perl

As a research scientist at a major pharmaceutical company, I became involved with microbial genomics four years ago. I have become familar with bioinformatics by talking and working with colleagues in my company, but on more than one occasion in the past, I found myself baffled by some detail or aspect of this new and rapidly evolving field. This book, Developing Bioinformatics Computer Skills is an outstanding introduction for the biologist attempting to become broadly familar with the basics of the bioinformatics field. The authors begin with a highly informative introduction to the Unix operating system, and then proceed to describe many of the basic tools for sequence analysis, database searching, multiple sequence alignments and phylogenetic analysis. This section has an outstanding non-mathematical explanation of scoring matrices and dynamic programming for alignments. This is followed by chapters on protein structure and predicting protein structure and function from sequence. They also discuss tools for sequence assembly, annotating genomes, proteomics and biochemical pathway databases. There is an excellent chapter on analysis of large data sets using Perl scripts. The book closes with chapters on building relational databases and data visualization. The material is well written and clearly presented, and can serve as an excellent springboard to more advanced texts in the field. I highly recommend it to those who are beginning to use bioinformatics, as well as to those more experienced who would like a ready reference with the basics all under one cover. Well worth the modest price!!

This book is the worst I've ever purchased. It has been no help whatsoever. It had a couple examples of PERL programming...big deal.

The 5-star ratings are obvious shills (one reviewer wrote a very long review and has never reviewed anything else)

This book is a good introduction to Bioinformatics and to what it takes to get started in the field. Some reviewers deride it as too superficial or as too Unix-centric, but I think those are two of its strengths. The authors lay no claim to having written the definitive work on the subject of Bioinformatics, and they freely admit that they come in with a certain bias. If you are serious about Bioinformatics this won't be your last book anyway, but it'll get you started.

That said, I found the material a bit uneven. The authors tend to jump from almost trivial stuff to very complex in a heartbeat, and they sometimes use a concept or command before it can be properly understood One example: Introducing the Unix commands head and tail, then moving on to split and csplit. The introduction to regular expressions as needed by csplit follows a few pages later.

Nevertheless, I plan to use this book as a companion text to my own sequence of computer classes for biologists, and I think it will serve that purpose very well.