Chad Clark's Open Journal : 2008-02-02

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February 02, 2008 :
1) Book review : Introduction to Bioinformatics by Anna Tramontano

The book packs a lot into 170 pages.  It was published in 2007 so I expect
it to be reasonably up to date.  It does mention a few web sites with the
comment that web resources quickly change in the lifetime of a book.

A few kinds of databases are discussed. eg: nucleotide, protein sequence,
protein structure, and protein interaction.

High level descriptions of algorithms are include.  eg: searching for and
comparing similar sequences, statistical calculations to determine if two
sequences are probably closely related through evolution.

A few computer science methods get explained including Artificial Neural
Networks, Markov Models, and Genetic Algorithms.

Roughly the last third of the book is about protein folding prediction.
This part discusses evolutionary related folds, energy calculations, and
empirically determined properties of amino acids.

I suspect the intended audience is someone with a background mostly in
biology, a statistics course or two, and maybe a tiny bit of computer
programming.

The algorithm descriptions are high level but there are some formulas and
statistical discussion.  The descriptions are mostly to describe how data
is searched or compared an where the calculated results come from.  The
book mentions that database with search tools exist and does not document
any particular tools because it will quickly become out of date.

The book really is an introduction.  I like that each chapter lists
references for historical contributions and suggestions for further
reading.  Each chapter also starts with a glossary of terms used in the
chapter.



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