# Provides theoretical introductions followed by step-by-step tutorials and sample datasets of practical applications in each chapter
# Demonstrates how to screen out genes of interest from genomics, transcriptomics, proteomics, and other integrative databases
# Shows how to retrieve single nucleotide polymorphism and haploytype data
# Covers the most commonly used biocomputing tools and program languages, including Perl, Java, and R
# Contains a list of useful websites and databases as well as more than 250 figures to complement the text
An emerging, ever-evolving branch of science, bioinformatics has paved the way for the explosive growth in the distribution of biological information to a variety of biological databases, including the National Center for Biotechnology Information. For growth to continue in this field, biologists must obtain basic computer skills while computer specialists must possess a fundamental understanding of biological problems. Bridging the gap between biology and computer science, Bioinformatics: A Practical Approach assimilates current bioinformatics knowledge and tools relevant to the omics age into one cohesive, concise, and self-contained volume.
Written by expert contributors from around the world, this practical book presents the most state-of-the-art bioinformatics applications. The first part focuses on genome analysis, common DNA analysis tools, phylogenetics analysis, and SNP and haplotype analysis. After chapters on microarray, SAGE, regulation of gene expression, miRNA, and siRNA, the book presents widely applied programs and tools in proteome analysis, protein sequences, protein functions, and functional annotation of proteins in murine models. The last part introduces the programming languages used in biology, website and database design, and the interchange of data between Microsoft Excel and Access.
Keeping complex mathematical deductions and jargon to a minimum, this accessible book offers both the theoretical underpinnings and practical applications of bioinformatics.
Table of Contents
GENOME AND DNA SEQUENCE ANALYSIS
Genome Analysis
Genome structure analysis by genome browser
Sequence similarity searching by BLAST
Two Common DNA Analysis Tools
Restriction mapping
PCR application
Phylogenetics Analysis
Multiple sequence alignments
Building phylogenetics tree
SNP and Haplotype Analysis
SNP analysis
Haplotype analysis
TRANSCRIPTOME AND RNA SEQUENCE ANALYSIS
Gene Expression Profiling by Microarray
Experimental design
Data acquisition and preprocessing
Data analysis
Tutorial
Gene Expression Profiling by SAGE
SAGE experimentation
SAGE data analysis
Retrieve data from SAGE database
Regulation of Gene Expression
Alternative promoters
Alternatively splicing
Alternative translation initiation
RNA editing
MicroRNoma Genome-Wide Profiling by Microarray
What are miRNAs?
microRNAs and human diseases
Significance of microRNA profiling
Significance of microRNA CGH assay
Genome-wide microRNA profiling by microarray
RNAi
Introduction of RNAi and siRNA
Search for siRNA information
PROTEOME AND PROTEIN SEQUENCE ANALYSIS
Proteome Analysis
Analyzing 2DE-derived data
Analyzing mass spectrometry derived data
Analyzing data derived from protein microarrays
Protein Sequence Analysis
Primary structure analysis
Secondary and tertiary structure analysis
Pattern and profile search
Protein Function Analysis
Protein function annotation
Protein posttranslational modifications
Protein-protein interactions
Functional Annotation of Proteins in Murine Models
Various murine models of human diseases
Search for murine databases
BASIC BIOCOMPUTING TOOLS
Application of Programming Languages in Biology
Application of Perl in biology
Application of Java in biology
Application of R in biology
Website and Database Design
Personal website design
Nuts and bolts of biological databases and their constructions
Microsoft Excel and Access
Microsoft Excel
Microsoft Access
Interchange data between Microsoft Excel and Access
APPENDICES
Abbreviations
Selected glossary
Websites for selected bioinformatics softwares
INDEX