- Paperback: 356 pages
- Publisher: Cambridge University Press; 1 edition (May 13, 1998)
- Language: English
- ISBN-10: 0521629713
- ISBN-13: 978-0521629713
- Product Dimensions: 6.8 x 0.8 x 9.7 inches
- Shipping Weight: 1.7 pounds (View shipping rates and policies)
- Average Customer Review: 25 customer reviews
- Amazon Best Sellers Rank: #184,216 in Books (See Top 100 in Books)
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Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids 1st Edition
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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.
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One chapter covers the basics of dynamic programming for string matching: a staple of bioinformatics computing. The authors come back to it a number of times as they introduce new variations on the string-matching theme. They give about the clearest description of the Needleman-Wunsch and basic variants (including Smith-Waterman) of any book I know.
The bulk of the book is devoted to Hidden Markov Models (HMMs), as one might have guessed in a book with Eddy as co-author. It covers the basics of model construction, motif finding, and various uses for decoding. Again, it covers all the basics so clearly you'll want to start coding as soon as you read it.
The later sections of the book cover phylogeny and tree building, along with the relationships to multiple alignment. Good, solid, clear writing prepares the reader for texts that may be more specialized, but possibly less transparent.
The next-to-last chapter, on RNA folding, is weaker than the ones before, in my opinion. It ties to the other chapters reasonably well in terms of algorithms, but I don't think it does justice to the thermodynamic models of RNA folding. If there is any weakness in this chapter, though, it does not detract from the strengths elsewhere.
The final chapter, the "background on probability", is the one that I think needs the most support. If you don't already understand its topics, I doubt that this will help very much. (If you do understand them, you won 't need the help.) There's nothing inherently tricky about probability, but individual distributions carry many assumptions, and I did not see those spelled out well.
This shouldn't be the only book in your bioinformatics library. If you really want algorithms, though, it's a good book to have in the collection and one you'll keep coming back to.
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.