, analytical tools, and tables used in sequence analysis.The book is partitioned into three fundamental areas to help you maximize your use of the content. The first section, Databases contains examples of flatfiles from key databases (GenBank, EMBL, SWISS-PROT), the definitions of the codes or fields used in each database, and the sequence feature types/terms and qualifiers for the nucleotide and protein databases.The second section, Tools provides the command line syntax for popular applications such as ReadSeq, MEME/MAST, BLAST, ClustalW, and the EMBOSS suite of analytical tools. The third section, Appendixes concentrates on information essential to understanding the individual components that make up a biological sequence. The tables in this section include nucleotide and protein codes, genetic codes, as well as other relevant information.Written in O'Reilly's enormously popular, straightforward Nutshell format, this book draws together essential information for bioinformaticians in industry and academia, as well as for students.If sequence analysis is part of your daily life, you'll want this easy-to-use book on your desk.

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.

Sequence analysis (SA) was developed to study social processes that unfold over time as sequences of events. It has gained increasing attention as the availability of longitudinal data made it possible to address sequence-oriented questions. This volume introduces the basics of SA to guide practitioners and support instructors through the basic workflow of sequence analysis. In addition to the basics, this book outlines recent advances and innovations in SA. The presentation of statistical, substantive, and theoretical foundations is enriched by examples to help the reader understand the repercussions of specific analytical choices. The extensive ancillary material supports self-learning based on real-world survey data and research questions from the field of life course research. Data and code and a variety of additional resources to enrich the use of this book are available on an accompanying website.

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.

This open access book provides innovative methods and original applications of sequence analysis (SA) and related methods for analysing longitudinal data describing life trajectories such as professional careers, family paths, the succession of health statuses, or the time use. The applications as well as the methodological contributions proposed in this book pay special attention to the combined use of SA and other methods for longitudinal data such as event history analysis, Markov modelling, and sequence network. The methodological contributions in this book include among others original propositions for measuring the precarity of work trajectories, Markov-based methods for clustering sequences, fuzzy and monothetic clustering of sequences, network-based SA, joint use of SA and hidden Markov models, and of SA and survival models. The applications cover the comparison of gendered occupational trajectories in Germany, the study of the changes in women market participation in Denmark, the study of typical day of dual-earner couples in Italy, of mobility patterns in Togo, of internet addiction in Switzerland, and of the quality of employment career after a first unemployment spell. As such this book provides a wealth of information for social scientists interested in quantitative life course analysis, and all those working in sociology, demography, economics, health, psychology, social policy, and statistics.; Provides new perspectives and methods for sequence analysis Focusses on the link between sequence analysis and other methods for longitudinal data, especially event history analysis and Markov models Stresses the complementarity of sequence analysis and other models for longitudinal data Applications of sequence analysis in a whole range of different domains This work was published by Saint Philip Street Press pursuant to a Creative Commons license permitting commercial use. All rights not granted by the work's license are retained by the author or authors.

Social sequence analysis includes a diverse and rapidly growing body of methods that social scientists have developed to help study complex ordered social processes, including chains of transitions, trajectories and other ordered phenomena. Social sequence analysis is not limited by content or time scale and can be used in many different fields, including sociology, communication, information science and psychology. Social Sequence Analysis aims to bring together both foundational and recent theoretical and methodological work on social sequences from the last thirty years. A unique reference book for a new generation of social scientists, this book will aid demographers who study life-course trajectories and family histories, sociologists who study career paths or work/family schedules, communication scholars and micro-sociologists who study conversation, interaction structures and small-group dynamics, as well as social epidemiologists.

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.

′This book provides an excellent reference guide to basic theoretical arguments, practical quantitative techniques and the methodologies that the majority of social science researchers are likely to require for postgraduate study and beyond′ - Environment and Planning ′The book provides researchers with guidance in, and examples of, both quantitative and qualitative modes of analysis, written by leading practitioners in the field. The editors give a persuasive account of the commonalities of purpose that exist across both modes, as well as demonstrating a keen awareness of the different things that each offers the practising researcher′ - Clive Seale, Brunel University ′With the appearance of this handbook, data analysts no longer have to consult dozens of disparate publications to carry out their work. The essential tools for an intelligent telling of the data story are offered here, in thirty chapters written by recognized experts. ′ - Michael Lewis-Beck, F Wendell Miller Distinguished Professor of Political Science, University of Iowa ′This is an excellent guide to current issues in the analysis of social science data. I recommend it to anyone who is looking for authoritative introductions to the state of the art. Each chapter offers a comprehensive review and an extensive bibliography and will be invaluable to researchers wanting to update themselves about modern developments′ - Professor Nigel Gilbert, Pro Vice-Chancellor and Professor of Sociology, University of Surrey This is a book that will rapidly be recognized as the bible for social researchers. It provides a first-class, reliable guide to the basic issues in data analysis, such as the construction of variables, the characterization of distributions and the notions of inference. Scholars and students can turn to it for teaching and applied needs with confidence. The book also seeks to enhance debate in the field by tackling more advanced topics such as models of change, causality, panel models and network analysis. Specialists will find much food for thought in these chapters. A distinctive feature of the book is the breadth of coverage. No other book provides a better one-stop survey of the field of data analysis. In 30 specially commissioned chapters the editors aim to encourage readers to develop an appreciation of the range of analytic options available, so they can choose a research problem and then develop a suitable approach to data analysis.

Sequence Analysis in Molecular Biology ...