Essential bioinformatics:
Saved in:
| Main Author: | |
|---|---|
| Format: | Book |
| Language: | English |
| Published: |
Cambridge [u.a.]
Cambridge Univ. Press
2006
|
| Edition: | 1. publ. |
| Subjects: | |
| Online Access: | Table of contents Publisher description Inhaltsverzeichnis |
| Item Description: | Includes bibliographical references and index |
| Physical Description: | XI, 339 S. Ill., graph. Darst. |
| ISBN: | 0521840988 0521600820 9780521840989 |
Staff View
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| adam_text | Contents
Preface ¦ ix
SECTION I INTRODUCTION AND BIOLOGICAL DATABASES
1 Introduction ¦ 3
What Is Bioinformatics? ¦ 4
Goal ¦ 5
Scope ¦ 5
Applications ¦ 6
Limitations ¦ 7
NewThemes ¦ 8
Further Reading ¦ 8
2 Introduction to Biological Databases ¦ 10
What Is a Database? «10
Typesof Databases «10
Biological Databases «13
Pitfallsof Biological Databases «17
Information Retrieval from Biological Databases «18
Summary ¦ 27
Further Reading ¦ 27
SECTION II SEQUENCE ALIGNMENT
3 Pairwise Sequence Alignment «31
Evolutionary Basis »31
Sequence Homology versus Sequence Similarity ¦ 32
Sequence Similarity versus Sequence Identity ¦ 33
Methods ¦ 34
Scoring Matrices «41
Statistical Significance of Sequence Alignment ¦ 47
Summary ¦ 48
Further Reading ¦ 49
4 Database Similarity Searching ¦ 51
Unique Requirements of Database Searching «51
Heuristic Database Searching ¦ 52
Basic Local Alignment Search Tool (BLAST) ¦ 52
FASTA ¦ 57
ComparisonofFASTA and BLAST ¦ 60
Database Searching with the Smith Waterman Method ¦ 61
Summary ¦ 61
Further Reading ¦ 62
5 Multiple Sequence Alignment ¦ 63
Scoring Function ¦ 63
Exhaustive Algorithms ¦ 64
Heuristic Algorithms ¦ 65
Practical Issues «71
Summary ¦ 73
Further Reading ¦ 74
6 Proflies and Hidden Markov Models ¦ 75
Position Specific Scoring Matrices ¦ 75
Profiles ¦ 77
Markov Model and Hidden Markov Model ¦ 79
Summary ¦ 84
Further Reading ¦ 84
7 Protein Motifs and Domain Prediction ¦ 85
Identification of Motifs and Domains in Multiple Sequence
Alignment ¦ 86
Motifand Domain Databases Using Regulär Expressions ¦ 86
Motif and Domain Databases Using Statistical Models ¦ 87
Protein Family Databases ¦ 90
Motif Discovery in Unaligned Sequences ¦ 91
Sequence Logos ¦ 92
Summary ¦ 93
Further Reading ¦ 94
SECTION III GENE AND PROMOTER PREDICTION
8 Gene Prediction ¦ 97
Categories of Gene Prediction Programs ¦ 97
Gene Prediction in Prokaryotes ¦ 98
Gene Prediction in Eukaryotes «103
Summary ¦ 111
Further Reading ¦ 111
9 Promoter and Regulatory Element Prediction «113
Promoter and Regulatory Elements in Prokaryotes ¦ 113
Promoter and Regulatory Elements in Eukaryotes ¦ 114
Prediction Algorithms ¦ 115
Summary ¦ 123
Further Reading ¦ 124
SECTION IV MOLECULAR PHYLOGENETICS
10 Phylogenetics Basics ¦ 127
Molecular Evolution and Molecular Phylogenetics ¦ 127
Terminology ¦ 128
Gene Phylogeny versus Species Phylogeny ¦ 130
i
i
FormsofTree Repräsentation ¦ 131
WhyFindingaTrueTreelsDifficult «132
Procedure «133
Summary «140
Further Reading «141
