Abbreviations Preface Section A-Overview of bioinformatics A1 The scoe 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 E1 Sequence similarity searches E2 Amino acid substitution matrices E3 Databases searches:FASTA and BLAST E4 Sequence filters E5 Iterative database searches and PSI-BLAST Section F-Multiple sequence alignment and family relationships 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 Adnanced 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 molecular pathways M2 Cheminformatics resources Section N-Bioinformatics in the pharmaceutical industry N1 Bioinformatics and drug discovery N2 Pharmainformatics resources Section O-Basic principles of computing in bioinformatics O1 Running computer software O2 Computer operating systems O3 Software downloading and installation O4 Database management Further reading Glossary Index
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