Excellent product, well supported by both Mathworks and the community, 14 Dec 2007
Matlab has become very popular in the engineering field. Whilst both Maple and Mathematica have stronger symbolic capabilities, Matlab excels in the numerics and so tends to be used for engineering more than pure maths.

The Matlab documentation is built into the program and is also available online. There is a very active newsgroup comp.soft-sys.matlab where Matlab users can ask for help. It is read by a lot of staff from Mathworks and they, or other Matlab users, answer questions quickly. The importance of good support on this sort of software can not be overstated. This is a serious issue with Mathematica, which is a similar(ish) product to Matlab. The Mathematica newsgroup is moderated, so help requests can take a day before anyone sees them. To get a satisfactory answer to a question can often take a long time.

Matlab is excellent value for money for students, being cheaper than the student versions of either Maple or Mathematica. Although this is is a "sprat to catch a mackerel", as the commercial version of Matlab is expensive. This student version includes various toolboxes and Simulink, all of which are optional extras if you buy the commercial version.

The commercial version of Matlab is available on Solaris, but only Windows, Linux and Mac are supported on the student version. Since I used Solaris as a student, I would have found this annoying. There would be no harm in asking if they would give a license for Solaris.

Excellent product, well supported by both Mathworks and the community, 14 Dec 2007
Matlab has become very popular in the engineering field. Whilst both Maple and Mathematica have stronger symbolic capabilities, Matlab excels in the numerics and so tends to be used for engineering more than pure maths.

The Matlab documentation is built into the program and is also available online. There is a very active newsgroup comp.soft-sys.matlab where Matlab users can ask for help. It is read by a lot of staff from Mathworks and they, or other Matlab users, answer questions quickly. The importance of good support on this sort of software can not be overstated. This is a serious issue with Mathematica, which is a similar(ish) product to Matlab. The Mathematica newsgroup is moderated, so help requests can take a day before anyone sees them. To get a satisfactory answer to a question can often take a long time.

Matlab is excellent value for money for students, being cheaper than the student versions of either Maple or Mathematica. Although this is is a "sprat to catch a mackerel", as the commercial version of Matlab is expensive. This student version includes various toolboxes and Simulink, all of which are optional extras if you buy the commercial version.

The commercial version of Matlab is available on Solaris, but only Windows, Linux and Mac are supported on the student version. Since I used Solaris as a student, I would have found this annoying. There would be no harm in asking if they would give a license for Solaris.


they say on the title "an excellent book for beginners and occasional practioners", 19 Jun 2007
... and I agree. This is a book for molecular biologist who want to analyse their data using bioinformatics tools. I would prefer Baxevanis/Oullette "Bioinformatics: A Practical Guide to the Analysis of Genes and Proteins", however, if this is too expensive for you than this "Bioinformatics for Dummies" is the second best choice. Layout and index is a bit more confused but it covers most stuff you will need.

A word of warning: if you want to learn how the programs work, you have to look for a different type of book, e.g. "Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids" by R. Durbin, Sean R. Eddy, Anders Krogh, and Graeme Mitchison or "Algorithmic Aspects of Bioinformatics" by Hans-Joachim Bockenhauer and Dirk Bongartz.

Clear and informative, 26 Dec 2005
So much of the information is this field (and indeed some of the applications which have been developed) seems almost intentially convoluted and difficult to understand. This book gives a very good overview of some of the more common programs that one will need to use if one is starting bioinformatics research in a way that is practical and easy understand. Despite the title, the authors have done some good work in the field (I use Notredame's T-Coffee alignment program often) and are credible authorities in this area.

Excellent product, well supported by both Mathworks and the community, 14 Dec 2007
Matlab has become very popular in the engineering field. Whilst both Maple and Mathematica have stronger symbolic capabilities, Matlab excels in the numerics and so tends to be used for engineering more than pure maths.

The Matlab documentation is built into the program and is also available online. There is a very active newsgroup comp.soft-sys.matlab where Matlab users can ask for help. It is read by a lot of staff from Mathworks and they, or other Matlab users, answer questions quickly. The importance of good support on this sort of software can not be overstated. This is a serious issue with Mathematica, which is a similar(ish) product to Matlab. The Mathematica newsgroup is moderated, so help requests can take a day before anyone sees them. To get a satisfactory answer to a question can often take a long time.

Matlab is excellent value for money for students, being cheaper than the student versions of either Maple or Mathematica. Although this is is a "sprat to catch a mackerel", as the commercial version of Matlab is expensive. This student version includes various toolboxes and Simulink, all of which are optional extras if you buy the commercial version.

The commercial version of Matlab is available on Solaris, but only Windows, Linux and Mac are supported on the student version. Since I used Solaris as a student, I would have found this annoying. There would be no harm in asking if they would give a license for Solaris.


they say on the title "an excellent book for beginners and occasional practioners", 19 Jun 2007
... and I agree. This is a book for molecular biologist who want to analyse their data using bioinformatics tools. I would prefer Baxevanis/Oullette "Bioinformatics: A Practical Guide to the Analysis of Genes and Proteins", however, if this is too expensive for you than this "Bioinformatics for Dummies" is the second best choice. Layout and index is a bit more confused but it covers most stuff you will need.

A word of warning: if you want to learn how the programs work, you have to look for a different type of book, e.g. "Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids" by R. Durbin, Sean R. Eddy, Anders Krogh, and Graeme Mitchison or "Algorithmic Aspects of Bioinformatics" by Hans-Joachim Bockenhauer and Dirk Bongartz.

Clear and informative, 26 Dec 2005
So much of the information is this field (and indeed some of the applications which have been developed) seems almost intentially convoluted and difficult to understand. This book gives a very good overview of some of the more common programs that one will need to use if one is starting bioinformatics research in a way that is practical and easy understand. Despite the title, the authors have done some good work in the field (I use Notredame's T-Coffee alignment program often) and are credible authorities in this area.

Brings strands of knowledge together, 11 Oct 2008
My science background is well out-of-date. In this book I can find several half understood concepts brought together, well explained and illuminating each other to an amazing extent. It's really rather exciting!

A great introductory book, 25 Jun 2004
This is an excellent introduction to this up-and-coming field. Bioinformatics one of many fields that is inherently inter-disciplinary, with biologists coming in and needing to learn computer science, and computer scientists coming in and needing to learn biology. I think that the book is very useful for both groups. I have a computer science background and did not find any of the biology overly difficult. So I highly recommend it for anyone, from the undergraduate to the postrgraduate or professional.

The book covers all of the major topics in bioinformatics, and touches on several of the minor ones. There are 5 long chapters:
Chapter 1 Introduction: introduces the basics of the field, describing the basics of data archiving, the WWW, computers and computer programming, biological classification and nomenclature, phylogenetic relationships and use of sequences, PSI-BLAST, and protein structure.
Chapter 2 Genome organization and evolution: genomics and proteomics, methods of genetic information transmission, genes and genomes, SNPs, genome evolution.
Chapter 3 Archives and information retrieval: this contains a detailed discussion of various databases and how to interact with them.
Chapter 4 Alignments and phylogenetic trees: this vast majority of this chapter covers many aspects of the important area of sequence alignment, including BLAST and HMMs. Then it has short sections on phylogeny and phylogenetic trees, again covering the basics.
Chapter 5 Protein structure and drug discovery: this starts with protein folding, and deals with hydrophobicity, structural alignments, DALI, and then evolution, classification and prediction of protein structures and function. Finally it touches on drug discovery in this context.

One of the nice things about this book is the code samples, written in the bioinformatician's favorite language, Perl. These are printed and discussed in the book, but then also available on the web site that is associated with the book, so you don't have to type it in yourself. In addition to the programs, the website also has graphics from the book, many of which rotate so you can see them from different positions (can't get that in a book!). It also has the web links mentioned in the book, so you can explore them more conveniently than having to flip through the book and type the URLs in.

