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Bioinformatics: Sequence, Structure and Databanks

Article  in  Briefings in Bioinformatics · January 2001

DOI: 10.1093/bib/2.2.202

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Book reviews
have a strange karyotype made up of
macro and micro-chromosomes? Why are
some syntenies conserved between
mammals and invertebrates? Of course in
many speci®c cases, algorithmic
modelling will not be suf®cient; we will
need to know about the biology of the
region and what makes it tick.
From a different angle Leslie Lyons
looks at `Companion Animal Genetics'
describing what is being done with horse,
cat and dog genomes, and what these
projects might tell us. Our obsession with
generating ever more bizarre dog breeds
in particular has provided us with an
accelerated evolutionary model. Both
crops and agricultural livestock are also
represented, with progress reports on the
various genome projects underway in
these commercially lucrative and
important arenas.
The ®nal section deals with gene and
genome duplication and all the associated
mathematical horrors of different
genomes having not only different
numbers of homologous genes, but more
than one copy of each gene in most cases
and many copies of some. The various
evolutionary contributors to this state of
affairs are exposed and to an extent
modelled, including whole genome
duplications/polyploidy, chromosomal,
regional and tandem duplications.
In summary, `Comparative Genomics'
covers a broad range of topics very well.
It is a little light in one or two areas and
perhaps (for the reviewer at least) a little
heavy on algorithms. One minor criticism
of the layout of the book is that all ®gures
are in black and white, while some
legends refer to coloured lines or bands
which are therefore not clearly
recognisable. That said, it is a timely
publication in an era where
computational competence is an essential
part of genomic comparison. As the
genomes get ticked off by the sequencers
ever more rapidly, we will need all the
help we can get.
Greg Elgar
Fugu Genomics Group, Hinxton, UK
202 & HENRY STEWART PUBLICATIONS 1467-5463. B R I E F I N G S I N B I O I N F O R M A T I C S . VOL 2. NO 2. 199±208. MAY 2001
Bioinformatics: Sequence,
Structure and Databanks
edited by Des Higgins and Willie
Taylor
Oxford University Press, Oxford;
ISBN 0 19 963791 1 (hardback),
ISBN 0 19 963790 3 (paperback);
hardback US$115; 269 pp.
With the increasing importance of
bioinformatics in biological research,
there is a de®nite need for `how-to'
guides that can introduce molecular
biologists to the computational techniques
that are fast becoming essential in their
®eld. This installment in the Practical
Approach series from OUP attempts to
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®ll this role with a collection of chapters
that present both theoretical overviews
and practical descriptions of selected
sequence and structure analysis
procedures. However, practical emphasis
notwithstanding, the book is far from
being a `Bioinformatics for Dummies'. It
covers a selection of important topics in
detail, but may be daunting for beginners
with no previous exposure to
bioinformatics terminology.
The `practical approach' of the book
varies from chapter to chapter. Some
chapters provide descriptions of UNIX
command line options; others provide
lists of URLs for accessing relevant web
sites. Unfortunately no central web site is
provided that lists and updates all the
URLs given in the book. Some chapters
contain protocols, but these are not
consistent throughout the book: in some
chapters they provide step-by-step
instructions, in others general guidelines,
and in others they describe a computer
algorithm.
The reader lured by the title into
expecting a full coverage of the current
state of bioinformatics may be
disappointed: the emphasis of the book is
clearly on protein sequence and structure
analysis. Nucleotide databanks are
mentioned, but nucleotide sequence
methods central to current genomic
efforts such as gene prediction techniques
and contig assembly are conspicuously