11 Phylogenetic Tree Construction Methods and Programs «142
Distance Based Methods ¦ 142
Character Based Methods ¦ 150
Phylogenetic Tree Evaluation ¦ 163
Phylogenetic Programs ¦ 167
Summary ¦ 168
Further Reading ¦ 169
SECTION V STRUCTURAL BIOINFORMATICS
12 Protein Structure Basics ¦ 173
AminoAcids ¦ 173
Peptide Formation «174
DihedralAngles ¦ 175
Hierarchy ¦ 176
Secondary Structures «178
Tertiary Structures «180
Determination of Protein Three Dimensional Structure ¦ 181
Protein Structure Database «182
Summary ¦ 185
Further Reading «186
13 Protein Structure Visualization, Comparison,
and Classification ¦ 187
Protein Structural Visualization ¦ 187
Protein Structure Comparison ¦ 190
Protein Structure Classification ¦ 195
Summary ¦ 199
Further Reading «199
14 Protein Secondary Structure Prediction ¦ 200
Secondary Structure Prediction for Globular Proteins «201
Secondary Structure Prediction for Transmembrane Proteins ¦ 208
Coiled Coil Prediction ¦ 211
Summary ¦ 212
Further Reading «213
15 Protein Tertiary Structure Prediction «214
Methods «215
Homology Modeling »215
Threading and Fold Recognition ¦ 223
Ab Initio Protein Structural Prediction ¦ 227
CASP ¦ 228
Summary ¦ 229
Further Reading ¦ 230
16 RNA Structure Prediction «231
Introduction «231
TypesofRNAStructures ¦ 233
RNA Secondary Structure Prediction Methods ¦ 234
Ab Initio Approach ¦ 234
Comparative Approach ¦ 237
Performance Evaluation ¦ 239
Summary ¦ 239
Further Reading ¦ 240
SECTION VI GENOMICS AND PROTEOMICS
17 Genome Mapping, Assembly, and Comparison ¦ 243
Genome Mapping ¦ 243
Genome Sequencing ¦ 245
Genome Sequence Assembly ¦ 246
Genome Annotation ¦ 250
Comparative Genomics ¦ 255
Summary ¦ 259
Further Reading ¦ 259
18 Functional Genomics ¦ 261
Sequence Based Approaches ¦ 261
Microarray Based Approaches ¦ 267
Comparison of SAGE and DNA Microarrays ¦ 278
Summary ¦ 279
Further Reading ¦ 280
19 Proteomics «281
Technology of Protein Expression Analysis ¦ 281
Posttranslational Modifikation ¦ 287
Protein Sorting ¦ 289
Protein Protein Interactions «291
Summary ¦ 296
Further Reading ¦ 296
APPENDIX
Appendix 1. Practical Exercises «301
Appendix 2. Glossary ¦ 318
Index «331
i
i
|
| adam_txt |
Contents
Preface ¦ ix
SECTION I INTRODUCTION AND BIOLOGICAL DATABASES
1 Introduction ¦ 3
What Is Bioinformatics? ¦ 4
Goal ¦ 5
Scope ¦ 5
Applications ¦ 6
Limitations ¦ 7
NewThemes ¦ 8
Further Reading ¦ 8
2 Introduction to Biological Databases ¦ 10
What Is a Database? «10
Typesof Databases «10
Biological Databases «13
Pitfallsof Biological Databases «17
Information Retrieval from Biological Databases «18
Summary ¦ 27
Further Reading ¦ 27
SECTION II SEQUENCE ALIGNMENT
3 Pairwise Sequence Alignment «31
Evolutionary Basis »31
Sequence Homology versus Sequence Similarity ¦ 32
Sequence Similarity versus Sequence Identity ¦ 33
Methods ¦ 34
Scoring Matrices «41
Statistical Significance of Sequence Alignment ¦ 47
Summary ¦ 48
Further Reading ¦ 49
4 Database Similarity Searching ¦ 51
Unique Requirements of Database Searching «51
Heuristic Database Searching ¦ 52
