Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids

Book Description

Probablistic models are becoming increasingly important in analyzing 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 analyzing 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 is accessible to molecular biologists, computer scientists, and mathematicians with no formal knowledge of the other fields, and at the same time presents the state of the art in this new and important field.

Customer Reviews:

Great reference.......2007-09-06

A great reference and a good introduction to many important concepts in sequence analysis. However, if you don't have a reasonable grounding in math you may struggle with the terse notation.

Borodovsky's companion book is an excellent partner for this book. Get both.

One of the best available.......2007-08-17

Although this book is based primarily on work that was completed in 1998, and therefore somewhat out of date, it is the best book I have found for teaching bioinformatics. I selected this as the best of the available books on the subject for use in my bioinformatics and numerical methods course which is to be taught in the fall of 2007 at Univ. of Conn. This course is an upper division undergraduate and first year graduate course. That is roughly the level of this text and the comparative advantage of this book is the excellent presentation and thorough discussion of the algorithms. A student armed with Matlab or MathScriptor can take this book and start writing algorithms for sequence alignment and Hidden Markov Method (HMM) analysis after only the first three or four chapters. This book is in its 11th printing and is nearly error free (I found only a few in the figures). This book is strongly recommended for both students and researchers, particularly those interested in protein alignment, phylogenic analysis or an introduction to Hidden Markov Methods.

Biological Sequence Analysis.......2006-03-07

This is a very good book. I got it for a class and it is very helpful and insightful.

Truly an Excellent Book.......2006-02-18

I will agree and submit: this is an invaluable introduction to the field of bioinformatics. With introductions to everything from sequence analysis to hidden markov models and even a primer on grammars, this is a useful introduction both to biological applications for computer scientists *as well as* computational methods for biologists.

I am in a joint graduate-level biology/computer science class and we are using this book as a foundation to bring both groups up to speed and it seems to be working out nicely.

However, one criticism is that sometimes Durbin et al jump into subjects without an adequate introduction or with one that is overcomplexified. In other words, they sometimes break Einstein's the rule of "make everything as simple as possible but not simpler". Durbin et al do not always make things as simple as possible. And it is annoying when they do not. Especially when I see them confusing the bejebus out of the biology people over computer science concepts that are really not that complicated through overly technical jargon.

But this is rare and they provide many insightful diagrams to clear up their algorithms as well as lucid ways to introduce biological concepts. Sometimes the introduction of an algorithm/theory *and* a biological concept molds together beautifully such that the reader is simultaneously being infused with both. An example of this phenomenon is their dual introduction to CpG islands and markov models.

Excellent book ... a little boring to read ..........2005-09-30

I bought "Biological Sequence Analysis" for my introductory bioinformatics course. AS the course covers almost everything mentioned in the book I have (almost) finished reading and studying it.

I find this book an excellent textbook but wouldn't consider it a classic. There are some important topics missing or some topics are just briefly touched upon. (e.g. heuristic pairwaise alignment) Maybe it's just because of my theoretical background, but I find that the book does a poor job in explaining/proving the intuition behind certain aspects of the algorithms (e.d. why does a convex gap penalty lead to a different complexity than a strictly increasing gap penalty ...) . On the other hand, the probabilistic foundations of the different techniques is well written.

My final remark is that the book is not fun to read at all. The authors have made no effort to spice up the content with some historical background, some explanations of how the theory fits in the bigger picture ...

Summarized: an excellent textbook for anyone taking a course in bioinformatics but do not use this book to wet your appetite for the field ...

Bioinformatics: A Practical Guide to the Analysis of Genes and Proteins

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Somewhat more than an out-of-date catalog of tools
A survey for tool users
Bioinformatic for the beginner...
Poorly organized overpriced book
...

Bioinformatics: A Practical Guide to the Analysis of Genes and Proteins

Manufacturer: Wiley-Interscience
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Binding: Hardcover

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ASIN: 0471478784

Book Description

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.

Customer Reviews:

Somewhat more than an out-of-date catalog of tools.......2004-03-27

The book is a collection of chapters by different authors addressing software tools for various problems: database search, multiple sequence alignment, gene prediction, protein structure prediction, etc. A big flaw is that all of the authors assume a different level of prior background and have rather different emphases.

I'd have to agree with the other reviewer that Chapters 1 & 17, which constitute 10% of the book, are wasted paper. No one in 2001 (when the book was published), let alone 2004, needs Chapter 1's lengthy explanation of what e-mail and web browsers are. And the perl program at the anticlimax of Chapter 17 was ... anticlimactic.