An excellent beginner's guide to bioinformatics, 27 Apr 2002
This is a superb introduction to the subject of bioinformatics. It is very well written, and for the first time (thanks to this book) I can understand what hidden Markov models are about. It invites comparison with another book of the same name, namely "Introduction to Bioinformatics" by Attwood and Parry-Smith. The book by Lesk has two advantages (three, I suppose, if you include the fact that it is a more recent publication): it uses everyday, non-biological analogies to explain many of the concepts that are otherwise difficult to grasp, and it also covers molecular modelling.

Advanced undergraduate students tackling bioinformatics for the first time, or research students whose experience of bioinformatics is limited to the odd BLAST search and surfing through genomes, will find this book a must have. You will wonder how you ever got by without it.

Excellent product, well supported by both Mathworks and the community, 14 Dec 2007
Matlab has become very popular in the engineering field. Whilst both Maple and Mathematica have stronger symbolic capabilities, Matlab excels in the numerics and so tends to be used for engineering more than pure maths.

The Matlab documentation is built into the program and is also available online. There is a very active newsgroup comp.soft-sys.matlab where Matlab users can ask for help. It is read by a lot of staff from Mathworks and they, or other Matlab users, answer questions quickly. The importance of good support on this sort of software can not be overstated. This is a serious issue with Mathematica, which is a similar(ish) product to Matlab. The Mathematica newsgroup is moderated, so help requests can take a day before anyone sees them. To get a satisfactory answer to a question can often take a long time.

Matlab is excellent value for money for students, being cheaper than the student versions of either Maple or Mathematica. Although this is is a "sprat to catch a mackerel", as the commercial version of Matlab is expensive. This student version includes various toolboxes and Simulink, all of which are optional extras if you buy the commercial version.

The commercial version of Matlab is available on Solaris, but only Windows, Linux and Mac are supported on the student version. Since I used Solaris as a student, I would have found this annoying. There would be no harm in asking if they would give a license for Solaris.


they say on the title "an excellent book for beginners and occasional practioners", 19 Jun 2007
... and I agree. This is a book for molecular biologist who want to analyse their data using bioinformatics tools. I would prefer Baxevanis/Oullette "Bioinformatics: A Practical Guide to the Analysis of Genes and Proteins", however, if this is too expensive for you than this "Bioinformatics for Dummies" is the second best choice. Layout and index is a bit more confused but it covers most stuff you will need.

A word of warning: if you want to learn how the programs work, you have to look for a different type of book, e.g. "Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids" by R. Durbin, Sean R. Eddy, Anders Krogh, and Graeme Mitchison or "Algorithmic Aspects of Bioinformatics" by Hans-Joachim Bockenhauer and Dirk Bongartz.

Clear and informative, 26 Dec 2005
So much of the information is this field (and indeed some of the applications which have been developed) seems almost intentially convoluted and difficult to understand. This book gives a very good overview of some of the more common programs that one will need to use if one is starting bioinformatics research in a way that is practical and easy understand. Despite the title, the authors have done some good work in the field (I use Notredame's T-Coffee alignment program often) and are credible authorities in this area.

Brings strands of knowledge together, 11 Oct 2008
My science background is well out-of-date. In this book I can find several half understood concepts brought together, well explained and illuminating each other to an amazing extent. It's really rather exciting!

A great introductory book, 25 Jun 2004
This is an excellent introduction to this up-and-coming field. Bioinformatics one of many fields that is inherently inter-disciplinary, with biologists coming in and needing to learn computer science, and computer scientists coming in and needing to learn biology. I think that the book is very useful for both groups. I have a computer science background and did not find any of the biology overly difficult. So I highly recommend it for anyone, from the undergraduate to the postrgraduate or professional.

The book covers all of the major topics in bioinformatics, and touches on several of the minor ones. There are 5 long chapters:
Chapter 1 Introduction: introduces the basics of the field, describing the basics of data archiving, the WWW, computers and computer programming, biological classification and nomenclature, phylogenetic relationships and use of sequences, PSI-BLAST, and protein structure.
Chapter 2 Genome organization and evolution: genomics and proteomics, methods of genetic information transmission, genes and genomes, SNPs, genome evolution.
Chapter 3 Archives and information retrieval: this contains a detailed discussion of various databases and how to interact with them.
Chapter 4 Alignments and phylogenetic trees: this vast majority of this chapter covers many aspects of the important area of sequence alignment, including BLAST and HMMs. Then it has short sections on phylogeny and phylogenetic trees, again covering the basics.
Chapter 5 Protein structure and drug discovery: this starts with protein folding, and deals with hydrophobicity, structural alignments, DALI, and then evolution, classification and prediction of protein structures and function. Finally it touches on drug discovery in this context.

One of the nice things about this book is the code samples, written in the bioinformatician's favorite language, Perl. These are printed and discussed in the book, but then also available on the web site that is associated with the book, so you don't have to type it in yourself. In addition to the programs, the website also has graphics from the book, many of which rotate so you can see them from different positions (can't get that in a book!). It also has the web links mentioned in the book, so you can explore them more conveniently than having to flip through the book and type the URLs in.

An excellent beginner's guide to bioinformatics, 27 Apr 2002
This is a superb introduction to the subject of bioinformatics. It is very well written, and for the first time (thanks to this book) I can understand what hidden Markov models are about. It invites comparison with another book of the same name, namely "Introduction to Bioinformatics" by Attwood and Parry-Smith. The book by Lesk has two advantages (three, I suppose, if you include the fact that it is a more recent publication): it uses everyday, non-biological analogies to explain many of the concepts that are otherwise difficult to grasp, and it also covers molecular modelling.

Advanced undergraduate students tackling bioinformatics for the first time, or research students whose experience of bioinformatics is limited to the odd BLAST search and surfing through genomes, will find this book a must have. You will wonder how you ever got by without it.

Learn Bioinformatics in a week, 30 Apr 2008
This book beats it. At 40 years I turned my career from molecular plant biology to Bioinformatics. Obviously this book does not teach you how to do BI but with the basic biological knowledge I had and this book it really gets piece of cake. I actually started with a bit of Perl for Dummies, also good but I felt a bit lost after Chapter 7, went on with Tisdall's Beginning Perl and in half a day I ran my first scripts. It actually does explain what most things do (for instance what a filehandle is for). The clear English, the code available online all contribute to a learning BI on the fast track. It is specially the combination of text that does not go too deep, and the examples and exercises that guide you through dry material like it is all very simple, which it is of course.

Cum laude!

Good to go., 05 Dec 2004
I'm one of those people who should be doing something better! But since this book is good, because my copy is bent to pieces, I thought I would offer up my vote for a good read.

clear follow through, gives you coded programs - not just snipits! that don't work on there own. Lets you cut the bits out you don't need etc... up to speed fast with the little bit of code you needed. No point learning everthing perl can do! only to chop some sequences etc... otherwise you wouldn't be buying this book, you'd buy a specific perl book

fun read too, with websites you might not yet know about.

A great way to get started in bioinformatics programming, 26 Jun 2004
I think this is a really good introduction to both Perl and Bioinformatics programming. I already know several other languages, and have been meaning to pick up Perl for a while. So I thought this book might be too basic for me, but because I was new to the field of Bioinformatics, I did not find it terribly basic. I also do believe that it would be very good for someone with a biology background wanting to learn perl for bioinformatics (this is the audience the book claims to be targeting). Perl is a very powerful language, and I do think that it could be hard for programming beginner to learn. However, I think this book does a very good job of introducing several important topics in Perl gently. The best thing about it is the extremely numerous examples, which can all be downloaded from the book's website, so you don't have to waste time typing them in. This provides a great source of learning and experimenting with the code, but it also provides a platform for developing more advanced programs. You can just build new programs on top of much of the code from the book, which is very convenient, and is also what programming efficiently is all about.