Basic Local Alignment Search Tool (BLAST) ¦ 52
FASTA ¦ 57
ComparisonofFASTA and BLAST ¦ 60
Database Searching with the Smith Waterman Method ¦ 61
Summary ¦ 61
Further Reading ¦ 62
5 Multiple Sequence Alignment ¦ 63
Scoring Function ¦ 63
Exhaustive Algorithms ¦ 64
Heuristic Algorithms ¦ 65
Practical Issues «71
Summary ¦ 73
Further Reading ¦ 74
6 Proflies and Hidden Markov Models ¦ 75
Position Specific Scoring Matrices ¦ 75
Profiles ¦ 77
Markov Model and Hidden Markov Model ¦ 79
Summary ¦ 84
Further Reading ¦ 84
7 Protein Motifs and Domain Prediction ¦ 85
Identification of Motifs and Domains in Multiple Sequence
Alignment ¦ 86
Motifand Domain Databases Using Regulär Expressions ¦ 86
Motif and Domain Databases Using Statistical Models ¦ 87
Protein Family Databases ¦ 90
Motif Discovery in Unaligned Sequences ¦ 91
Sequence Logos ¦ 92
Summary ¦ 93
Further Reading ¦ 94
SECTION III GENE AND PROMOTER PREDICTION
8 Gene Prediction ¦ 97
Categories of Gene Prediction Programs ¦ 97
Gene Prediction in Prokaryotes ¦ 98
Gene Prediction in Eukaryotes «103
Summary ¦ 111
Further Reading ¦ 111
9 Promoter and Regulatory Element Prediction «113
Promoter and Regulatory Elements in Prokaryotes ¦ 113
Promoter and Regulatory Elements in Eukaryotes ¦ 114
Prediction Algorithms ¦ 115
Summary ¦ 123
Further Reading ¦ 124
SECTION IV MOLECULAR PHYLOGENETICS
10 Phylogenetics Basics ¦ 127
Molecular Evolution and Molecular Phylogenetics ¦ 127
Terminology ¦ 128
Gene Phylogeny versus Species Phylogeny ¦ 130
i
i
FormsofTree Repräsentation ¦ 131
WhyFindingaTrueTreelsDifficult «132
Procedure «133
Summary «140
Further Reading «141
11 Phylogenetic Tree Construction Methods and Programs «142
Distance Based Methods ¦ 142
Character Based Methods ¦ 150
Phylogenetic Tree Evaluation ¦ 163
Phylogenetic Programs ¦ 167
Summary ¦ 168
Further Reading ¦ 169
SECTION V STRUCTURAL BIOINFORMATICS
12 Protein Structure Basics ¦ 173
AminoAcids ¦ 173
Peptide Formation «174
DihedralAngles ¦ 175
Hierarchy ¦ 176
Secondary Structures «178
Tertiary Structures «180
Determination of Protein Three Dimensional Structure ¦ 181
Protein Structure Database «182
Summary ¦ 185
Further Reading «186
13 Protein Structure Visualization, Comparison,
and Classification ¦ 187
Protein Structural Visualization ¦ 187
Protein Structure Comparison ¦ 190
Protein Structure Classification ¦ 195
Summary ¦ 199
Further Reading «199
14 Protein Secondary Structure Prediction ¦ 200
Secondary Structure Prediction for Globular Proteins «201
Secondary Structure Prediction for Transmembrane Proteins ¦ 208
Coiled Coil Prediction ¦ 211
Summary ¦ 212
Further Reading «213
15 Protein Tertiary Structure Prediction «214
Methods «215
Homology Modeling »215
Threading and Fold Recognition ¦ 223
Ab Initio Protein Structural Prediction ¦ 227
CASP ¦ 228
Summary ¦ 229
Further Reading ¦ 230
16 RNA Structure Prediction «231
Introduction «231
TypesofRNAStructures ¦ 233
RNA Secondary Structure Prediction Methods ¦ 234
Ab Initio Approach ¦ 234
Comparative Approach ¦ 237
Performance Evaluation ¦ 239
Summary ¦ 239
