Bioinformatics: A Practical Approach, 1st Edition (Hardback) book cover

Bioinformatics

A Practical Approach, 1st Edition

Edited by Shui Qing Ye

Chapman and Hall/CRC

648 pages | 263 B/W Illus.

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Hardback: 9781584888109
pub: 2007-08-20
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pub: 2007-08-20
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Description

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

About the Originator

About the Series

Chapman & Hall/CRC Mathematical and Computational Biology

Learn more…

Subject Categories

BISAC Subject Codes/Headings:
MAT029000
MATHEMATICS / Probability & Statistics / General
SCI008000
SCIENCE / Life Sciences / Biology / General
SCI010000
SCIENCE / Biotechnology