There are 13 chapters in the book, and I'll give a quick summary and insight into each below:
Chapter 1 Biology and computer science: This gives a quick and gentle introduction to the goals of the field of bioinformatics, and how the two fields of biology and computer science contribute to it. It sets the context of the book.
Chapter 2 Getting started with Perl: This is a good chapter which details how to set up Perl on your computer, and get started using it.
Chapter 3 The art of programming: This chapter discusses the common approaches that people take to programming, and open source programming. Design, pseudocode, algorithms, and implementation are all discussed.
Chapter 4 Sequences and strings: This provides a dual introduction to the string variable type in Perl and basic sequence analysis in bioinformatics. The general basics of Perl are covered as well, but the focus is on working with strings (actually scalars, and also arrays), which are very important in bioinformatics.
Chapter 5 Motifs and loops: This chapter covers further topics in Perl (such as control structures (conditional stetments and loops), and searching DNA and proteins for sequences (motifs).
Chapter 6 Subroutines and bugs: This chapter covers the important topic of subroutines, or breaking your code into small, reusable chunks. This is quite important in programming. The chapter also introduces debuggin, which is also (unfortunately) a very important part of programming.
Chapter 7 Mutations and randomization: This chapter introduces the concept of mutation in bioinformatics, and how to model that with a computer, via a random number generator. It does a good job of explaining the (sort of strange) way that random number generators work, and the importance of using them correctly in order to get genuinely random numbers (which you obviously want!).
Chapter 8 The genetic code: This chapter talks more about the genetic code in terms of translating DNA into protein. It also introduces hashes, which are another important variable type in Perl. It provides some good examples, and also deals with reading files in the FASTA data format, which is commonly used.
Chapter 9 Restriction maps and regular expressions: Regular expressions were introduced and used in earlier chapters, but are covered more deeply here. It also introduces restriction enzymes and restriction maps, which are important for designing effective and efficient laboratory experiments. The chapter explains the process of developing a program for computing restriction maps, and provides some good example code.
Chapter 10 GenBank: This chapter basically covers the methods you need to go through in order to extract information from GenBank, one of the most important databanks of genetic sequence information.

Chapter 11 Protein data bank: This chapter is similar to the last, except that it deals with the Protein Data Bank instead of GenBank.
Chapter 12 BLAST: This is another specific chapter, dealing with the Basic Local Alignment Search Tool (BLAST), a pervasive tool in bioinformatics.
Chapter 13 Further Topics: Gives a cursory discussion of several "advanced" topics, like DNA computing, graphics pogramming and relational databases.

You can see from the above chapters how the book proceeds, covering both aspects of Perl and tasks in bioinformatics one step at a time, which means that it's good for beginners with any background, really. All of the chapters (except the very early ones) have lots of sample code. Obviously this book isn't intended to be the only book you own on bioinformatics or Perl. It doesn't provide a thorough discussion of either, and you will especially need another book on bioinformatics if you are new to the biological sciences. You will need a more solid reference for the Perl language, which you can get from Programming Perl, or you can use the online documentation. If you are new to programming, you would also possibly benefit from using another beginning book, like Learning Perl, but I still believe that having a targeted book like this is invaluable to the starting bioinformatician.

Not far from Awful..., 21 Oct 2003
I was advised to buy this book by my supervisor when I started my PhD in Bioinformatics. I had no previous programing experience and I was told that perl was the best way forward. It turned out perl was the best way forward, but not using this book. Perl is a very simple and intuitive language which a joy to work with.

This book tackles biological problems but with a poor approach. It forces you to copy down pages of code to form your first programs, and barely explains why you are doing it. What happens is that you miss out a word or spell something wrong and your program doesn't work, you get annoyed, you smash something! In contrast, the world renouned "learning perl" book teaches you why you do things and you build up your perl from a solid base. Yes this book focuses on the problem of using perl for biological problems, but that really isn't necessary. What you need is to learn the programming language, then when you are sure you know enough, you can apply it to your own problems. A solve them easily.

Buy "learning perl, O'reilly press" and then proceed to "programming perl, O'reilly press", there are far better books and will give you a solid grounding to tackle bioinformatics problems.

Perfect for all those biologists frightened of perl!!!, 22 Dec 2001
I found this book excellent, it contains the solution to most programmes required for bioinformatics and creating a web-site. I mean as a biologist with no experience in computer programming i was scared when it came to programme using perl but this book is literally a god-send and provided most of the solutions to build biological web-sites from finding pattern matching restriction sites in a nucleotide sequence to extracting specific information from sequences and transforming nucleotide sequences into amino acid sequences and building web pages from it.
You have to buy this book if you are new to the world of perl or bioinformatics.

Excellent product, well supported by both Mathworks and the community, 14 Dec 2007
Matlab has become very popular in the engineering field. Whilst both Maple and Mathematica have stronger symbolic capabilities, Matlab excels in the numerics and so tends to be used for engineering more than pure maths.

The Matlab documentation is built into the program and is also available online. There is a very active newsgroup comp.soft-sys.matlab where Matlab users can ask for help. It is read by a lot of staff from Mathworks and they, or other Matlab users, answer questions quickly. The importance of good support on this sort of software can not be overstated. This is a serious issue with Mathematica, which is a similar(ish) product to Matlab. The Mathematica newsgroup is moderated, so help requests can take a day before anyone sees them. To get a satisfactory answer to a question can often take a long time.

Matlab is excellent value for money for students, being cheaper than the student versions of either Maple or Mathematica. Although this is is a "sprat to catch a mackerel", as the commercial version of Matlab is expensive. This student version includes various toolboxes and Simulink, all of which are optional extras if you buy the commercial version.

The commercial version of Matlab is available on Solaris, but only Windows, Linux and Mac are supported on the student version. Since I used Solaris as a student, I would have found this annoying. There would be no harm in asking if they would give a license for Solaris.


they say on the title "an excellent book for beginners and occasional practioners", 19 Jun 2007
... and I agree. This is a book for molecular biologist who want to analyse their data using bioinformatics tools. I would prefer Baxevanis/Oullette "Bioinformatics: A Practical Guide to the Analysis of Genes and Proteins", however, if this is too expensive for you than this "Bioinformatics for Dummies" is the second best choice. Layout and index is a bit more confused but it covers most stuff you will need.

A word of warning: if you want to learn how the programs work, you have to look for a different type of book, e.g. "Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids" by R. Durbin, Sean R. Eddy, Anders Krogh, and Graeme Mitchison or "Algorithmic Aspects of Bioinformatics" by Hans-Joachim Bockenhauer and Dirk Bongartz.

Clear and informative, 26 Dec 2005
So much of the information is this field (and indeed some of the applications which have been developed) seems almost intentially convoluted and difficult to understand. This book gives a very good overview of some of the more common programs that one will need to use if one is starting bioinformatics research in a way that is practical and easy understand. Despite the title, the authors have done some good work in the field (I use Notredame's T-Coffee alignment program often) and are credible authorities in this area.

Brings strands of knowledge together, 11 Oct 2008
My science background is well out-of-date. In this book I can find several half understood concepts brought together, well explained and illuminating each other to an amazing extent. It's really rather exciting!

A great introductory book, 25 Jun 2004
This is an excellent introduction to this up-and-coming field. Bioinformatics one of many fields that is inherently inter-disciplinary, with biologists coming in and needing to learn computer science, and computer scientists coming in and needing to learn biology. I think that the book is very useful for both groups. I have a computer science background and did not find any of the biology overly difficult. So I highly recommend it for anyone, from the undergraduate to the postrgraduate or professional.

