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Although this book is based primarily on work that was completed in 1998, and therefore somewhat out of date, it is the best book I have found for teaching bioinformatics.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 ...

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Nucleic Acid Testing for Human Disease

Manufacturer: CRC
ProductGroup: Book
Binding: Hardcover

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ASIN: 157444543X

Book Description

Nucleic Acid Testing for Human Disease describes various techniques including target and signal amplification-based NAT procedures, microarrays, bead-based multiplex assays, in situ hybridization, and SNP techniques. This book discusses RNA expression profiling and laboratory issues such as the need for proper validation of tests intended for routine use. It focuses on specific applications of NATs to human disease diagnosis and treatment, from viral, bacterial, fungal, and protozoan detection to genetic exploration by SNP determinations, patterns of RNA expression, and the growing relevance of epigenetic changes. It also offers different perspectives on future directions in the field.

Nucleic Acids: Structures, Properties, and Functions

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An excellent text

Nucleic Acids: Structures, Properties, and Functions
Victor A. Bloomfield , Donald M. Crothers , Ignacio Tinoco , John E. Hearst , David E. Wemmer , Peter A. Killman , and Douglas H. Turner
Manufacturer: University Science Books
ProductGroup: Book
Binding: Hardcover

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ASIN: 0935702490

Book Description

Nucleic Acids presents an up-to-date and comprehensive account of the structures and physical chemistry properties of nucleic acids, with special emphasis on biological function. With a targeted audience of 1)molecular biologists, 2)physical biochemists, and 3)physical chemists, the book has been carefully organized to reach three different audiences while requiring only introductory physical chemistry and molecular biology as prerequisites. Nucleic Acids will serve as a textbook in physical biochemistry and biophysical chemistry classes, as well as a supplemental text in courses on nucleic acid biochemistry or molecular biology, and as a personal reference for students and researchers in these fields.

Customer Reviews:

Link to review.......2000-11-30

Authors are well known researchers in the field of nucleic acid biophysics. For detailed review of the book, look at J. Am. Chem. Soc., 122 (46), 11570 (2000).

An excellent text.......2000-11-28

This book is a revised edition of the original text by Bloomfield, Crothers, and Tinoco. A previous book written by this team discusses the Physical Chemistry of Nucleic Acids. The team continues in that tradition of good writing here.

It seems that the standard text for the study of nucleic acids is that by Saenger. But this text is also strong, to use either side by side with Saenger, or even on its own.

Illustrations are clear (although, no really pretty pictures except at the very end), and the writing is quite fluid and intelligible. This book, however, is not a book for beginners (ie. a person who's never read up on nucleic acids before). There tends to be some presupposition in the knowledge and technical jargon such that I think it would better serve as a reference for more advanced students and scientists.

The authors are recognized in the scientific world as being experts in their field, so it comes as no surprise that the text is full of good information.

Where the book falls short is as follows. The book is not very even in terms of the topics it covers. Another downside is that the book fails to discuss many of the newer experimental methods and discoveries, and in that sense is more out of date than you would like.

A good way to compensate for the two aforementioned problems is to supplement your reading with a text like Saenger, and to keep up to date with the current journal literature (if you're interested in methods, the first place to look is a place like Meth. Enzym.; if you're interested in reviews and other articles, turn to journals like Cell, Nature, Science, PNAS, and Biochemistry. If you're into more specialized stuff, consider these journals: 1)Nucleic Acids Research, and 2)RNA ).

Book Description

In recent years Molecular Biology has experienced an unprecedented revolution by the discovery of functional small RNAs. The number of cellular processes in which non-coding RNAs are involved is growing rapidly and include gene regulation on the transcriptional, post-transcriptional and translational level. To complicate matters, these processes seem to be strongly interconnected on the one hand, and diverse among different organisms on the other. This volume describes strategies for the discovery and validation of small RNAs and provides a snapshot of our current understanding of the different mechanisms triggered by small RNAs.

Nucleic Acid Research: Future Development

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Nucleic Acid Research: Future Development

Manufacturer: Academic Pr
ProductGroup: Book
Binding: Hardcover

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ASIN: 0125016506

Fluorescent Energy Transfer Nucleic Acid Probes: Designs And Protocols (Methods in Molecular Biology) (Methods in Molecular Biology)

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Fluorescent Energy Transfer Nucleic Acid Probes: Designs And Protocols (Methods in Molecular Biology) (Methods in Molecular Biology)

Manufacturer: Humana Press
ProductGroup: Book
Binding: Hardcover

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ASIN: 1588293807

Book Description

The first comprehensive treatment of energy transfer (ET) nucleic acid probes. Hands-on experts thoroughly describe all the major probes, both fluorescence resonance energy transfer (FRET)-based and non-FRET-based, and provide a complete set of techniques to monitor DNA and RNA reactions, including hybridization, amplification, cleavage, folding, and associations with proteins, other molecules, and metal ions. Optimal design strategies for customized ET probes are presented, as well as techniques for distance determination in protein-DNA complexes and the detection of topological DNA alterations, mutations, DNA breaks and single nucleotide polymorphisms. Merging work on nanotechnology, and fluorescent probes, authors describe in detail the design and application of ET-using molecular devices, such as biosensors, molecular machines, and logic gates for molecular scale computation.