The book is to a great extent a catalog of available software tools. With the exception of the chapters on multiple alignment and phylogeny, the emphasis is on not on how the tools work but how to operate them -- to the of saying "at this URL there is a web page where you can either paste in your sequence or upload a file". The idea of invoking a program through a Unix command line is more than once presented as a truly daunting prospect. The authors generally do a good job of emphasizing that the programs are the beginning of analysis and not the end; the results must always be viewed somewhat skeptically with an expert eye.

If you're coming at the book as a biologist, you will probably find it to be a useful catalog of software, though undoubtedly dated by now. If you're coming at it from the informatics side, you're going to need some background... a book like Dwyer's, Setubal and Meidanis's, or Mount's will get you up to speed on the algorithm aspects of the field with simplified versions of many of the big problems. Then you can look at this book to find good pointers to the ways the real-world versions have been addressed.

The book was published three years ago and, being to a large extent an index of the work of others, is necessarily no longer up to date in a fast-moving field. It needs a revision and, in the meantime, it would make more sense to snag a used copy than to pay full price for a new book.

A survey for tool users.......2003-10-09

Like any survey, it seems to touch the major features only. And, as others have pointed out, the tools change but the book doesn't.

I think this is a good, brief introduction to the wide variety of bioinformatic tools and databases on the internet. It describes the major features of each, and the kinds of results that each tool is good for. After that, the serious user will go to the sources of each tool or database, to learn more about the specifics as of the moment. No book can hope to keep up with the weekly enhancements at the major repositories.

I emphasize that this is for tools users, not tool makers. It addresses the working scientists who already know their subjects and their needs. This skips over the algorithms in favor of higher level descriptions, and skips over many of the biological reasons for the tools described. Better-informed tool users get better answers from the tools, true. At some point, though, the biologists want to skip the theory, skip the introduction to subjects in which they're experts, and get on with their science. I don't think this book was ever meant for people - and I'm one - who want full details of the algorithms.

I agree, the book treats its many subjects in a shallow way. I think that is by intent, since the book's real goal is breadth and its target is a reader who knows the basic science. It's a bit off the center of my interests, but I've found it helpful.

Bioinformatic for the beginner..........2003-01-31

I guess that everybody interrested by this kind of book knows already a little about bioinformatic and wants to improve his bioinformatician skill. So forget about this book:
This is really a well-documented introduction to all the methods currently used by every biologist or biology student, such as Blast, Clustal, multiple alignement or use of web-interface for submiting sequence.
So get it if you need a clear introduction to the field, but if you already know a little bit about bioinfo, immediately choose a more detailed book.

Poorly organized overpriced book.......2002-09-30

Although the book is presented as an introduction to the topic, its organization assumes that the reader has already been working in the area. Two of the chapters (1 and 17) are a waste of space. The first chapter presents a (useless) introduction to internet, while chapter 17 attempts (and fails to do so) to explain Perl in the context of bioinformatics. For the same money you can find far better books in the market. The good thing is that I only borrowed the book :)

..........2002-06-27

I used the Baxevanis volume in coursework at Johns Hopkins Biotechnology program...several of the chapter authors are associated with the school. There's no doubt that the editor and authors are experts in their fields, but the volume seems somewhat dated, and is disjointed. I found a couple of the chapters virtually unreadable. The real killer is the price. The book is GROSSLY overpriced...

Book Description

Protein NMR Spectroscopy combines a comprehensive theoretical treatment of NMR spectroscopy with an extensive exposition of the experimental techniques applicable to proteins and other biological macromolecules in solution. Beginning with simple theoretical models and experimental techniques, Protein NMR Spectroscopy develops the complete repertoire of theoretical principles and experimental techniques necessary for understanding and implementing the most sophisticated NMR experiments.

Important new techniques and applications of NMR spectroscopy have emerged since the first edition of this extremely successful book was published in 1996. The second edition includes new sections describing measurement and use of residual dipolar coupling constants for structure determination, TROSY and deuterium labeling for application to large macromolecules, and experimental techniques for characterizing conformational dynamics. In addition, the treatments of instrumentation and signal acquisition, field gradients, multidimensional spectroscopy, and structure calculation are updated and enhanced.

Protein NMR Spectroscopy is written as a graduate-level textbook and will be of interest to biochemists, chemists, biophysicists, and structural biologists who utilize NMR spectroscopy or who wish to understand the latest developments in this field.