The book covers all of the major topics in bioinformatics, and touches on several of the minor ones. There are 5 long chapters:
Chapter 1 Introduction: introduces the basics of the field, describing the basics of data archiving, the WWW, computers and computer programming, biological classification and nomenclature, phylogenetic relationships and use of sequences, PSI-BLAST, and protein structure.
Chapter 2 Genome organization and evolution: genomics and proteomics, methods of genetic information transmission, genes and genomes, SNPs, genome evolution.
Chapter 3 Archives and information retrieval: this contains a detailed discussion of various databases and how to interact with them.
Chapter 4 Alignments and phylogenetic trees: this vast majority of this chapter covers many aspects of the important area of sequence alignment, including BLAST and HMMs. Then it has short sections on phylogeny and phylogenetic trees, again covering the basics.
Chapter 5 Protein structure and drug discovery: this starts with protein folding, and deals with hydrophobicity, structural alignments, DALI, and then evolution, classification and prediction of protein structures and function. Finally it touches on drug discovery in this context.

One of the nice things about this book is the code samples, written in the bioinformatician's favorite language, Perl. These are printed and discussed in the book, but then also available on the web site that is associated with the book, so you don't have to type it in yourself. In addition to the programs, the website also has graphics from the book, many of which rotate so you can see them from different positions (can't get that in a book!). It also has the web links mentioned in the book, so you can explore them more conveniently than having to flip through the book and type the URLs in.

An excellent beginner's guide to bioinformatics, 27 Apr 2002
This is a superb introduction to the subject of bioinformatics. It is very well written, and for the first time (thanks to this book) I can understand what hidden Markov models are about. It invites comparison with another book of the same name, namely "Introduction to Bioinformatics" by Attwood and Parry-Smith. The book by Lesk has two advantages (three, I suppose, if you include the fact that it is a more recent publication): it uses everyday, non-biological analogies to explain many of the concepts that are otherwise difficult to grasp, and it also covers molecular modelling.

Advanced undergraduate students tackling bioinformatics for the first time, or research students whose experience of bioinformatics is limited to the odd BLAST search and surfing through genomes, will find this book a must have. You will wonder how you ever got by without it.

Learn Bioinformatics in a week, 30 Apr 2008
This book beats it. At 40 years I turned my career from molecular plant biology to Bioinformatics. Obviously this book does not teach you how to do BI but with the basic biological knowledge I had and this book it really gets piece of cake. I actually started with a bit of Perl for Dummies, also good but I felt a bit lost after Chapter 7, went on with Tisdall's Beginning Perl and in half a day I ran my first scripts. It actually does explain what most things do (for instance what a filehandle is for). The clear English, the code available online all contribute to a learning BI on the fast track. It is specially the combination of text that does not go too deep, and the examples and exercises that guide you through dry material like it is all very simple, which it is of course.

Cum laude!

Good to go., 05 Dec 2004
I'm one of those people who should be doing something better! But since this book is good, because my copy is bent to pieces, I thought I would offer up my vote for a good read.

clear follow through, gives you coded programs - not just snipits! that don't work on there own. Lets you cut the bits out you don't need etc... up to speed fast with the little bit of code you needed. No point learning everthing perl can do! only to chop some sequences etc... otherwise you wouldn't be buying this book, you'd buy a specific perl book

fun read too, with websites you might not yet know about.

A great way to get started in bioinformatics programming, 26 Jun 2004
I think this is a really good introduction to both Perl and Bioinformatics programming. I already know several other languages, and have been meaning to pick up Perl for a while. So I thought this book might be too basic for me, but because I was new to the field of Bioinformatics, I did not find it terribly basic. I also do believe that it would be very good for someone with a biology background wanting to learn perl for bioinformatics (this is the audience the book claims to be targeting). Perl is a very powerful language, and I do think that it could be hard for programming beginner to learn. However, I think this book does a very good job of introducing several important topics in Perl gently. The best thing about it is the extremely numerous examples, which can all be downloaded from the book's website, so you don't have to waste time typing them in. This provides a great source of learning and experimenting with the code, but it also provides a platform for developing more advanced programs. You can just build new programs on top of much of the code from the book, which is very convenient, and is also what programming efficiently is all about.

There are 13 chapters in the book, and I'll give a quick summary and insight into each below:
Chapter 1 Biology and computer science: This gives a quick and gentle introduction to the goals of the field of bioinformatics, and how the two fields of biology and computer science contribute to it. It sets the context of the book.
Chapter 2 Getting started with Perl: This is a good chapter which details how to set up Perl on your computer, and get started using it.
Chapter 3 The art of programming: This chapter discusses the common approaches that people take to programming, and open source programming. Design, pseudocode, algorithms, and implementation are all discussed.
Chapter 4 Sequences and strings: This provides a dual introduction to the string variable type in Perl and basic sequence analysis in bioinformatics. The general basics of Perl are covered as well, but the focus is on working with strings (actually scalars, and also arrays), which are very important in bioinformatics.
Chapter 5 Motifs and loops: This chapter covers further topics in Perl (such as control structures (conditional stetments and loops), and searching DNA and proteins for sequences (motifs).
Chapter 6 Subroutines and bugs: This chapter covers the important topic of subroutines, or breaking your code into small, reusable chunks. This is quite important in programming. The chapter also introduces debuggin, which is also (unfortunately) a very important part of programming.
Chapter 7 Mutations and randomization: This chapter introduces the concept of mutation in bioinformatics, and how to model that with a computer, via a random number generator. It does a good job of explaining the (sort of strange) way that random number generators work, and the importance of using them correctly in order to get genuinely random numbers (which you obviously want!).
Chapter 8 The genetic code: This chapter talks more about the genetic code in terms of translating DNA into protein. It also introduces hashes, which are another important variable type in Perl. It provides some good examples, and also deals with reading files in the FASTA data format, which is commonly used.
Chapter 9 Restriction maps and regular expressions: Regular expressions were introduced and used in earlier chapters, but are covered more deeply here. It also introduces restriction enzymes and restriction maps, which are important for designing effective and efficient laboratory experiments. The chapter explains the process of developing a program for computing restriction maps, and provides some good example code.
Chapter 10 GenBank: This chapter basically covers the methods you need to go through in order to extract information from GenBank, one of the most important databanks of genetic sequence information.

Chapter 11 Protein data bank: This chapter is similar to the last, except that it deals with the Protein Data Bank instead of GenBank.
Chapter 12 BLAST: This is another specific chapter, dealing with the Basic Local Alignment Search Tool (BLAST), a pervasive tool in bioinformatics.
Chapter 13 Further Topics: Gives a cursory discussion of several "advanced" topics, like DNA computing, graphics pogramming and relational databases.

You can see from the above chapters how the book proceeds, covering both aspects of Perl and tasks in bioinformatics one step at a time, which means that it's good for beginners with any background, really. All of the chapters (except the very early ones) have lots of sample code. Obviously this book isn't intended to be the only book you own on bioinformatics or Perl. It doesn't provide a thorough discussion of either, and you will especially need another book on bioinformatics if you are new to the biological sciences. You will need a more solid reference for the Perl language, which you can get from Programming Perl, or you can use the online documentation. If you are new to programming, you would also possibly benefit from using another beginning book, like Learning Perl, but I still believe that having a targeted book like this is invaluable to the starting bioinformatician.

Not far from Awful..., 21 Oct 2003
I was advised to buy this book by my supervisor when I started my PhD in Bioinformatics. I had no previous programing experience and I was told that perl was the best way forward. It turned out perl was the best way forward, but not using this book. Perl is a very simple and intuitive language which a joy to work with.

This book tackles biological problems but with a poor approach. It forces you to copy down pages of code to form your first programs, and barely explains why you are doing it. What happens is that you miss out a word or spell something wrong and your program doesn't work, you get annoyed, you smash something! In contrast, the world renouned "learning perl" book teaches you why you do things and you build up your perl from a solid base. Yes this book focuses on the problem of using perl for biological problems, but that really isn't necessary. What you need is to learn the programming language, then when you are sure you know enough, you can apply it to your own problems. A solve them easily.

Buy "learning perl, O'reilly press" and then proceed to "programming perl, O'reilly press", there are far better books and will give you a solid grounding to tackle bioinformatics problems.

