Algorithmic aspects of bioinformatics: with 118 figures and 9 tables
Gespeichert in:
| Hauptverfasser: | , |
|---|---|
| Format: | Buch |
| Sprache: | English German |
| Veröffentlicht: |
Berlin [u.a.]
Springer
2007
|
| Schriftenreihe: | Natural computing series
|
| Schlagworte: | |
| Online-Zugang: | Inhaltsverzeichnis |
| Beschreibung: | X, 396 Seiten Illustrationen, Diagramme |
| ISBN: | 9783642091001 3540719121 |
Internformat
MARC
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| 240 | 1 | 0 | |a Algorithmische Grundlagen der Bioinformatik |
| 245 | 1 | 0 | |a Algorithmic aspects of bioinformatics |b with 118 figures and 9 tables |c Hans-Joachim Böckenhaue, Dirk Bongartz |
| 264 | 1 | |a Berlin [u.a.] |b Springer |c 2007 | |
| 300 | |a X, 396 Seiten |b Illustrationen, Diagramme | ||
| 336 | |b txt |2 rdacontent | ||
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Datensatz im Suchindex
| _version_ | 1804137205799583744 |
|---|---|
| adam_text | Contents
1
Introduction
............................................... 1
Part
I
Introduction and Basic
Algorithms
2
Basics of Molecular Biology
................................ 7
2.1
Proteins
................................................ 7
2.2
Nucleic Acids
........................................... 9
2.3
Hereditary Information and Protein Biosynthesis
............ 12
2.4
Experimental Techniques
................................. 15
2.4.1
Basic Terms and Methods
.......................... 15
2.4.2
Duplication of
DNA............................... 15
2.4.3
Gel Electrophoresis and Direct Sequencing
............ 16
2.4.4 DNA
Chips
....................................... 19
2.5
Bibliographic Notes
...................................... 20
3
Basic Concepts: Strings, Graphs, and Algorithms
.......... 23
3.1
Strings
................................................. 23
3.2
Graphs
................................................. 25
3.3
Algorithms and Complexity
............................... 28
3.4
Bibliographic Notes
...................................... 35
4
String Algorithms
......................................... 37
4.1
The String Matching Problem
............................. 37
4.2
String Matching Automata
............................... 39
4.3
The Boyer-Moore Algorithm
.............................. 44
4.4
Suffix Trees
............................................. 50
4.5
Further Applications of Suffix Trees
........................ 58
4.5.1
Generalized Suffix Trees and the Substring Problem
... 58
4.5.2
Longest Common Substrings
........................ 61
4.5.3
Efficient Computation of Overlaps
................... 63
4.5.4
Repeats in Strings
................................. 66
4.6
Suffix Arrays
............................................ 68
4.7
Summary
............................................... 77
4.8
Bibliographic Notes
...................................... 78
Alignment Methods
....................................... 81
5.1
Alignment of Two Strings
................................ 82
5.1.1
Basic Definitions
.................................. 82
5.1.2
Global Alignment
................................. 84
5.1.3
Local and
Semiglobal
Alignment
.................... 89
5.1.4
Generalized Scoring Functions
...................... 94
5.2
Heuristic Methods for Database Search
..................... 97
5.2.1
The
FASTA
Heuristic
.............................. 98
5.2.2
The BLAST Heuristic
.............................. 99
5.3
Multiple Alignments
.....................................101
5.3.1
Definition and Scoring of Multiple Alignments
........101
5.3.2
Exact Computation of Multiple Alignments
...........104
5.3.3
Combining Pairwise Alignments
.....................109
5.4
Summary
...............................................114
5.5
Bibliographic Notes
......................................114
Part II
DNA
Sequencing
6
Introduction and Overview