· Provides an understanding of the theoretical principles important for biological NMR spectroscopy
· Demonstrates how to implement, optimize and troubleshoot modern multi-dimensional NMR experiments
· Allows for the capability of designing effective experimental protocols for investigations of protein structures and dynamics
· Includes a comprehensive set of example NMR spectra of ubiquitin provides a reference for validation of experimental methods

Customer Reviews:

Satisfied.......2007-09-05

I have been reading this book for a while and decided to buy it. I am satisfied with the vendor, it arrived in good condition and fairly on time.

New 'Bible' for Protein NMR.......2007-06-16

This is the new standard for Protein NMR spectroscopists (the old one being Ernst). Everyone I've met who uses NMR in biology has nothing but praise for this book. It's not a perfect book and has some weakness, especially in the modelling portions. The math derivations are clear but the authors do not connect back to the physical phenomenon. I would recommend keeping a QM book nearby as a reference. However, this book is well written overall and very complete. Highly recommended!

Useful Handbook for Protein NMR study.......2000-04-29

The book is very complete, covers most of the field in protein NMR studies. The book is well organised, with plenty of figures to facilitate easy understanding of the subject. Overall, I find it is very helpful for anyone who will be interested in protein NMR research. I have actually seen quite a number of copies in a few NMR laboratories and I would recommand this book to all those who are looking for an complete introductory book in NMR and protein study.

Lectin Methods and Protocols (Methods in Molecular Medicine)

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Lectin Methods and Protocols (Methods in Molecular Medicine)

Manufacturer: Humana Press
ProductGroup: Book
Binding: Hardcover

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ASIN: 0896033961

Book Description

A comprehensive collection of optimized methods for using lectins in biomedical research. The techniques-fine-tuned by the researchers who developed them-apply lectins to the analysis of carbohydrates, to the isolation and quantification of glycoproteins, and to living cells. Also included are detailed methods for the separation of human bone marrow cells for clinical use, for the assessment of the biological effects of plant lectins, and for the use of light and electron microscopy in analyzing carbohydrate structures. Extremely useful tools for examining structural changes in glycosylation and their functional consequences for human pathophysiology.

Basic Protein and Peptide Protocols (Methods in Molecular Biology)

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Basic Protein and Peptide Protocols (Methods in Molecular Biology)

Manufacturer: Humana Press
ProductGroup: Book
Binding: Paperback

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ASIN: 0896032698

Book Description

Basic Protein and Peptide Protocols offers an excellent collection of reproducible, step-by-step laboratory methods covering three major areas: (1) the quantitation and characterization of proteins, (2) the electrophoretic and blotting procedures used in protein isolation and characterization, and (3) the analysis of protein and peptide structure. THOUSANDS of labs are already using Basic Protein and Peptide Protocols-you should be too!

Exploration and Analysis of DNA Microarray and Protein Array Data (Wiley Series in Probability and Statistics)

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Excellent!

Exploration and Analysis of DNA Microarray and Protein Array Data (Wiley Series in Probability and Statistics)
Dhammika Amaratunga , and Javier Cabrera
Manufacturer: Wiley-Interscience
ProductGroup: Book
Binding: Hardcover

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ASIN: 0471273988

Book Description

The emergence of genomics, the study of genes, is one of the major scientific revolutions of this century. Microarrays, a method used to analyze numerous DNA samples rapidly, enables scientists to make sense of this mountain of data using statistical analysis. They are being used in such areas of biomedical research as studying patterns for gene activity that cause cancers to spread. This book presents a comprehensive methodology for analyzing DNA microarray and protein array data.
The most comprehensive treatment of this important emerging field, Exploration and Analysis of DNA Microarray and Protein Array Data includes:
A review of basic molecular biology and a chapter introducing microarrays and their preparation
Chapters on processing scanned images, preprocessing microarray data, group comparative experiments, and other designs
Discussions of clustering, protein arrays, and applications for diagnostic tools
Ample exercises assist absorbtion

Customer Reviews:

Excellent!.......2004-03-30

This book provides an excellent overview of various methods in DNA microarray analysis. It explains most of the theories behind the algorithms, so that you know why the analyses are done in certain way. In fact, I find I get more insights from the book as compare to the research papers which tend to be brief.