Perfect for all those biologists frightened of perl!!!, 22 Dec 2001
I found this book excellent, it contains the solution to most programmes required for bioinformatics and creating a web-site. I mean as a biologist with no experience in computer programming i was scared when it came to programme using perl but this book is literally a god-send and provided most of the solutions to build biological web-sites from finding pattern matching restriction sites in a nucleotide sequence to extracting specific information from sequences and transforming nucleotide sequences into amino acid sequences and building web pages from it.
You have to buy this book if you are new to the world of perl or bioinformatics.

It tells you what can be done but not how to do it., 23 Jul 2002
I found this book to be little more than a very basic introduction to bioinformatics. If you want a book to tell you what can be done then it useful, but it goes into very little detail. The ground it attempts to cover is far too large, it runs through an introduction to databases, LINUX and PERL. If you are interested in these you will need to buy a proper book for each subject.

The book would have been a lot better if they had run through some examples of what you can do, showing you what can be done along the way.

The authors should also acknowledge that most biologists only use Windows PCs and Macs rather than just concentrate on LINUX. It should have also mentioned that OS-X is based upon UNIX and lots of the LINUX things can be done on that OS too.

A decent if cursory reference to current tools, 05 Jun 2001
Firstly this book is entirely Unix/Linux based, which may cut out many casual laboratory users. This is par for the course in bioinformatics but not strictly necessary. It has a few chapters to get you started on Linux set-up, and a very, very light grounding in molecular biology. The brief explanation of Perl programming, and databases is hardly sufficient other than as an eye-opener. It is a probable time saver as a good current reference to the available free bioinformatics web-sites and tools.

Possibly the authors are trying to cater to people who either know very little molecular biology (computing students), or very little computing (biologists). Perhaps there are two books yet to be written: one for each group.

Excellent product, well supported by both Mathworks and the community, 14 Dec 2007
Matlab has become very popular in the engineering field. Whilst both Maple and Mathematica have stronger symbolic capabilities, Matlab excels in the numerics and so tends to be used for engineering more than pure maths.

The Matlab documentation is built into the program and is also available online. There is a very active newsgroup comp.soft-sys.matlab where Matlab users can ask for help. It is read by a lot of staff from Mathworks and they, or other Matlab users, answer questions quickly. The importance of good support on this sort of software can not be overstated. This is a serious issue with Mathematica, which is a similar(ish) product to Matlab. The Mathematica newsgroup is moderated, so help requests can take a day before anyone sees them. To get a satisfactory answer to a question can often take a long time.

Matlab is excellent value for money for students, being cheaper than the student versions of either Maple or Mathematica. Although this is is a "sprat to catch a mackerel", as the commercial version of Matlab is expensive. This student version includes various toolboxes and Simulink, all of which are optional extras if you buy the commercial version.

The commercial version of Matlab is available on Solaris, but only Windows, Linux and Mac are supported on the student version. Since I used Solaris as a student, I would have found this annoying. There would be no harm in asking if they would give a license for Solaris.


they say on the title "an excellent book for beginners and occasional practioners", 19 Jun 2007
... and I agree. This is a book for molecular biologist who want to analyse their data using bioinformatics tools. I would prefer Baxevanis/Oullette "Bioinformatics: A Practical Guide to the Analysis of Genes and Proteins", however, if this is too expensive for you than this "Bioinformatics for Dummies" is the second best choice. Layout and index is a bit more confused but it covers most stuff you will need.

A word of warning: if you want to learn how the programs work, you have to look for a different type of book, e.g. "Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids" by R. Durbin, Sean R. Eddy, Anders Krogh, and Graeme Mitchison or "Algorithmic Aspects of Bioinformatics" by Hans-Joachim Bockenhauer and Dirk Bongartz.

Clear and informative, 26 Dec 2005
So much of the information is this field (and indeed some of the applications which have been developed) seems almost intentially convoluted and difficult to understand. This book gives a very good overview of some of the more common programs that one will need to use if one is starting bioinformatics research in a way that is practical and easy understand. Despite the title, the authors have done some good work in the field (I use Notredame's T-Coffee alignment program often) and are credible authorities in this area.

Brings strands of knowledge together, 11 Oct 2008
My science background is well out-of-date. In this book I can find several half understood concepts brought together, well explained and illuminating each other to an amazing extent. It's really rather exciting!

A great introductory book, 25 Jun 2004
This is an excellent introduction to this up-and-coming field. Bioinformatics one of many fields that is inherently inter-disciplinary, with biologists coming in and needing to learn computer science, and computer scientists coming in and needing to learn biology. I think that the book is very useful for both groups. I have a computer science background and did not find any of the biology overly difficult. So I highly recommend it for anyone, from the undergraduate to the postrgraduate or professional.

The book covers all of the major topics in bioinformatics, and touches on several of the minor ones. There are 5 long chapters:
Chapter 1 Introduction: introduces the basics of the field, describing the basics of data archiving, the WWW, computers and computer programming, biological classification and nomenclature, phylogenetic relationships and use of sequences, PSI-BLAST, and protein structure.
Chapter 2 Genome organization and evolution: genomics and proteomics, methods of genetic information transmission, genes and genomes, SNPs, genome evolution.
Chapter 3 Archives and information retrieval: this contains a detailed discussion of various databases and how to interact with them.
Chapter 4 Alignments and phylogenetic trees: this vast majority of this chapter covers many aspects of the important area of sequence alignment, including BLAST and HMMs. Then it has short sections on phylogeny and phylogenetic trees, again covering the basics.
Chapter 5 Protein structure and drug discovery: this starts with protein folding, and deals with hydrophobicity, structural alignments, DALI, and then evolution, classification and prediction of protein structures and function. Finally it touches on drug discovery in this context.

One of the nice things about this book is the code samples, written in the bioinformatician's favorite language, Perl. These are printed and discussed in the book, but then also available on the web site that is associated with the book, so you don't have to type it in yourself. In addition to the programs, the website also has graphics from the book, many of which rotate so you can see them from different positions (can't get that in a book!). It also has the web links mentioned in the book, so you can explore them more conveniently than having to flip through the book and type the URLs in.

An excellent beginner's guide to bioinformatics, 27 Apr 2002
This is a superb introduction to the subject of bioinformatics. It is very well written, and for the first time (thanks to this book) I can understand what hidden Markov models are about. It invites comparison with another book of the same name, namely "Introduction to Bioinformatics" by Attwood and Parry-Smith. The book by Lesk has two advantages (three, I suppose, if you include the fact that it is a more recent publication): it uses everyday, non-biological analogies to explain many of the concepts that are otherwise difficult to grasp, and it also covers molecular modelling.

Advanced undergraduate students tackling bioinformatics for the first time, or research students whose experience of bioinformatics is limited to the odd BLAST search and surfing through genomes, will find this book a must have. You will wonder how you ever got by without it.

Learn Bioinformatics in a week, 30 Apr 2008
This book beats it. At 40 years I turned my career from molecular plant biology to Bioinformatics. Obviously this book does not teach you how to do BI but with the basic biological knowledge I had and this book it really gets piece of cake. I actually started with a bit of Perl for Dummies, also good but I felt a bit lost after Chapter 7, went on with Tisdall's Beginning Perl and in half a day I ran my first scripts. It actually does explain what most things do (for instance what a filehandle is for). The clear English, the code available online all contribute to a learning BI on the fast track. It is specially the combination of text that does not go too deep, and the examples and exercises that guide you through dry material like it is all very simple, which it is of course.

Cum laude!

Good to go., 05 Dec 2004
I'm one of those people who should be doing something better! But since this book is good, because my copy is bent to pieces, I thought I would offer up my vote for a good read.

clear follow through, gives you coded programs - not just snipits! that don't work on there own. Lets you cut the bits out you don't need etc... up to speed fast with the little bit of code you needed. No point learning everthing perl can do! only to chop some sequences etc... otherwise you wouldn't be buying this book, you'd buy a specific perl book

fun read too, with websites you might not yet know about.