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Should be on any biotechnology practicioner's shelf
A practicing MA biotech user
Excellent book for basic FAB, MALDI, and ESI
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REVIEW

Mass Spectrometry for Biotechnology
Gary Siuzdak
Manufacturer: Academic Press
ProductGroup: Book
Binding: Paperback

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ASIN: 0126474710

Book Description

If you investigate biological systems and might use mass spectrometry in your research but need to know more about it, this book is for you. It introduces the fundamental concepts of mass spectrometry and how mass spectrometers work. It also presents recent advancements particularly interesting to bio-researchers in an easy-to-understand manner that does not require extensive background in chemistry, math, or physics.

Key Features
* Glossary of basic terms
* Abundant illustrations
* Examples of applications
* Practical tips on using mass spectrometric techniques
* Useful for peptide, protein, oligonucleotide, and carbohydrate analysis
* Simplified description of mass spectrometry including:
* Matrix-Assisted Laser Desorption/Ionization (MALDI)
* Electrospray Ionization (ESI)
* Fast Atom/Ion Bombardment (FAB)

Customer Reviews:

Should be on any biotechnology practicioner's shelf.......2003-08-28

I love this book. I spent years selling GC-MS and LC-MS, then worked on software applications. But coming from a biology background, I appreciated the simple yet thorough introduction in Siuzdak's text for the applications commonly used in biotechnology. This is an excellent, well-written introductory text. I recommend it highly.

A practicing MA biotech user.......2002-08-14

A well written book that clearly explains the basics in addition to interesting examples of advanced applications.

Excellent book for basic FAB, MALDI, and ESI.......2001-10-17

This book is easy to read and packed with information. I especially like the table of different kinds of compounds and which ionization technique is the best for each of them. It is obvious that the author has actually run mass spectrometers, and he gives several good tips.

review.......2001-04-26

A very good book for the beginner in mass spectrometry. I've used it in numerous classes and the feedback from the students has been very positive.

REVIEW.......2001-04-24

Siuzdak has written a useful book for the novice or a student without a background in biological mass spectrometry. The book's small size and concise treatise, however, gives rise to many trite and overly simplistic explanations of aspects of the field and some errors. Consider, for example, page 37 that describes that a limitation of magnetic mass analyzers is their relatively "low" resolution. This is contradicted in Table 2.1 where a correct representation of the resolution is made. Also on page, Siuzdak describes the "physics behind" ion trap and conventional quadrupole analyzers as being "similar" when ion motion and dynamics in each analyzer is quite different. A textbook to be read with caution!

Protocols for Nucleic Acid Analysis by Nonradioactive Probes (Methods in Molecular Biology)

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Protocols for Nucleic Acid Analysis by Nonradioactive Probes (Methods in Molecular Biology)
Peter G. Isaac
Manufacturer: Humana Press
ProductGroup: Book
Binding: Paperback

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ASIN: 089603254X

Book Description

This book provides an exceptionally useful collection of tried and tested protocols for nucleic acid analysis that avoid the use of radioisotopes. Southern (i.e., DNA) and Northern (i.e., RNA) blotting protocols are covered in detail, from how to isolate good quality nucleic acids from plant and animal sources, to the use of the widest range of probe systems (involving digoxigenin, biotin, fluorescein, horseradish peroxidase labeling, and colorimetric and chemiluminescent detection). Other techniques treated in detail include hybridization in situ to chromosomes and transcribed RNA, newer and less conventional technologies, such as Randomly Amplified Polymorphic DNA (RAPD), reverse dot blots, bacterial identification using magnetic bead and dipstick assays, and nucleic acid sequence-based amplification.

Diagnostic Molecular Microbiology: Principles and Applications

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Diagnostic Molecular Microbiology: Principles and Applications
David H. Persing , Thomas F. Smith , Fred C. Tenover , and Thomas J. White
Manufacturer: American Society Microbiology
ProductGroup: Book
Binding: Plastic Comb

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ASIN: 155581056X

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Nucleic Acid Structure and Recognition
Stephen Neidle
Manufacturer: Oxford University Press, USA
ProductGroup: Book
Binding: Paperback

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ASIN: 019850635X

Book Description

This book provides a detailed view of the molecular structures of DNA and RNA and how they are recognised by small molecules and proteins. Extensive source material is provided, including information on relevant web sites and computer programmes. The major methods of structural investigation for nucleic acids: X-ray crystallography, NMR, and molecular modelling are reviewed and their scope and limitations (in the context of nucleic acids) discussed. Also covered are the conformational features of nucleic acid building blocks, including a description of how base-pair morphologies are analysed; the structures of DNA double helices and helical oligonucleotides, emphasising current ideas on sequence-dependent structure; and DNA-DNA interactions, including triplexes and quadruplexes. The principles of RNA folding, ribosome, and ribozyme structure are also surveyed. Both covalent and non-covalent nucleic acid interactions with small molecules are described, with the emphasis on recognition principles and sequence specific gene recognition. The principles of protein - nucleic acid are covered, focussing on regulatory proteins. Nucleic Acid Structure and Recognition will therefore equip readers with a good understanding of all the important aspects of this major field. The Nucleic Acid Database (NDB) crystallographic and NMR structures for the nucleic acid structures described in the book are freely available through the Nucleic Acid Structure and Recognition website.

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