Table Of ContentSYSTEMS AND
COMPUTATIONAL BIOLOGY
– BIOINFORMATICS AND
COMPUTATIONAL
MODELING
Edited by Ning-Sun Yang
Systems and Computational Biology –
Bioinformatics and Computational Modeling
Edited by Ning-Sun Yang
Published by InTech
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Copyright © 2011 InTech
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First published August, 2011
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Systems and Computational Biology – Bioinformatics and Computational Modeling,
Edited by Ning-Sun Yang
p. cm.
ISBN 978-953-307-875-5
free online editions of InTech
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Contents
Preface IX
Part 1 Tools and Design for Bioinformatics Studies 1
Chapter 1 Parallel Processing of Complex Biomolecular Information:
Combining Experimental and Computational Approaches 3
Jestin Jean-Luc and Lafaye Pierre
Chapter 2 Bioinformatics Applied to Proteomics 25
Simone Cristoni and Silvia Mazzuca
Chapter 3 Evolutionary Bioinformatics
with a Scientific Computing Environment 51
James J. Cai
Part 2 Computational Design and
Combinational Approaches for Systems Biology 75
Chapter 4 Strengths and Weaknesses of Selected
Modeling Methods Used in Systems Biology 77
Pascal Kahlem, Alessandro DiCara, Maxime Durot,
John M. Hancock, Edda Klipp, Vincent Schächter,
Eran Segal, Ioannis Xenarios, Ewan Birney and Luis Mendoza6
Chapter 5 Unifying Bioinformatics and
Chemoinformatics for Drug Design 99
J.B. Brown and Yasushi Okuno
Chapter 6 Estimating Similarities in DNA Strings
Using the Efficacious Rank Distance Approach 121
Liviu P. Dinu and Andrea Sgarro
Chapter 7 The Information Systems for DNA Barcode Data 139
Di Liu and Juncai Ma
VI Contents
Chapter 8 Parallel Processing of Multiple Pattern
Matching Algorithms for Biological
Sequences: Methods and Performance Results 161
Charalampos S. Kouzinopoulos,
Panagiotis D. Michailidis and Konstantinos G. Margaritis
Part 3 Techniques for Analysis of
Protein Families and Small Molecules 183
Chapter 9 Understanding Tools and
Techniques in Protein Structure Prediction 185
Geraldine Sandana Mala John, Chellan Rose
and Satoru Takeuchi
Chapter 10 Protein Progressive MSA Using 2-Opt Method 213
Gamil Abdel-Azim, Aboubekeur Hamdi-Cherif,
Mohamed Ben Othman and Z.A. Aboeleneen
Chapter 11 Clustering Libraries of Compounds
into Families: Asymmetry-Based Similarity
Measure to Categorize Small Molecules 229
Wieczorek Samuel, Aci Samia, Bisson Gilles,
Gordon Mirta, Lafanechère Laurence,
Maréchal Eric and Roy Sylvaine
Chapter 12 Systematic and Phylogenetic Analysis
of the Ole e 1 Pollen Protein Family Members in Plants 245
José Carlos Jiménez-López,
María Isabel Rodríguez-García and Juan de Dios Alché
Chapter 13 Biological Data Modelling and Scripting in R 261
Srinivasan Ramachandran, Rupanjali Chaudhuri,
Srikant Prasad Verma, Ab Rauf Shah, Chaitali Paul,
Shreya Chakraborty, Bhanwar Lal Puniya
and Rahul Shubhra Mandal
Chapter 14 Improving Bio-technology
Processes Using Computational Techniques 289
Avinash Shankaranarayanan and Christine Amaldas
Chapter 15 Signal Processing Methods for Capillary Electrophoresis 311
Robert Stewart, Iftah Gideoni and Yonggang Zhu
Preface
Immediately after the first drafts of the human genome sequence were reported almost
a decade ago, the importance of genomics and functional genomics studies became
well recognized across the broad disciplines of biological sciences research. The
initiatives of Leroy Hood and other pioneers on developing systems biology
approaches for evaluating or addressing global and integrated biological activities,
mechanisms, and network systems have motivated many of us, as bioscientists, to re-
examine or revisit a whole spectrum of our previous experimental findings or
observations in a much broader, link-seeking and cross-talk context. Soon thereafter,
these lines of research efforts generated interesting, fancy and sometimes misleading
new names for the now well-accepted “omics” research areas, including functional
genomics, (functional) proteomics, metabolomics, transcriptomics, glycomics,
lipidomics, and cellomics. It may be interesting for us to try to relate these “omics”
approaches to one of the oldest omics studies that we all may be quite familiar with,
and that is “economics”, in a way that all “omics” indeed seemed to have meant to
address the mechanisms/activities/constituents in a global, inter-connected and
regulated way or manner.