................................119
7
Physical Mapping
.........................................123
7.1
Restriction Site Mapping
.................................123
7.1.1
The Double Digest Approach
.......................124
7.1.2
The Partial Digest Approach
.......................131
7.1.3
Comparison of Methods for Restriction Site Mapping
.. 141
7.2
Hybridization Mapping
...................................143
7.2.1
Mapping with Unique Probes
.......................146
7.2.2
Mapping with Unique Probes and Errors
.............157
7.2.3
Mapping with Non-unique Probes
...................165
7.3
Summary
...............................................166
7.4
Bibliographic Notes
......................................168
8 DNA
Sequencing
..........................................171
8.1
Shotgun Sequencing
.....................................171
8.1.1
Crucial Points to Be Considered in a Suitable Model
... 174
8.1.2
The Shortest Common Superstring Problem
..........176
8.1.3
Refined Models for Fragment Assembly
..............196
8.2
Sequencing by Hybridization
..............................201
8.3
Summary
...............................................207
8.4 Bibliographie Notes......................................208
Part III Analyzing Biological Data
9
Finding
Signals in DNA
Sequences
........................213
9.1
Identical and Similar Substrings
...........................213
9.2
Tandem Repeats
........................................217
9.3
Frequent and Infrequent Substrings
........................223
9.4
Hidden Markov Models
...................................228
9.5
Summary
...............................................235
9.6
Bibliographic Notes
......................................235
10
Genome Rearrangements
..................................237
10.1
Modeling
...............................................237
10.2
Sorting Undirected Permutations
..........................239
10.3
Sorting Directed Permutations
............................247
10.4
Computing the Syntenic Distance
.........................249
10.5
Summary
...............................................255
10.6
Bibliographic Notes
......................................255
11
Phylogenetic Trees
........................................257
11.1
Ultrametric Distances
....................................258
11.2
Additive Trees
..........................................265
11.3
Characters with Binary States
............................268
11.4
The Parsimony Principle and the Quartet Method
...........275
11.5
Summary
...............................................283
11.6
Bibliographic Notes
......................................285
12
Haplotyping
...............................................287
12.1
Inferring Haplotypes from a Population
....................288
12.2
Haplotyping a Single Individual
...........................305
12.3
Summary
...............................................316
12.4
Bibliographic Notes
......................................316
13
Molecular Structures
......................................319
13.1
RNA
Secondary Structure Prediction
......................320
13.1.1
Minimizing the Free Energy
........................322
13.1.2
Stochastic Context-Free Grammars
..................329
13.2
Structure-Based Comparison of Biomolecules
................337
13.3
Protein Structure Prediction
..............................349
13.3.1
De Novo
Structure Prediction
—
The HP Model
......352
13.3.2
Protein Threading
.................................363
13.4
Summary
...............................................369
13.4.1
RNA
Secondary Structure Prediction
................369
13.4.2
Structure-Based Comparison of Biomolecules
.........371
13.4.3
Protein Structure Prediction
........................371
13.5
Bibliographic Notes
......................................372
13.5.1
RNA
Secondary Structure Prediction
................372