Protein Phosphatase Protocols (Methods in Molecular Biology)

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Protein Phosphatase Protocols (Methods in Molecular Biology)

Manufacturer: Humana Press
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ASIN: 158829711X

Book Description

Protein Phosphatase Protocols presents a broad range of protocols for the study of protein phosphatases, all written by experts and innovators from phosphatase laboratories around the world. This volume is a compendium of resources for the study of protein phosphatases and their potential as drug targets. Experimental methodologies are taken from proteomics, bioinformatics, genomics, biochemistry, RNAi, and genetics. Included protocols utilize several model organisms, including yeast, Drosophila, and various plant and human cells. Protein Phosphatase Protocols provides a concise introduction to protein phosphatase research, with particular attention to phosphatase families. Assays for identification, quantification, purification, and functional characterization are presented throughout in specific detail.

Protein Biochemistry and Proteomics (The Experimenter Series)

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good book - misprinted edition - missing / blank pages in Ch.2
really helpful

Protein Biochemistry and Proteomics (The Experimenter Series)
Hubert Rehm
Manufacturer: Academic Press
ProductGroup: Book
Binding: Paperback

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ASIN: 012088545X

Book Description

Hubert Rehm's Protein Biochemistry and Proteomics is more than a laboratory manual; it is a strategic guide that provides the reader with tips and tricks for more successful lab experiments. Using a conversational yet professional tone, Rehm provides an overview of a variety of methods in protein biochemistry/proteomics. He provides short and precise summaries of routine procedures as well as listings of the advantages and disadvantages of alternative methods. Readers will immediately sense that the author if very familiar with the challenges, and frustration of the daily lab routine. Never before has such an honest, tactical guide been available for those conducting lab experiments within the field of biochemistry.

· Shows how to avoid experimental dead ends and helps users develop an instinct for the right experiment at the right time
· Contains short and precise summaries of routine procedures (e.g. column chromatography, gel electrophoresis), and lists the advantages and disadvantages of alternative methods
· Includes over 100 detailed figures and tables
· Contains a chapter on proteomics

Customer Reviews:

good book - misprinted edition - missing / blank pages in Ch.2.......2007-07-30

In the chapter 2, a number of important pages (50-51, 54-55, 58-59, 62-63, 66-67, 70-71, 74-75, 78-79) is missed / left blank - apparently by the publisher's fault! This is really frustrating - a good book is ruined by a printing mishap!

really helpful.......2006-10-31

I've found this book really very helpful. I'm essentially a geneticist/molecular biologist, but with this book I've been able to develop a multistep protocol for affinity purifying my protein of interest. The book is clear and concise, I would highly recommend it.

Proteome Research: Two-Dimensional Gel Electrophoresis and Identification Methods (Principles and Practice)

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Necessary Text for the Neophyte

Proteome Research: Two-Dimensional Gel Electrophoresis and Identification Methods (Principles and Practice)

Manufacturer: Springer
ProductGroup: Book
Binding: Paperback

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ASIN: 3540657924

Book Description

Two-dimensional electrophoresis is the central methodology in proteome research, and the state of the art is described in detail in this text, together with extensive coverage of the detection methods available. Sufficient detail is given to allow the readers to apply these technologies to their own particular requirements.

Customer Reviews:

Necessary Text for the Neophyte.......2000-07-03

After reading the book, I better understood the fundamentals of proteomics. The book over all is well written and provides information into the new technology of proteomics that have been poorly described in other texts. Professor Rabilloud, Thanks.

Protein and Peptide Analysis by Mass Spectrometry (Methods in Molecular Biology)

Average customer rating:

A good hand-book on protein analysis by MS

Protein and Peptide Analysis by Mass Spectrometry (Methods in Molecular Biology)

Manufacturer: Humana Press
ProductGroup: Book
Binding: Hardcover

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ASIN: 0896033457

Book Description

Leading practitioners authoritatively describe the newest and most effective spectrometric techniques for the analysis of proteins and peptides. The areas covered range from the elucidation of primary and secondary protein structure and the rapid identification of proteins using database techniques to methods for sequencing, as well as methods for the quantitative determination of peptides. Other chapters provide detailed information on the analysis of glycoproteins and glycopeptides and on the use of mass spectrometry to probe the interactions of proteins, both covalent and noncovalent.

Customer Reviews:

A good hand-book on protein analysis by MS.......2000-04-21

"Protein and Peptide Analysis by Mass Spectrometry" is a very good handbook for beginners, as well as experienced people. It is written by some of the best world specialists in the field. Volume 61 of the famous "Methods in Molecular Biology" series, it is built on the usual format: Introduction, Materials, Methods and Notes. Very clear and very practical, this up-to-date book should content most people interested in protein analysis.

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