A great way to get started in bioinformatics programming, 26 Jun 2004
I think this is a really good introduction to both Perl and Bioinformatics programming. I already know several other languages, and have been meaning to pick up Perl for a while. So I thought this book might be too basic for me, but because I was new to the field of Bioinformatics, I did not find it terribly basic. I also do believe that it would be very good for someone with a biology background wanting to learn perl for bioinformatics (this is the audience the book claims to be targeting). Perl is a very powerful language, and I do think that it could be hard for programming beginner to learn. However, I think this book does a very good job of introducing several important topics in Perl gently. The best thing about it is the extremely numerous examples, which can all be downloaded from the book's website, so you don't have to waste time typing them in. This provides a great source of learning and experimenting with the code, but it also provides a platform for developing more advanced programs. You can just build new programs on top of much of the code from the book, which is very convenient, and is also what programming efficiently is all about.

There are 13 chapters in the book, and I'll give a quick summary and insight into each below:
Chapter 1 Biology and computer science: This gives a quick and gentle introduction to the goals of the field of bioinformatics, and how the two fields of biology and computer science contribute to it. It sets the context of the book.
Chapter 2 Getting started with Perl: This is a good chapter which details how to set up Perl on your computer, and get started using it.
Chapter 3 The art of programming: This chapter discusses the common approaches that people take to programming, and open source programming. Design, pseudocode, algorithms, and implementation are all discussed.
Chapter 4 Sequences and strings: This provides a dual introduction to the string variable type in Perl and basic sequence analysis in bioinformatics. The general basics of Perl are covered as well, but the focus is on working with strings (actually scalars, and also arrays), which are very important in bioinformatics.
Chapter 5 Motifs and loops: This chapter covers further topics in Perl (such as control structures (conditional stetments and loops), and searching DNA and proteins for sequences (motifs).
Chapter 6 Subroutines and bugs: This chapter covers the important topic of subroutines, or breaking your code into small, reusable chunks. This is quite important in programming. The chapter also introduces debuggin, which is also (unfortunately) a very important part of programming.
Chapter 7 Mutations and randomization: This chapter introduces the concept of mutation in bioinformatics, and how to model that with a computer, via a random number generator. It does a good job of explaining the (sort of strange) way that random number generators work, and the importance of using them correctly in order to get genuinely random numbers (which you obviously want!).
Chapter 8 The genetic code: This chapter talks more about the genetic code in terms of translating DNA into protein. It also introduces hashes, which are another important variable type in Perl. It provides some good examples, and also deals with reading files in the FASTA data format, which is commonly used.
Chapter 9 Restriction maps and regular expressions: Regular expressions were introduced and used in earlier chapters, but are covered more deeply here. It also introduces restriction enzymes and restriction maps, which are important for designing effective and efficient laboratory experiments. The chapter explains the process of developing a program for computing restriction maps, and provides some good example code.
Chapter 10 GenBank: This chapter basically covers the methods you need to go through in order to extract information from GenBank, one of the most important databanks of genetic sequence information.

Chapter 11 Protein data bank: This chapter is similar to the last, except that it deals with the Protein Data Bank instead of GenBank.
Chapter 12 BLAST: This is another specific chapter, dealing with the Basic Local Alignment Search Tool (BLAST), a pervasive tool in bioinformatics.
Chapter 13 Further Topics: Gives a cursory discussion of several "advanced" topics, like DNA computing, graphics pogramming and relational databases.

You can see from the above chapters how the book proceeds, covering both aspects of Perl and tasks in bioinformatics one step at a time, which means that it's good for beginners with any background, really. All of the chapters (except the very early ones) have lots of sample code. Obviously this book isn't intended to be the only book you own on bioinformatics or Perl. It doesn't provide a thorough discussion of either, and you will especially need another book on bioinformatics if you are new to the biological sciences. You will need a more solid reference for the Perl language, which you can get from Programming Perl, or you can use the online documentation. If you are new to programming, you would also possibly benefit from using another beginning book, like Learning Perl, but I still believe that having a targeted book like this is invaluable to the starting bioinformatician.

Not far from Awful..., 21 Oct 2003
I was advised to buy this book by my supervisor when I started my PhD in Bioinformatics. I had no previous programing experience and I was told that perl was the best way forward. It turned out perl was the best way forward, but not using this book. Perl is a very simple and intuitive language which a joy to work with.

This book tackles biological problems but with a poor approach. It forces you to copy down pages of code to form your first programs, and barely explains why you are doing it. What happens is that you miss out a word or spell something wrong and your program doesn't work, you get annoyed, you smash something! In contrast, the world renouned "learning perl" book teaches you why you do things and you build up your perl from a solid base. Yes this book focuses on the problem of using perl for biological problems, but that really isn't necessary. What you need is to learn the programming language, then when you are sure you know enough, you can apply it to your own problems. A solve them easily.

Buy "learning perl, O'reilly press" and then proceed to "programming perl, O'reilly press", there are far better books and will give you a solid grounding to tackle bioinformatics problems.

Perfect for all those biologists frightened of perl!!!, 22 Dec 2001
I found this book excellent, it contains the solution to most programmes required for bioinformatics and creating a web-site. I mean as a biologist with no experience in computer programming i was scared when it came to programme using perl but this book is literally a god-send and provided most of the solutions to build biological web-sites from finding pattern matching restriction sites in a nucleotide sequence to extracting specific information from sequences and transforming nucleotide sequences into amino acid sequences and building web pages from it.
You have to buy this book if you are new to the world of perl or bioinformatics.

It tells you what can be done but not how to do it., 23 Jul 2002
I found this book to be little more than a very basic introduction to bioinformatics. If you want a book to tell you what can be done then it useful, but it goes into very little detail. The ground it attempts to cover is far too large, it runs through an introduction to databases, LINUX and PERL. If you are interested in these you will need to buy a proper book for each subject.

The book would have been a lot better if they had run through some examples of what you can do, showing you what can be done along the way.

The authors should also acknowledge that most biologists only use Windows PCs and Macs rather than just concentrate on LINUX. It should have also mentioned that OS-X is based upon UNIX and lots of the LINUX things can be done on that OS too.

A decent if cursory reference to current tools, 05 Jun 2001
Firstly this book is entirely Unix/Linux based, which may cut out many casual laboratory users. This is par for the course in bioinformatics but not strictly necessary. It has a few chapters to get you started on Linux set-up, and a very, very light grounding in molecular biology. The brief explanation of Perl programming, and databases is hardly sufficient other than as an eye-opener. It is a probable time saver as a good current reference to the available free bioinformatics web-sites and tools.

Possibly the authors are trying to cater to people who either know very little molecular biology (computing students), or very little computing (biologists). Perhaps there are two books yet to be written: one for each group.

want to analyse your molbiol data? start here!, 19 Jun 2007
This is the best book for a molecular biologist looking for survey of online tools and databases available to support the analysis of molecular data. It is most useful. However, it is too expensive to be recommended as a "must have" for students (therefore only 4 stars).
The cheaper alternative might be "Bioinformatics for Dummies" by Jean-Michel Claverie, Cedric Notredame. But I would really recommend Baxevanis/Oullette.

Good solid reference, 27 Feb 2006
The second edition is a good solid introductory reference book. Particularly good chapters deal with PERL, sequence alignment and database searching and phylogenetics. Its small format and 450+ pages make it a portable yet useful reference.

Excellent bioinformatics text book, 07 Jul 2005
This new 3rd edition is a much improved an updated version of the 2nd edition, which was already a reference text.
It is easy to read, the layout is excellent, the illustrations are plenty and informative, and the web links, problem sets and worked examples make this our first choice for a text book for students of all levels in bioinformatics. Highly recommended!

