Review on ''Bioinformatics, Biocomputing and Perl'' by Michael Moorhouse and Paul Barry
BioMedical Engineering OnLine
Book review Review on ''Bioinformatics, Biocomputing and Perl'' by Michael Moorhouse and Paul Barry Artem Cherkasov*
0 Address: Division of Infectious Diseases, Faculty of Medicine, University of British Columbia. 2733, Heather street, Vancouver, British Columbia, V5Z 3J5 , Canada
The book aims at both biology- and computation-oriented audiences and is designed as a number of 'crashcourses' quickly updating the reader on the basics of bioinformatics. It starts with a preface outlining main biological and technological concepts of the modern computational biology. The rest is organized into four sections consisting of 18 chapters elaborating on essential bioinformatics tools and skills.
Book details; MoorhouseMBarryPBioinformatics Biocomputing and; PerlWiley2004506ISBN 047085331X
The section 'Working with Perl' presents an extended
tutorial with practical tips and useful references for Perl
beginners. Following this is 'Working with Data', which
familiarizes the reader with some public genomic and
proteomic databases and discusses important subjects of
database formats, non-redundancy, cross-referencing and
programmable access, etc. By working through the section,
the reader acquires basic skills for mySQL database use
and DBI Perl programming.
Next, the authors offer Perl-based solutions for remote
database access and for creation of WWW-based
bioinformatics services using Perl functionalities in 'Working with
The final topic of the book, 'Working with Applications',
features basic tools for sequence alignment, protein
homology modeling and data visualization, all
commonly used in bioinformatics practice. The section also
offers recent and relevant examples of BioPerl
In general, the book reflects the state of bioinformatics
field with its strengths and weaknesses. Many Perl
chapters, such as Perl regular expressions, modular
organization, DBI-programming, BioPerl and web-automation, are
excellent. The presented material is rather comprehensive
and yet easy to read the authors spent appreciative
efforts to make the book interesting and enjoyable. The
authors also acknowledge the open-source nature of Perl
and the bioinformatics community and offer on-line
support and direct feedback to the readers.
There are also certain aspects, in which the book could be
further improved. Several sections may be too advanced
for the beginner level (such as Perl basics and database
downloading), while others may contain too excessive
details (the Protein Databank section). In addition, it may
be of advantage to mention AcePerl ,
Perl-programmable access to the SRS as well as XML-  and distributed
data processing by Perl. The book would greatly benefit
from color illustrations. Several figures in the 'biological'
sections are not very informative or readable (such as
Figure 10.5), and one contains a critical error (Figure 1.1).
A very useful feature of the book is the use of maxims that
highlight key points throughout the text. The authors also
provide helpful technical comments where necessary and
offer practical exercises at the end of each chapter. The
book is concluded with six appendices covering the Linux
basics, Perl installation, operators, on-line support and
suggested reading materials which, in my mind, benefit
the book tremendously.
Thus, the overall product, the "Bioinformatics,
Biocomputing and Perl", serves well its purpose as an introductory
textbook and a resource of reference materials for
List of Abbreviations used
AcePerl is a Perl interface for the AceDB a popular
object-oriented bioinformatics database.
BioPerl a collection of Perl modules specifically
designed for several most common bioinformatics tasks.
XML Extensible Markup Language a popular standard
for documents containing structured information.
SRS the Sequence Retrieval System a popular
relational database for bioinformatics.
1. Moorhouse M , Barry P : Bioinformatics Biocomputing and Perl Wiley ; 2004 .
2. AcePerl - for more info visit the home page of the AcePerl developer Dr . L. Stein at the Cold Spring Harbor Laboratory [http://stein.cshl.org/AcePerl/]
3. Ray ET , McIntosh J : Perl & XML O'Reilly ; 2002 .