Table of contents for Applied bioinformatics : an introduction / P.M. Selzer, R.J. MarhoĢˆfer, A. Rohwer ; [translators, P.D. Frank Seeber, Conor Caffrey].


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1  Computers, Operating Systems and the Internet ....  1
1.1   Computers and Operating Systems .............  1
1.2   Internet and WWW .........................     5
1.3   The Physical Connection to the Internet.........  6
1.4   The Logical Connection to the Internet .........  8
1.5   Internet Services............................  8
1.5.1 E-mail .....................................   8
1.5.2  FTP  ......................................  11
1.5.3  World Wide Web ............................  16
1.6   Using UNIX ............................... .....  18
1.7   The History of Bioinformatics .................  23
WWW Links ................................    29
2  The Biological Foundations of Bioinformatics ......  31
2.1   Nucleic Acids and Proteins ....................  31
2.2   Structure of the Nucleic Acids DNA and RNA ....  31
2.3   The Storage of Genetic Information ............  33
2.4   The Structure of Proteins ....................  36
2.4.1  Primary Structure ...........................  36
2.4.2  Secondary Structure .........................  39
2.5   Tertiary and Quaternary Structure .............  41
WWW Links ................................    43
3  Biological Databases ...........................  45
3.1   Biological Knowledge is Stored in Global
Databases ..................................  45
3.2   Primary Databases ..........................   46
3.2.1  Nucleotide Sequence Databases ................  46
3.2.2  Protein Sequence Databases ..................  53
3.3   Secondary Databases ........................   58
3.3.1  PROSITE ..................................    58
3.3.2  PRINTS ....................................   60
3.3.3  Pfam   .......................................  61
3.3.4  Interpro  ...................................  61
3.4   Genotype-Phenotype Databases ...............   62
3.4.1  PhenomicDB ...............................    63
3.5   Molecular Structure Databases ................  64
3.5.1  Protein Data Bank (PDB)....................   64
3.5.2  SCO P  .......................................  65
3.5.3  CATH  .....................................   67
3.5.4  PubChem   ...................................  67
WWW Links ................................    72
4 Sequence Comparisons and Sequence-Based
Database Searches ..............................  75
4.1   Pairwise and Multiple Sequence Comparisons ...  75
4.2   Database Searches with Nucleotide and Protein
Sequences..................................   83
4.2.1 Important Algorithms for Database
Searching..................................   87
4.3   Software for Sequence Analysis ................  87
WWW Links ................................    92
5  The Decoding of Eukaryotic Genomes .............  95
5.1   The Sequencing of Complete Genomes. .........  95
5.2   The Characterization of Genomes using
STS and EST Sequences ......................  96
5.2.1  Sequence Tagged Sites are Landmarks
in the Human Genome .......................   96
5.2.2  Expressed Sequence Tags ................... ..  97
5.3   The Implementation of an EST Project ..........  99
5.4   The Identification of Unknown Genes ..........  103
5.5   The Discovery of Splice Variants ...............  105
5.6   Genetic Causes for Individual Differences .......  108
5.6.1 Pharmacogenetics and Individual
Medicine ...................................  110
WWW Links ................................   115
6 Protein Structures and Structure-Based Rational
Drug Design  ..................................  117
6.1   Protein Structure ...........................  117
6.2   Signal Peptides ..............................  118
6.3   Transmembrane Proteins ................. ...  122
6.4    Analyses of Protein Structures .................  123
6.4.1 Protein Modeling ...........................  124
6.4.2  The Determination of Protein Structures
by High Throughput Methods .................  125
6.5   Structure-Based Rational Drug Design..........  126
6.5.1 A Docking Example .........................  128
6.5.2  Pharmacophore Modeling ................... .  131
6.5.3  Successes of Structure-Based Rational
Drug Design ...............................  133
WWW Links ................................   136
7 Systems Biology: The Functional Analysis
of Genomes ...................................  139
7.1   The Identification of the Cellular Functions
of Gene Products ............................  139
7.1.1 Transcriptomics ............................  140
7.1.2  Proteomics .................................  153
7.1.3  Metabolomics ..............................  163
7.1.4  Phenomics .................................  166
7.2   Systems Biology ............................  170
WWW Links ................................    178
8  Comparative Genome Analyses ................... 181
8.1   The Era of Genome Sequencing ...............  181
8.2   Drug Research at the Target Protein ............  182
8.3   Comparative Genome Analyses Provide
Information about the Biology of Organisms ....  185
8.3.1 Genome Structure ..........................   185
8.3.2  Coding Regions ..............................  186
8.3.3  Noncoding Regions .........................  188
8.4   Comparative Metabolic Analyses ...............  188
8.4.1 Kyoto Encyclopedia of Genes and Genomes. .....  191
8.5   Groups of Orthologous Proteins ...............  195
WWW Links ................................   199
9  Solutions to the Exercises .......................  201



Library of Congress subject headings for this publication: Bioinformatics, Bioinformatics Problems, exercises, etc, Computational Biology, Computational Biology Problems and Exercises