Further Reading ¦ 240
SECTION VI GENOMICS AND PROTEOMICS
17 Genome Mapping, Assembly, and Comparison ¦ 243
Genome Mapping ¦ 243
Genome Sequencing ¦ 245
Genome Sequence Assembly ¦ 246
Genome Annotation ¦ 250
Comparative Genomics ¦ 255
Summary ¦ 259
Further Reading ¦ 259
18 Functional Genomics ¦ 261
Sequence Based Approaches ¦ 261
Microarray Based Approaches ¦ 267
Comparison of SAGE and DNA Microarrays ¦ 278
Summary ¦ 279
Further Reading ¦ 280
19 Proteomics «281
Technology of Protein Expression Analysis ¦ 281
Posttranslational Modifikation ¦ 287
Protein Sorting ¦ 289
Protein Protein Interactions «291
Summary ¦ 296
Further Reading ¦ 296
APPENDIX
Appendix 1. Practical Exercises «301
Appendix 2. Glossary ¦ 318
Index «331
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| spelling | Xiong, Jin Verfasser aut Essential bioinformatics Jin Xiong 1. publ. Cambridge [u.a.] Cambridge Univ. Press 2006 XI, 339 S. Ill., graph. Darst. txt rdacontent n rdamedia nc rdacarrier Includes bibliographical references and index Bio-informatica gtt Bioinformatics Computational Biology Molekulare Bioinformatik (DE-588)4531334-9 gnd rswk-swf Bioinformatik (DE-588)4611085-9 gnd rswk-swf (DE-588)4151278-9 Einführung gnd-content (DE-588)4123623-3 Lehrbuch gnd-content Molekulare Bioinformatik (DE-588)4531334-9 s DE-604 Bioinformatik (DE-588)4611085-9 s DE-188 http://www.loc.gov/catdir/toc/ecip061/2005029453.html Table of contents http://www.loc.gov/catdir/enhancements/fy0633/2005029453-d.html Publisher description HBZ Datenaustausch application/pdf http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=014768738&sequence=000004&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA Inhaltsverzeichnis |
| spellingShingle | Xiong, Jin Essential bioinformatics Bio-informatica gtt Bioinformatics Computational Biology Molekulare Bioinformatik (DE-588)4531334-9 gnd Bioinformatik (DE-588)4611085-9 gnd |
| subject_GND | (DE-588)4531334-9 (DE-588)4611085-9 (DE-588)4151278-9 (DE-588)4123623-3 |
| title | Essential bioinformatics |
| title_auth | Essential bioinformatics |
| title_exact_search | Essential bioinformatics |
| title_exact_search_txtP | Essential bioinformatics |
| title_full | Essential bioinformatics Jin Xiong |
| title_fullStr | Essential bioinformatics Jin Xiong |
| title_full_unstemmed | Essential bioinformatics Jin Xiong |
| title_short | Essential bioinformatics |
| title_sort | essential bioinformatics |
| topic | Bio-informatica gtt Bioinformatics Computational Biology Molekulare Bioinformatik (DE-588)4531334-9 gnd Bioinformatik (DE-588)4611085-9 gnd |
| topic_facet | Bio-informatica Bioinformatics Computational Biology Molekulare Bioinformatik Bioinformatik Einführung Lehrbuch |
| url | http://www.loc.gov/catdir/toc/ecip061/2005029453.html http://www.loc.gov/catdir/enhancements/fy0633/2005029453-d.html http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=014768738&sequence=000004&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA |
| work_keys_str_mv | AT xiongjin essentialbioinformatics |