A practical book and enormous collection of online resources, 12 Oct 2003
It is a good book, well-written and reasonably up-to-date.
A very good introduction for experimentalists who need to do some bioinformatics work. As promised in the title, the authors leave out detailed explanation of the theory and background and rather concentrate on most practical approaches.
The collection of online resources is impressive and fully appropriate for readers who want to find 'some' tool that fulfills the needed function. The more advance bioinformatician, however, will miss links to recently developed resources and is adviced to review the expert literature.

Excellent product, well supported by both Mathworks and the community, 14 Dec 2007
Matlab has become very popular in the engineering field. Whilst both Maple and Mathematica have stronger symbolic capabilities, Matlab excels in the numerics and so tends to be used for engineering more than pure maths.

The Matlab documentation is built into the program and is also available online. There is a very active newsgroup comp.soft-sys.matlab where Matlab users can ask for help. It is read by a lot of staff from Mathworks and they, or other Matlab users, answer questions quickly. The importance of good support on this sort of software can not be overstated. This is a serious issue with Mathematica, which is a similar(ish) product to Matlab. The Mathematica newsgroup is moderated, so help requests can take a day before anyone sees them. To get a satisfactory answer to a question can often take a long time.

Matlab is excellent value for money for students, being cheaper than the student versions of either Maple or Mathematica. Although this is is a "sprat to catch a mackerel", as the commercial version of Matlab is expensive. This student version includes various toolboxes and Simulink, all of which are optional extras if you buy the commercial version.

The commercial version of Matlab is available on Solaris, but only Windows, Linux and Mac are supported on the student version. Since I used Solaris as a student, I would have found this annoying. There would be no harm in asking if they would give a license for Solaris.


they say on the title "an excellent book for beginners and occasional practioners", 19 Jun 2007
... and I agree. This is a book for molecular biologist who want to analyse their data using bioinformatics tools. I would prefer Baxevanis/Oullette "Bioinformatics: A Practical Guide to the Analysis of Genes and Proteins", however, if this is too expensive for you than this "Bioinformatics for Dummies" is the second best choice. Layout and index is a bit more confused but it covers most stuff you will need.

A word of warning: if you want to learn how the programs work, you have to look for a different type of book, e.g. "Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids" by R. Durbin, Sean R. Eddy, Anders Krogh, and Graeme Mitchison or "Algorithmic Aspects of Bioinformatics" by Hans-Joachim Bockenhauer and Dirk Bongartz.

Clear and informative, 26 Dec 2005
So much of the information is this field (and indeed some of the applications which have been developed) seems almost intentially convoluted and difficult to understand. This book gives a very good overview of some of the more common programs that one will need to use if one is starting bioinformatics research in a way that is practical and easy understand. Despite the title, the authors have done some good work in the field (I use Notredame's T-Coffee alignment program often) and are credible authorities in this area.

Brings strands of knowledge together, 11 Oct 2008
My science background is well out-of-date. In this book I can find several half understood concepts brought together, well explained and illuminating each other to an amazing extent. It's really rather exciting!

A great introductory book, 25 Jun 2004
This is an excellent introduction to this up-and-coming field. Bioinformatics one of many fields that is inherently inter-disciplinary, with biologists coming in and needing to learn computer science, and computer scientists coming in and needing to learn biology. I think that the book is very useful for both groups. I have a computer science background and did not find any of the biology overly difficult. So I highly recommend it for anyone, from the undergraduate to the postrgraduate or professional.

The book covers all of the major topics in bioinformatics, and touches on several of the minor ones. There are 5 long chapters:
Chapter 1 Introduction: introduces the basics of the field, describing the basics of data archiving, the WWW, computers and computer programming, biological classification and nomenclature, phylogenetic relationships and use of sequences, PSI-BLAST, and protein structure.
Chapter 2 Genome organization and evolution: genomics and proteomics, methods of genetic information transmission, genes and genomes, SNPs, genome evolution.
Chapter 3 Archives and information retrieval: this contains a detailed discussion of various databases and how to interact with them.
Chapter 4 Alignments and phylogenetic trees: this vast majority of this chapter covers many aspects of the important area of sequence alignment, including BLAST and HMMs. Then it has short sections on phylogeny and phylogenetic trees, again covering the basics.
Chapter 5 Protein structure and drug discovery: this starts with protein folding, and deals with hydrophobicity, structural alignments, DALI, and then evolution, classification and prediction of protein structures and function. Finally it touches on drug discovery in this context.

One of the nice things about this book is the code samples, written in the bioinformatician's favorite language, Perl. These are printed and discussed in the book, but then also available on the web site that is associated with the book, so you don't have to type it in yourself. In addition to the programs, the website also has graphics from the book, many of which rotate so you can see them from different positions (can't get that in a book!). It also has the web links mentioned in the book, so you can explore them more conveniently than having to flip through the book and type the URLs in.

An excellent beginner's guide to bioinformatics, 27 Apr 2002
This is a superb introduction to the subject of bioinformatics. It is very well written, and for the first time (thanks to this book) I can understand what hidden Markov models are about. It invites comparison with another book of the same name, namely "Introduction to Bioinformatics" by Attwood and Parry-Smith. The book by Lesk has two advantages (three, I suppose, if you include the fact that it is a more recent publication): it uses everyday, non-biological analogies to explain many of the concepts that are otherwise difficult to grasp, and it also covers molecular modelling.

Advanced undergraduate students tackling bioinformatics for the first time, or research students whose experience of bioinformatics is limited to the odd BLAST search and surfing through genomes, will find this book a must have. You will wonder how you ever got by without it.

Learn Bioinformatics in a week, 30 Apr 2008
This book beats it. At 40 years I turned my career from molecular plant biology to Bioinformatics. Obviously this book does not teach you how to do BI but with the basic biological knowledge I had and this book it really gets piece of cake. I actually started with a bit of Perl for Dummies, also good but I felt a bit lost after Chapter 7, went on with Tisdall's Beginning Perl and in half a day I ran my first scripts. It actually does explain what most things do (for instance what a filehandle is for). The clear English, the code available online all contribute to a learning BI on the fast track. It is specially the combination of text that does not go too deep, and the examples and exercises that guide you through dry material like it is all very simple, which it is of course.

Cum laude!

Good to go., 05 Dec 2004
I'm one of those people who should be doing something better! But since this book is good, because my copy is bent to pieces, I thought I would offer up my vote for a good read.

clear follow through, gives you coded programs - not just snipits! that don't work on there own. Lets you cut the bits out you don't need etc... up to speed fast with the little bit of code you needed. No point learning everthing perl can do! only to chop some sequences etc... otherwise you wouldn't be buying this book, you'd buy a specific perl book

fun read too, with websites you might not yet know about.

A great way to get started in bioinformatics programming, 26 Jun 2004
I think this is a really good introduction to both Perl and Bioinformatics programming. I already know several other languages, and have been meaning to pick up Perl for a while. So I thought this book might be too basic for me, but because I was new to the field of Bioinformatics, I did not find it terribly basic. I also do believe that it would be very good for someone with a biology background wanting to learn perl for bioinformatics (this is the audience the book claims to be targeting). Perl is a very powerful language, and I do think that it could be hard for programming beginner to learn. However, I think this book does a very good job of introducing several important topics in Perl gently. The best thing about it is the extremely numerous examples, which can all be downloaded from the book's website, so you don't have to waste time typing them in. This provides a great source of learning and experimenting with the code, but it also provides a platform for developing more advanced programs. You can just build new programs on top of much of the code from the book, which is very convenient, and is also what programming efficiently is all about.

