生物信息學

本書是“精要速覽系列”中的《生物信息學》分冊，全書共15章，概括了該學科的核心內容和前沿動態，涉及生物學數據的獲得與處理、系統發生學、芯片數據分析、蛋白質組數據分析、生物信息學的應用等內容。

Abbreviations

Preface

Section A-Overview of bioinformatics

A1 The scope of bioinformatics

A2 Bioinformatics and the Internet

A3 Useful bioinformatics sites on the WWW

Section B-Data acquisition

B1 Sequencing DNA, RNA and proteins

B2 Determination of protein structure

B3 Gene and protein expression data

B4 Protein interaction data

Section C-Databases-contents, structure and annotation

C1 File formats

C2 Annotated sequence databases

C3 Genome and organism-specific databases

C4 Miscellaneous databases

Section D-Retrieval of biological data

D1 Data retrieval with Entrez and DBGET/LinkDB

D2 Data retrieval with SRS (sequence retrieval system)

Section E-Searching sequence databases by sequence similarity criteria

E1 Sequence similarity searches

E2 Amino acid substitution matrices

E3 Database searches：FASTA and BLAST

E4 Sequence filters

E5 Iterative database searches and PSI-BLAST

Section F-Multiple sequence alignment：gene and protein families

F1 Multiple sequence alignment and family relationships

F2 Protein families and pattern databases

F3 Protein domain families

Section G-Phylogenetics

G1 Phylogenetics, cladistics and ontology

G2 Building phylogenetic trees

G3 Evolution of macromolecular sequences

Section H-Sequence annotation

H1 Principles of genome annotation

H2 Annotation tools and resources

Section I-Structural bioinformatics

I1 Conceptual models of protein structure

I2 The relationship of protein three-dimensional structure to protein function

I3 The evolution of protein structure and function

I4 Obtaining, viewing and analyzing structural data

I5 Structural alignment

I6 Classification of proteins of known three-dimensional structure：CATH and SCOp

I7 Introduction to protein structure prediction

I8 Structure prediction by comparative modeling

I9 Secondary structure prediction

I10 Advanced protein structure prediction and prediction strategies

Section J-Microarray data analysis

J1 Microarray data：analysis methods

J2 Microarray data：tools and resources

J3 Sequence sampling and SAGE

Section K-Proteomic data analysis

K1 Analyzing data from 2D-PAGE gels

K2 Analyzing protein mass spectrometry data

Section L-Higher-order systems

L1 Modeling and reconstructing molecular pathways

L2 Protein interaction informatics

L3 Higher-order models

Section M-Cheminformatics in biology

M1 Conventions for representing molecules

M2 Cheminformatics resources

Section N-Bioinformatics in the pharmaceutical industry

N1 Boinformatics and drug discovery

N2 pharmainformatics resources

Section O-Basic principles of computing in bioinformatics

O1 Running computer software

02 Computer operating systems

03 Software downloading and installation

04 Database management

Further reading

Glossary

Index