13.5.2
Structure-Based Comparison of Biomolecules
.........373
13.5.3
Protein Structure Prediction
........................374
References
.....................................................377
Index
..........................................................389
|
| adam_txt |
Contents
1
Introduction
. 1
Part
I
Introduction and Basic
Algorithms
2
Basics of Molecular Biology
. 7
2.1
Proteins
. 7
2.2
Nucleic Acids
. 9
2.3
Hereditary Information and Protein Biosynthesis
. 12
2.4
Experimental Techniques
. 15
2.4.1
Basic Terms and Methods
. 15
2.4.2
Duplication of
DNA. 15
2.4.3
Gel Electrophoresis and Direct Sequencing
. 16
2.4.4 DNA
Chips
. 19
2.5
Bibliographic Notes
. 20
3
Basic Concepts: Strings, Graphs, and Algorithms
. 23
3.1
Strings
. 23
3.2
Graphs
. 25
3.3
Algorithms and Complexity
. 28
3.4
Bibliographic Notes
. 35
4
String Algorithms
. 37
4.1
The String Matching Problem
. 37
4.2
String Matching Automata
. 39
4.3
The Boyer-Moore Algorithm
. 44
4.4
Suffix Trees
. 50
4.5
Further Applications of Suffix Trees
. 58
4.5.1
Generalized Suffix Trees and the Substring Problem
. 58
4.5.2
Longest Common Substrings
. 61
4.5.3
Efficient Computation of Overlaps
. 63
4.5.4
Repeats in Strings
. 66
4.6
Suffix Arrays
. 68
4.7
Summary
. 77
4.8
Bibliographic Notes
. 78
Alignment Methods
. 81
5.1
Alignment of Two Strings
. 82
5.1.1
Basic Definitions
. 82
5.1.2
Global Alignment
. 84
5.1.3
Local and
Semiglobal
Alignment
. 89
5.1.4
Generalized Scoring Functions
. 94
5.2
Heuristic Methods for Database Search
. 97
5.2.1
The
FASTA
Heuristic
. 98
5.2.2
The BLAST Heuristic
. 99
5.3
Multiple Alignments
.101
5.3.1
Definition and Scoring of Multiple Alignments
.101
5.3.2
Exact Computation of Multiple Alignments
.104
5.3.3
Combining Pairwise Alignments
.109
5.4
Summary
.114
5.5
Bibliographic Notes
.114
Part II
DNA
Sequencing
6
Introduction and Overview
.119
7
Physical Mapping
.123
7.1
Restriction Site Mapping
.123
7.1.1
The Double Digest Approach
.124
7.1.2
The Partial Digest Approach
.131
7.1.3
Comparison of Methods for Restriction Site Mapping
. 141
7.2
Hybridization Mapping
.143
7.2.1
Mapping with Unique Probes
.146
7.2.2
Mapping with Unique Probes and Errors
.157
7.2.3
Mapping with Non-unique Probes
.165
7.3
Summary
.166
7.4
Bibliographic Notes
.168
8 DNA
Sequencing
.171
8.1
Shotgun Sequencing
.171
8.1.1
Crucial Points to Be Considered in a Suitable Model
. 174
8.1.2
The Shortest Common Superstring Problem
.176
8.1.3
Refined Models for Fragment Assembly
.196
8.2
Sequencing by Hybridization
.201
8.3
Summary
.207
8.4 Bibliographie Notes.208
Part III Analyzing Biological Data
9
Finding
Signals in DNA
Sequences
.213
9.1
Identical and Similar Substrings
.213
9.2
Tandem Repeats
.217
9.3
Frequent and Infrequent Substrings
.223
9.4
Hidden Markov Models
.228
9.5
Summary
.235
9.6
Bibliographic Notes
.235
10
Genome Rearrangements
.237
10.1
Modeling
.237
10.2
Sorting Undirected Permutations
.239
10.3
Sorting Directed Permutations
.247
10.4
Computing the Syntenic Distance
.249
10.5
Summary
.255
10.6
Bibliographic Notes
.255
11
Phylogenetic Trees
.257
11.1
Ultrametric Distances
.258
11.2
Additive Trees
.265
11.3
Characters with Binary States
.268
11.4
The Parsimony Principle and the Quartet Method
.275
11.5
Summary
.283
11.6
Bibliographic Notes
.285
12
Haplotyping
.287
12.1
Inferring Haplotypes from a Population
.288
12.2
Haplotyping a Single Individual
.305
12.3
Summary
.316
12.4
Bibliographic Notes
.316
13
Molecular Structures
.319
13.1
RNA
Secondary Structure Prediction
.320
13.1.1
Minimizing the Free Energy
.322
13.1.2
Stochastic Context-Free Grammars
.329
13.2
Structure-Based Comparison of Biomolecules
.337
13.3
Protein Structure Prediction
.349
13.3.1
De Novo
Structure Prediction
—
The HP Model
.352
13.3.2
Protein Threading
.363
13.4
Summary
.369
13.4.1
RNA
Secondary Structure Prediction
.369
13.4.2
Structure-Based Comparison of Biomolecules