There are 13 chapters in the book, and I'll give a quick summary and insight into each below:
Chapter 1 Biology and computer science: This gives a quick and gentle introduction to the goals of the field of bioinformatics, and how the two fields of biology and computer science contribute to it. It sets the context of the book.
Chapter 2 Getting started with Perl: This is a good chapter which details how to set up Perl on your computer, and get started using it.
Chapter 3 The art of programming: This chapter discusses the common approaches that people take to programming, and open source programming. Design, pseudocode, algorithms, and implementation are all discussed.
Chapter 4 Sequences and strings: This provides a dual introduction to the string variable type in Perl and basic sequence analysis in bioinformatics. The general basics of Perl are covered as well, but the focus is on working with strings (actually scalars, and also arrays), which are very important in bioinformatics.
Chapter 5 Motifs and loops: This chapter covers further topics in Perl (such as control structures (conditional stetments and loops), and searching DNA and proteins for sequences (motifs).
Chapter 6 Subroutines and bugs: This chapter covers the important topic of subroutines, or breaking your code into small, reusable chunks. This is quite important in programming. The chapter also introduces debuggin, which is also (unfortunately) a very important part of programming.
Chapter 7 Mutations and randomization: This chapter introduces the concept of mutation in bioinformatics, and how to model that with a computer, via a random number generator. It does a good job of explaining the (sort of strange) way that random number generators work, and the importance of using them correctly in order to get genuinely random numbers (which you obviously want!).
Chapter 8 The genetic code: This chapter talks more about the genetic code in terms of translating DNA into protein. It also introduces hashes, which are another important variable type in Perl. It provides some good examples, and also deals with reading files in the FASTA data format, which is commonly used.
Chapter 9 Restriction maps and regular expressions: Regular expressions were introduced and used in earlier chapters, but are covered more deeply here. It also introduces restriction enzymes and restriction maps, which are important for designing effective and efficient laboratory experiments. The chapter explains the process of developing a program for computing restriction maps, and provides some good example code.
Chapter 10 GenBank: This chapter basically covers the methods you need to go through in order to extract information from GenBank, one of the most important databanks of genetic sequence information.

Chapter 11 Protein data bank: This chapter is similar to the last, except that it deals with the Protein Data Bank instead of GenBank.
Chapter 12 BLAST: This is another specific chapter, dealing with the Basic Local Alignment Search Tool (BLAST), a pervasive tool in bioinformatics.
Chapter 13 Further Topics: Gives a cursory discussion of several "advanced" topics, like DNA computing, graphics pogramming and relational databases.

You can see from the above chapters how the book proceeds, covering both aspects of Perl and tasks in bioinformatics one step at a time, which means that it's good for beginners with any background, really. All of the chapters (except the very early ones) have lots of sample code. Obviously this book isn't intended to be the only book you own on bioinformatics or Perl. It doesn't provide a thorough discussion of either, and you will especially need another book on bioinformatics if you are new to the biological sciences. You will need a more solid reference for the Perl language, which you can get from Programming Perl, or you can use the online documentation. If you are new to programming, you would also possibly benefit from using another beginning book, like Learning Perl, but I still believe that having a targeted book like this is invaluable to the starting bioinformatician.

Not far from Awful..., 21 Oct 2003
I was advised to buy this book by my supervisor when I started my PhD in Bioinformatics. I had no previous programing experience and I was told that perl was the best way forward. It turned out perl was the best way forward, but not using this book. Perl is a very simple and intuitive language which a joy to work with.

This book tackles biological problems but with a poor approach. It forces you to copy down pages of code to form your first programs, and barely explains why you are doing it. What happens is that you miss out a word or spell something wrong and your program doesn't work, you get annoyed, you smash something! In contrast, the world renouned "learning perl" book teaches you why you do things and you build up your perl from a solid base. Yes this book focuses on the problem of using perl for biological problems, but that really isn't necessary. What you need is to learn the programming language, then when you are sure you know enough, you can apply it to your own problems. A solve them easily.

Buy "learning perl, O'reilly press" and then proceed to "programming perl, O'reilly press", there are far better books and will give you a solid grounding to tackle bioinformatics problems.

Perfect for all those biologists frightened of perl!!!, 22 Dec 2001
I found this book excellent, it contains the solution to most programmes required for bioinformatics and creating a web-site. I mean as a biologist with no experience in computer programming i was scared when it came to programme using perl but this book is literally a god-send and provided most of the solutions to build biological web-sites from finding pattern matching restriction sites in a nucleotide sequence to extracting specific information from sequences and transforming nucleotide sequences into amino acid sequences and building web pages from it.
You have to buy this book if you are new to the world of perl or bioinformatics.

It tells you what can be done but not how to do it., 23 Jul 2002
I found this book to be little more than a very basic introduction to bioinformatics. If you want a book to tell you what can be done then it useful, but it goes into very little detail. The ground it attempts to cover is far too large, it runs through an introduction to databases, LINUX and PERL. If you are interested in these you will need to buy a proper book for each subject.

The book would have been a lot better if they had run through some examples of what you can do, showing you what can be done along the way.

The authors should also acknowledge that most biologists only use Windows PCs and Macs rather than just concentrate on LINUX. It should have also mentioned that OS-X is based upon UNIX and lots of the LINUX things can be done on that OS too.

A decent if cursory reference to current tools, 05 Jun 2001
Firstly this book is entirely Unix/Linux based, which may cut out many casual laboratory users. This is par for the course in bioinformatics but not strictly necessary. It has a few chapters to get you started on Linux set-up, and a very, very light grounding in molecular biology. The brief explanation of Perl programming, and databases is hardly sufficient other than as an eye-opener. It is a probable time saver as a good current reference to the available free bioinformatics web-sites and tools.

Possibly the authors are trying to cater to people who either know very little molecular biology (computing students), or very little computing (biologists). Perhaps there are two books yet to be written: one for each group.

want to analyse your molbiol data? start here!, 19 Jun 2007
This is the best book for a molecular biologist looking for survey of online tools and databases available to support the analysis of molecular data. It is most useful. However, it is too expensive to be recommended as a "must have" for students (therefore only 4 stars).
The cheaper alternative might be "Bioinformatics for Dummies" by Jean-Michel Claverie, Cedric Notredame. But I would really recommend Baxevanis/Oullette.

Good solid reference, 27 Feb 2006
The second edition is a good solid introductory reference book. Particularly good chapters deal with PERL, sequence alignment and database searching and phylogenetics. Its small format and 450+ pages make it a portable yet useful reference.

Excellent bioinformatics text book, 07 Jul 2005
This new 3rd edition is a much improved an updated version of the 2nd edition, which was already a reference text.
It is easy to read, the layout is excellent, the illustrations are plenty and informative, and the web links, problem sets and worked examples make this our first choice for a text book for students of all levels in bioinformatics. Highly recommended!

A practical book and enormous collection of online resources, 12 Oct 2003
It is a good book, well-written and reasonably up-to-date.
A very good introduction for experimentalists who need to do some bioinformatics work. As promised in the title, the authors leave out detailed explanation of the theory and background and rather concentrate on most practical approaches.
The collection of online resources is impressive and fully appropriate for readers who want to find 'some' tool that fulfills the needed function. The more advance bioinformatician, however, will miss links to recently developed resources and is adviced to review the expert literature.

One of the best books on the subject, 16 May 2007
I teach bioinformatics, and have a special interest in protein structure. In most texts, the two things barely overlap. In this book, proteins, and especially their structures, take centre stage, in contrast to the 'protein sequence as a data string' view of the world so often taken. This is hardly a surprise, given the authors, but it is a viewpoint I whole-heartedly endorse. Putting the approach to the subject aside, the book is excellent in its own right. Concise, lucid coverage, unified by a set of excellent diagrams and illustrations. Criticisms would be lack of colour throughout, the relatively small format and the lack of web support, but these are minor quibbles.

Invaluable resource for students and researchers, 22 Mar 2004
As an MSc Bioinformatics student, this book proves to be invaluable in understanding my course. Covering topics from all fields of Bioinformatics, this book goes deep into the details necessary for any serious researcher or student. This would be especially useful to someone coming from a computing background; quickly covering the biology required and moving into how this can be integrated with technology to complete the amalgumation of these two sciences. This book is both informative and the perfect resource for quick reference to details when they slip your mind. With such an easy to understand layout, this book is the end to my worries of understanding both sciences to such a high level. This was the best use of my limited student money I have ever made.