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Author: Michael Gribskov Publisher: Oxford University Press ISBN: 0195356837 Category : Science Languages : en Pages : 297
Book Description
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.
Author: Michael Gribskov Publisher: Oxford University Press ISBN: 0195356837 Category : Science Languages : en Pages : 297
Book Description
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.
Author: Richard Durbin Publisher: Cambridge University Press ISBN: 113945739X Category : Science Languages : en Pages : 372
Book Description
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.
Author: Cedric Gondro Publisher: Springer ISBN: 3319144758 Category : Medical Languages : en Pages : 283
Book Description
Through this book, researchers and students will learn to use R for analysis of large-scale genomic data and how to create routines to automate analytical steps. The philosophy behind the book is to start with real world raw datasets and perform all the analytical steps needed to reach final results. Though theory plays an important role, this is a practical book for graduate and undergraduate courses in bioinformatics and genomic analysis or for use in lab sessions. How to handle and manage high-throughput genomic data, create automated workflows and speed up analyses in R is also taught. A wide range of R packages useful for working with genomic data are illustrated with practical examples. The key topics covered are association studies, genomic prediction, estimation of population genetic parameters and diversity, gene expression analysis, functional annotation of results using publically available databases and how to work efficiently in R with large genomic datasets. Important principles are demonstrated and illustrated through engaging examples which invite the reader to work with the provided datasets. Some methods that are discussed in this volume include: signatures of selection, population parameters (LD, FST, FIS, etc); use of a genomic relationship matrix for population diversity studies; use of SNP data for parentage testing; snpBLUP and gBLUP for genomic prediction. Step-by-step, all the R code required for a genome-wide association study is shown: starting from raw SNP data, how to build databases to handle and manage the data, quality control and filtering measures, association testing and evaluation of results, through to identification and functional annotation of candidate genes. Similarly, gene expression analyses are shown using microarray and RNAseq data. At a time when genomic data is decidedly big, the skills from this book are critical. In recent years R has become the de facto tool for analysis of gene expression data, in addition to its prominent role in analysis of genomic data. Benefits to using R include the integrated development environment for analysis, flexibility and control of the analytic workflow. Included topics are core components of advanced undergraduate and graduate classes in bioinformatics, genomics and statistical genetics. This book is also designed to be used by students in computer science and statistics who want to learn the practical aspects of genomic analysis without delving into algorithmic details. The datasets used throughout the book may be downloaded from the publisher’s website.
Author: Eugene V. Koonin Publisher: Springer Science & Business Media ISBN: 1475737831 Category : Science Languages : en Pages : 482
Book Description
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.
Author: Chhandak Basu Publisher: Humana ISBN: 9781493947553 Category : Medical Languages : en Pages : 0
Book Description
This volume provides an overview on design PCR primers for successful DNA amplification. Chapters focus on primer design strategies for quantitative PCR, in silico PCR primer design, and primer design using software. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and easily accessible, PCR Primer Design, Second Edition seeks to aid molecular biology students, researchers, professors and PCR enthusiasts.
Author: G.P. Pfeifer Publisher: Springer Science & Business Media ISBN: 9780306452376 Category : Medical Languages : en Pages : 476
Book Description
''Useful and timely.'' ---Mutagenesis ''Of considerable value.'' ---Journal of Medical Genetics ''Quite readable....a comprehensive overview....perfectly covers the needs of those researchers who have to decide on the best strategy to identify damage or mutations at the molecular level.'' ---Trends in Cell Biology ''The formats of the presentations are uniform and ample and up-to-date references are provided at the end of each chapter...will be welcomed by postgraduate researchers of all ages and should retain its usefulness for a long time.'' ---Endeavour, 21(4), 1997 This important resource thoroughly reviews a wide range of techniques used in mutagenesis research-ranging from established techniques to recently developed methodologies-based on the polymerase chain reaction. DNA damage analysis, DNA repair assays, and mutation detection are a few of the techniques featured. Chapters present detailed experimental protocols benefiting researchers and students in the fields of toxicology, biotechniques, molecular biology, photobiology, medical genetics, and oncology.
Author: Scott Markel Publisher: "O'Reilly Media, Inc." ISBN: 9780596004941 Category : Computers Languages : en Pages : 308
Book Description
This work pulls together all of the vital information about the most commonly used databases, analytical tools, and tables used in sequence analysis.
Author: Shawn T. O'Neil Publisher: ISBN: 9780870719264 Category : Science Languages : en Pages : 0
Book Description
A Primer for Computational Biology aims to provide life scientists and students the skills necessary for research in a data-rich world. The text covers accessing and using remote servers via the command-line, writing programs and pipelines for data analysis, and provides useful vocabulary for interdisciplinary work. The book is broken into three parts: Introduction to Unix/Linux: The command-line is the "natural environment" of scientific computing, and this part covers a wide range of topics, including logging in, working with files and directories, installing programs and writing scripts, and the powerful "pipe" operator for file and data manipulation. Programming in Python: Python is both a premier language for learning and a common choice in scientific software development. This part covers the basic concepts in programming (data types, if-statements and loops, functions) via examples of DNA-sequence analysis. This part also covers more complex subjects in software development such as objects and classes, modules, and APIs. Programming in R: The R language specializes in statistical data analysis, and is also quite useful for visualizing large datasets. This third part covers the basics of R as a programming language (data types, if-statements, functions, loops and when to use them) as well as techniques for large-scale, multi-test analyses. Other topics include S3 classes and data visualization with ggplot2.
Author: Emanuel A. Schegloff Publisher: Cambridge University Press ISBN: 1139459589 Category : Language Arts & Disciplines Languages : en Pages : 317
Book Description
Much of our daily lives are spent talking to one another, in both ordinary conversation and more specialized settings such as meetings, interviews, classrooms, and courtrooms. It is largely through conversation that the major institutions of our society - economy, religion, politics, family and law - are implemented. This book Emanuel Schegloff, the first in a series and first published in 2007, introduces the findings and theories of conversation analysis. Together, the volumes in the series constitute a complete and authoritative 'primer' in the subject. The topic of this first volume is 'sequence organization' - the ways in which turns-at-talk are ordered and combined to make actions take place in conversation, such as requests, offers, complaints, and announcements. Containing many examples from real-life conversations, it will be invaluable to anyone interested in human interaction and the workings of conversation.
Author: Michael Gribskov
Author: Michael Gribskov
Author: Richard Durbin
Author: Cedric Gondro
Author: Eugene V. Koonin
Author: Chhandak Basu
Author: Antoon D. L. Akkermans
Author: G.P. Pfeifer
Author: Scott Markel
Author: Shawn T. O'Neil
Author: Emanuel A. Schegloff