.371
13.4.3
Protein Structure Prediction
.371
13.5
Bibliographic Notes
.372
13.5.1
RNA
Secondary Structure Prediction
.372
13.5.2
Structure-Based Comparison of Biomolecules
.373
13.5.3
Protein Structure Prediction
.374
References
.377
Index
.389 |
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| discipline_str_mv | Biologie Chemie-Ingenieurwesen Biotechnologie |
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| id | DE-604.BV022959668 |
| illustrated | Illustrated |
| index_date | 2024-07-02T19:04:14Z |
| indexdate | 2024-07-09T21:08:36Z |
| institution | BVB |
| isbn | 9783642091001 3540719121 |
| language | English German |
| oai_aleph_id | oai:aleph.bib-bvb.de:BVB01-016164051 |
| oclc_num | 318389261 |
| open_access_boolean | |
| owner | DE-1028 DE-11 DE-83 |
| owner_facet | DE-1028 DE-11 DE-83 |
| physical | X, 396 Seiten Illustrationen, Diagramme |
| publishDate | 2007 |
| publishDateSearch | 2007 |
| publishDateSort | 2007 |
| publisher | Springer |
| record_format | marc |
| series2 | Natural computing series |
| spelling | Böckenhauer, Hans-Joachim 1970- Verfasser (DE-588)122738365 aut Algorithmische Grundlagen der Bioinformatik Algorithmic aspects of bioinformatics with 118 figures and 9 tables Hans-Joachim Böckenhaue, Dirk Bongartz Berlin [u.a.] Springer 2007 X, 396 Seiten Illustrationen, Diagramme txt rdacontent n rdamedia nc rdacarrier Natural computing series Algoritmos Bioinformática - Matemáticas Algorithmus (DE-588)4001183-5 gnd rswk-swf Bioinformatik (DE-588)4611085-9 gnd rswk-swf Bioinformatik (DE-588)4611085-9 s Algorithmus (DE-588)4001183-5 s DE-604 Bongartz, Dirk 1974- Verfasser (DE-588)131753282 aut Erscheint auch als Online-Ausgabe 978-3-540-71913-7 Digitalisierung UB Passau application/pdf http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=016164051&sequence=000002&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA Inhaltsverzeichnis |
| spellingShingle | Böckenhauer, Hans-Joachim 1970- Bongartz, Dirk 1974- Algorithmic aspects of bioinformatics with 118 figures and 9 tables Algoritmos Bioinformática - Matemáticas Algorithmus (DE-588)4001183-5 gnd Bioinformatik (DE-588)4611085-9 gnd |
| subject_GND | (DE-588)4001183-5 (DE-588)4611085-9 |
| title | Algorithmic aspects of bioinformatics with 118 figures and 9 tables |
| title_alt | Algorithmische Grundlagen der Bioinformatik |
| title_auth | Algorithmic aspects of bioinformatics with 118 figures and 9 tables |
| title_exact_search | Algorithmic aspects of bioinformatics with 118 figures and 9 tables |
| title_exact_search_txtP | Algorithmic aspects of bioinformatics with 118 figures and 9 tables |
| title_full | Algorithmic aspects of bioinformatics with 118 figures and 9 tables Hans-Joachim Böckenhaue, Dirk Bongartz |
| title_fullStr | Algorithmic aspects of bioinformatics with 118 figures and 9 tables Hans-Joachim Böckenhaue, Dirk Bongartz |
| title_full_unstemmed | Algorithmic aspects of bioinformatics with 118 figures and 9 tables Hans-Joachim Böckenhaue, Dirk Bongartz |
| title_short | Algorithmic aspects of bioinformatics |
| title_sort | algorithmic aspects of bioinformatics with 118 figures and 9 tables |
| title_sub | with 118 figures and 9 tables |
| topic | Algoritmos Bioinformática - Matemáticas Algorithmus (DE-588)4001183-5 gnd Bioinformatik (DE-588)4611085-9 gnd |
| topic_facet | Algoritmos Bioinformática - Matemáticas Algorithmus Bioinformatik |
| url | http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=016164051&sequence=000002&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA |
| work_keys_str_mv | AT bockenhauerhansjoachim algorithmischegrundlagenderbioinformatik AT bongartzdirk algorithmischegrundlagenderbioinformatik AT bockenhauerhansjoachim algorithmicaspectsofbioinformaticswith118figuresand9tables AT bongartzdirk algorithmicaspectsofbioinformaticswith118figuresand9tables |