Bioinformatics: A Practical Approach

Series:
Chapman & Hall/CRC Mathematical & Computational Biology
Published:
August 20, 2007 by Chapman and Hall/CRC - 648 Pages
Editor(s):
Shui Qing Ye, University of Missouri, Columbia, USA

Purchasing Options

Hardback
$94.95
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ISBN 9781584888109
Cat# C8105
 

Features

  • 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

    • Summary

    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 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

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