Bioinformatics: Principles and Applications
by: Harshawardhan P. Bal
Abstract: The International Human Genome Project (IHGP), accomplished in 2003, was undoubtedly a giant step for mankind in the sequencing and assembly of the entire human genome. This event has fundamentally altered the manner in which we analyze biological systems, our approach to the many unsolved problems, and indeed, our attempt to unravel the closely held mysteries of evens the simplest of living organisms. However, deriving biological meaning from the raw stack of three billion bases of human DNA would not have been possible without the development of new algorithms for data mining and analysis. This book is about those fundamental tools and techniques that revolutionized biomedical research, and enable us today to perform biology in silico. The book uses an integrative approach to illustrate the use of these tools, and binds them together to create a coherent strategy to tackle the overwhelming problem of biological information overload. Divided into two parts, the book covers the core set of tools that have become indispensable to scientific discovery in the post-genome era, and also demonstrates how these tools can be integrated programmatically with BioPerl to be used in an enhanced, truly high throughput- biology on steroids- manner. With this coverage, the book will be useful to a diverse array of life science professionals, computational biologists, bioinformaticists, as well as students.
Full details
Table of Contents
- A. Author's Profile
- B. Dedication
- C. Preface
- D. Acknowledgements
- A. Part One: Principles
- 1. Web-based Sequence Analysis: BLAST I
- 2. Web-based Sequence Analysis: BLAST II
- 3. Web-based Sequence Analysis: BLAST III
- 4. Web-based Sequence Analysis: Gene Prediction
- 5. Web-based Sequence Analysis: HMMER
- 6. PSI-BLAST
- B. Part Two: Applications
- 7. Accessing Sequence Information Using BioPerl
- 8. Bio::DB::GenBank
- 9. Accessing GenBank Data
- 10. BioPerl BLAST Modules
- 11. Parsing BLAST Output
Tools & Media
Expanded Table of Contents
- A. Author's Profile
- B. Dedication
- C. Preface
- D. Acknowledgements
- A. Part One: Principles
- 1. Web-based Sequence Analysis: BLAST I
- 2. Web-based Sequence Analysis: BLAST II
- BASIC LOCAL ALIGNMENT SEARCH TOOL (BLAST)
- SCORING MATRICES
- PAM OR PER CENT ACCEPTED MUTATION MATRICES
- BLOSUM (BLOCKS SUBSTITUTION MATRICES)
- THE RELATIONSHIP BETWEEN BLOSUM AND PAM SUBSTITUTION MATRICES
- WORKING OF THE BLAST ALGORITHM
- A PRACTICAL BLASTN EXERCISE
- EXPLANATION OF THE BLAST OUTPUT
- ADVANCED BLASTN
- BIOLOGICAL ANALYSIS OF BLASTN: CYSTIC FIBROSIS
- AUTOMATING BLAST ANALYSES WITH PERL
- Assignments
- 3. Web-based Sequence Analysis: BLAST III
- 4. Web-based Sequence Analysis: Gene Prediction
- 5. Web-based Sequence Analysis: HMMER
- 6. PSI-BLAST
- B. Part Two: Applications
- 7. Accessing Sequence Information Using BioPerl
- 8. Bio::DB::GenBank
- 9. Accessing GenBank Data
- 10. BioPerl BLAST Modules
- 11. Parsing BLAST Output
Book Details
Title: Bioinformatics: Principles and Applications
Publisher: McGraw Hill Education (India) Private Limited
Copyright / Pub. Date: 2005 McGraw Hill Education (India) Private Limited
ISBN: 9780070583207
Authors:
Harshawardhan P. Bal
is currently a management and strategy consultant at Booz Allen Hamilton Inc., Rockville, MD. He has more than a decade of experience in biotechnology and bioinformatics, both in academia and in the industry. Through his research, he has made direct contributions to the annotation of the important food crop rice- and in mining the human genome to identify novel target proteins for new drug development.
At Millennium Pharmaceuticals Inc., Cambridge, MA, Harshawardhan acquired considerable experience in design and deployment of enterprise-wide knowledge management systems in the pharma industry.
Harshawardhan has a Master's degree in pharmaceutical sciences and was a formulation scientist in the pharma industry in Bombay. He has a Ph.D. in molecular biology from the National Institute of Immunology, New Delhi. He pursued research on HIV/AIDS and gene therapy at the University of Rochester Medical Center, Rochester, NY, and moved on to Cold Spring Harbor Laboratory, Cold Spring Harbor, NY. At Cold Spring, he worked on whole genome sequencing projects and received training from experts such as Prof. W. Richard McCombie, Dr. Andy Baxevanis, Dr. William Pearson, Dr. Randall Smith, and Dr. Stephen Altschul.
Harshawardhan is the author of several peer-reviewed publications in scientific journals, and a book titled Perl Programming for Bioinformatics.
Description: The International Human Genome Project (IHGP), accomplished in 2003, was undoubtedly a giant step for mankind in the sequencing and assembly of the entire human genome. This event has fundamentally altered the manner in which we analyze biological systems, our approach to the many unsolved problems, and indeed, our attempt to unravel the closely held mysteries of evens the simplest of living organisms. However, deriving biological meaning from the raw stack of three billion bases of human DNA would not have been possible without the development of new algorithms for data mining and analysis. This book is about those fundamental tools and techniques that revolutionized biomedical research, and enable us today to perform biology in silico. The book uses an integrative approach to illustrate the use of these tools, and binds them together to create a coherent strategy to tackle the overwhelming problem of biological information overload. Divided into two parts, the book covers the core set of tools that have become indispensable to scientific discovery in the post-genome era, and also demonstrates how these tools can be integrated programmatically with BioPerl to be used in an enhanced, truly high throughput- biology on steroids- manner. With this coverage, the book will be useful to a diverse array of life science professionals, computational biologists, bioinformaticists, as well as students.