The advancement of a spectrum of technological methodologies and assay systems for
various omics studies has been literally astonishing, including next-generation DNA
sequencing platforms, whole transcriptome microarrays, micro-RNA arrays, various
protein chips, polysaccharide or glycomics arrays, advanced LC-MS/MS, GC-MS/MS,
MALDI-TOF, 2D-NMR, FT-IR, and other systems for proteome and metabolome
research and investigations on related molecular signaling and networking
bioactivities. Even more excitingly and encouragingly, many outstanding researchers
previously trained as mathematicians, information or computation scientists have
courageously re-educated themselves and turned into a new generation of
bioinformatics scientists. The collective achievements and breakthroughs made by our
colleagues have created a number of wonderful database systems which are now
routinely and extensively used by not only young but also “old” researchers. It is very
difficult to miss the overwhelming feeling and excitement of this new era in systems
biology and computational biology research.
It is now estimated, with good supporting evidence by omics information, that there
are approximately 25,000 genes in the human genome, about 45,000 total proteins in
X Preface
the human proteome, and around 3000 species of primary and between 3000 and 6000
species of secondary metabolites, respectively, in the human body fluid/tissue
metabolome. These numbers and their relative levels to each other are now helping us
to construct a more comprehensive and realistic view of human biology systems.
Likewise, but maybe to a lesser extent, various baseline omics databases on mouse,
fruit fly, Arabidopsis plant, yeast, and E. coli systems are being built to serve as model
systems for molecular, cellular and systems biology studies; these efforts are projected
to result in very interesting and important research findings in the coming years.
Good findings in a new research area may not necessarily translate quickly into good
or high-impact benefits pertaining to socio-economic needs, as may be witnessed now
by many of us with regard to research and development in omics science/technology.
To some of us, the new genes, novel protein functions, unique metabolite profiles or
PCA clusters, and their signaling systems that we have so far revealed seemed to have
yielded less than what we have previously (only some 5 to 10 years ago) expected, in
terms of new targets or strategies for drug or therapeutics development in medical
sciences, or for improvement of crop plants in agricultural science. Nonetheless, some
useful new tools for diagnosis and personalized medicine have been developed as a
result of genomics research. Recent reviews on this subject have helped us more
realistically and still optimistically to address such issues in a socially responsible
academic exercise. Therefore, whereas some “microarray” or “bioinformatics”
scientists among us may have been criticized as doing “cataloging research”, the
majority of us believe that we are sincerely exploring new scientific and technological
systems to benefit human health, human food and animal feed production, and
environmental protections. Indeed, we are humbled by the complexity, extent and
beauty of cross-talks in various biological systems; on the other hand, we are
becoming more educated and are able to start addressing honestly and skillfully the
various important issues concerning translational medicine, global agriculture, and the
environment.
I am very honored to serve as the editor of these two volumes on Systems and
Computational Biology: (I) Molecular and Cellular Experimental Systems, and (II)
Bioinformatics and Computational Modeling. I believe that we have collectively
contributed a series of high-quality research or review articles in a timely fashion to
this emerging research field of our scientific community.
I sincerely hope that our colleagues and readers worldwide will help us in future
similar efforts, by providing us feedback in the form of critical comments,
interdisciplinary ideas and innovative suggestions on our book chapters, as a way to
pay our high respect to the biological genomes on planet earth.
Dr. Ning-Sun Yang
Agricultural Biotechnology Research Center, Academia Sinica
Taiwan, R.O.C