absent. Molecular phylogeny is
mentioned only brie¯y, and there is no
mention of topics such as microarray data
analysis, which are increasingly perceived
as `bioinformatics'. This is a minor
quibble: the back cover clearly identi®es
the target reader as `any researcher who is
involved with protein structural or
functional analysis', and it is likely that
readers ®tting this description will ®nd at
least some sections of the book very
valuable.
The book is an edited volume with
different chapters written by different
authors. The downside of this approach is
the lack of cohesion between different
chapters. For example there are no less
than four different (but overlapping) lists
of web sites for protein family
identi®cation in different chapters.
Different authors give different de®nitions
of the same terms (for example `pro®le'
and `motif').
The advantage of the multi-author
approach is the level of expertise that
authors bring to their topic, and in this
regard `Bioinformatics' is no exception.
The book kicks off with an introduction
to threading for protein structure
prediction by Jones and Hadley, who do a
great job of explaining the challenges in
protein structure prediction and the major
fold recognition methods that have been
used so far. Structure prediction is also
discussed in Chapter 6 by Jaap Heringa,
who reviews secondary structure
prediction methods, from the early Chou-
Fasman and Lim approaches to modern
methods combining neural networks and
information from multiple sequences.
This overview also includes testing
methodologies and some coverage of
transmembrane domain and coiled-coil
detection. The author summarises the
guidelines for structure prediction into a
handy protocol that concludes the
chapter, and provides a concise list of web
sites to access the resources discussed.
In the second chapter, Mark Johnson
and Jukka Lehtonen discuss techniques for
comparing three-dimensional protein
structures, not only for validating
& HENRY STEWART PUBLICATIONS 1467-5463. B R I E F I N G S I N B I O I N F O R M A T I C S . VOL 2. NO 2. 199±208. MAY 2001
Book reviews
structure prediction methods, but also for
identifying conserved and convergent
structural features. This can be unfamiliar
ground for biologists working primarily
with sequence data, but the very practical
treatment given to the topic should make
it accessible to biologists who can deal
with a little mathematical notation.
In Chapter 3, Duret and Abdeddaim
provide an extensive overview of multiple
sequence alignment methods, including a
discussion of the main parameter settings
that in¯uence the results. This chapter is
clearly targeted at the less experienced
user, and contains a wealth of well-
organised information, including a good
collection of web sites. Yona and Brenner
Downloaded from http://bib.oxfordjournals.org/ by guest on November 12, 2012
cover some of the same ground in more
depth in their chapter on protein
sequence comparison and database
searching (Chapter 8). They add a
discussion of alignment statistics, database
search algorithms, and practical
information for setting up and
interpreting database searches. However
the chapter shows a little bit of a split
personality: its theory section appears to
be targeted more towards computer
scientists than biologists (for example,
terms such as `hash table' are used without
any explanation). In contrast its practical
section is targeted at biologists who want
to get the most out of their database
searches and understand the pitfalls of the
approach.
The main emphasis of the book is on
protein families, especially the various
ways to represent these families and use
them to search databases or characterise
new proteins. In Chapter 4, Ewan Birney
focuses on hidden Markov models
(especially the HMMER package) and
provides a clear summary of the issues
associated with their use. Henikoff and
Henikoff follow in Chapter 5 with a
review of different protein family
methods for identifying homologues and
analysing proteins. Their chapter starts
with an amusing discussion of rival
sequence alignment philosophies
(`gappers' v. `blockers') and includes an
anecdotal comparison of different protein
203
 Book reviews
family databases and of their performance
in characterising a new protein. Protein
families are also discussed by Inge
Jonassen in Chapter 7, but with an
emphasis on PROSITE-type patterns
rather than on the probabilistic methods
discussed in previous chapters. The author
describes in detail his own pattern
discovery program Pratt as well as SPratt,
which searches for conserved motifs in
protein structures rather than sequences.
The last two chapters of the book are
fully practical. In Chapter 9, under the
heading of `Networking for the biologist',
Rob Harper discusses how to `avoid the
World Wide Wait while using World
Wide Web'. The recipes outlined here
include the use of email servers,
accelerated search sites and local servers
for database searches and sequence
submission. Chapter 10 by Kreil and
Etzold demonstrates the use of the
authors' software, SRS, for sequence
retrieval and analysis, and includes several
step-by-step `how-to-use' protocols as
well as a technical section on installing the
system locally. Both chapters are
illustrated with screen captures, which are
in many cases out of date, a common
curse of books attempting to document
the ever-changing Internet. In particular,
the SRS chapter describes version 5 of
SRS (version 6 is the current version).
Fortunately many of the protocols can still
be used with minor modi®cations, but the
version change casts doubts on whether
the SRS server installation instructions are
still current.
Overall, `Bioinformatics: Sequence,
Structure and Databanks' appears to have
been written with the biologist in mind
rather than the computer scientist.
However the book still requires more
than a passing level of familiarity with
UNIX command line operations,
mathematical expressions and
bioinformatics terminology, and readers
without this familiarity are likely to ®nd it
daunting in places. A glossary would
certainly have been useful in this context
(more useful than the list of biological
reagent and equipment suppliers oddly
204 & HENRY STEWART PUBLICATIONS 1467-5463. B R I E F I N G S I N B I O I N F O R M A T I C S . VOL 2. NO 2. 199±208. MAY 2001
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found at the end of the book). At three
pages, the index is also disappointing and
does not list many important words or
references: for example, the words `motif'
and `pattern' in the index point only to
Chapter 7, when Chapter 5 also deals
extensively with the topic. Nevertheless,
if you are looking for a review of current
topics in protein characterisation and
structure prediction, together with a
useful summary of guidelines for practical
analysis (and don't mind the US$115
price tag), this book is likely to be a
worthwhile addition to your library.
Bruno Gaeta
Director of Education and Senior Scientist,
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eBioinformatics, Australia
Computational Molecular
Biology: An Introduction
Peter Clote and Rolf Backofen
Wiley & Sons; ISBN 0471 872520;
paperback; US$59.99; 279 pp.
This is a volume in the Wiley series,
edited by Simon Levin, on mathematical
and computational biology. It is 267 pages
long, including appendices, a
comprehensive reference list and index.
The Wiley web site (http://
www.wiley.co.uk/statistics) provides
further information, including a limited
selection of links and the source code (in
C/C‡‡ or Java) of the various example
programs described in the text.
Clote and Backofen state in the preface
that their book is a self-contained
introduction to computational molecular
biology, intended to provide the
mathematical background to the
algorithms commonly used in
bioinformatics so that the student may
understand how and why these algorithms
work. The book is divided into six
chapters. The ®rst two are primers in
molecular biology and the essential
mathematics. The other chapters
concentrate on sequence alignment
(Chapter 3), phylogenetic analysis