Computational promoter recognition in eukaryotic genomic DNA:
Saved in:
| Main Author: | |
|---|---|
| Format: | Book |
| Language: | English |
| Published: |
Berlin
Logos-Verl.
2002
|
| Series: | Studien zur Mustererkennung
7 |
| Subjects: | |
| Online Access: | Inhaltsverzeichnis |
| Item Description: | Zugl.: Erlangen, Nürnberg, Univ., Diss., 2002. - Zsfassung in dt. Sprache |
| Physical Description: | III, 186 S. Ill., graph. Darst. |
| ISBN: | 3897229889 |
Staff View
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| 100 | 1 | |a Ohler, Uwe |e Verfasser |4 aut | |
| 245 | 1 | 0 | |a Computational promoter recognition in eukaryotic genomic DNA |c from Uwe Ohler |
| 264 | 1 | |a Berlin |b Logos-Verl. |c 2002 | |
| 300 | |a III, 186 S. |b Ill., graph. Darst. | ||
| 336 | |b txt |2 rdacontent | ||
| 337 | |b n |2 rdamedia | ||
| 338 | |b nc |2 rdacarrier | ||
| 490 | 1 | |a Studien zur Mustererkennung |v 7 | |
| 500 | |a Zugl.: Erlangen, Nürnberg, Univ., Diss., 2002. - Zsfassung in dt. Sprache | ||
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Record in the Search Index
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| adam_text |
CONTENTS
1
INTRODUCTION
1
1.1
CONTRIBUTIONS
AND
GOALS
OF
THIS
THESIS
.
3
1.2
OUTLINE
OF
THIS
WORK
.
4
2
BACKGROUND
IN
MOLECULAR
BIOLOGY
AND
BIOINFORMATICS
7
2.1
FROM
DNA
TO
PROTEINS
.
7
2.1.1
STRUCTURE
OF
DNA
AND
CHROMOSOMES
.
7
2.1.2
PROTEINS,
TRANSCRIPTION
AND
TRANSLATION
.
10
2.2
COMPUTER-BASED
ANNOTATION
OF
GENOMES
.
13
2.2.1
STRUCTURAL
ANNOTATION
.
13
2.2.2
FUNCTIONAL
ANNOTATION
.
17
2.2.3
ASSESSMENT
OF
GENOME
ANNOTATIONS
.
18
3
PROMOTERS
AND
PROMOTER
RECOGNITION
21
3.1
GENE
REGULATION
IN
EUKARYOTES
.
21
3.2
REGULATION
AT
THE
TRANSCRIPTIONAL
LEVEL
.
24
3.2.1
THE
BASAL
TRANSCRIPTION
MACHINERY
.
25
3.2.2
CHROMATIN
STRUCTURE
IN
PROMOTER
REGIONS
.
28
3.2.3
SEQUENCE
ELEMENTS
AND
TRANSCRIPTION
FACTORS
.
30
3.3
APPROACHES
FOR
COMPUTATIONAL
PROMOTER
RECOGNITION
.
34
3.3.1
AB
INITIO
PREDICTION
.
34
3.3.2
PREDICTION
BY
HOMOLOGY
.
41
3.3.3
MODELS
FOR
PROMOTER
SUB-CLASSES
.
42
4
DATA
SETS
45
4.1
DROSOPHILA
DATA
SETS
.
46
4.2
VERTEBRATE
DATA
SETS
.
48
5
DISCRETE
DENSITIES
FOR
BIOPOLYMER
SEQUENCES
51
5.1
INTRODUCTION
.
52
5.2
STATIONARY
MARKOV
CHAINS
.
54
5.2.1
BASICS
.
54
5.2.2
INTERPOLATED
MARKOV
CHAINS
.
57
5.2.3
VARIABLE
LENGTH
MARKOV
CHAINS
.
59
5.2.4
DISCRIMINATIVE
ESTIMATION
OF
MARKOV
CHAIN
PARAMETERS
.
64
5.3
STOCHASTIC
SEGMENT
MODELS
.
68
5.3.1
FROM
HIDDEN
MARKOV
TO
SEGMENT
MODELS
.
68
5.3.2
ALGORITHMS
FOR
TRAINING
AND
EVALUATION
.
72
5.3.3
RUNTIME
CONSIDERATIONS
.
79
6
EXTRACTION
AND
MODELING
OF
CONTINUOUS
FEATURES
81
6.1
CPG
ISLAND
FEATURES
.
81
6.2
CALCULATION
OF
PROPERTY
PROFILES
.
82
6.3
FEATURES
FOR
PROPERTY
PROFILES
.
85
6.4
CONTINUOUS
DENSITIES
FOR
PROFILE
FEATURES
.
89
7
CLASSIFICATION
AND
EVALUATION
91
7.1
BAYES
CLASSIFIER
.
91
7.2
NEURAL
NETWORKS
.
94
7.2.1
ARCHITECTURE
.
94
7.2.2
LEARNING
THE
WEIGHTS
.
96
7.2.3
FEATURE
PRE-PROCESSING
.
98
7.3
CRITERIA
OF
SUCCESS
.
99
8
THE
SYSTEM
FOR
PROMOTER
RECOGNITION
101
8.1
GENERAL
REMARKS
.
101
8.1.1
OUTLINE
OF
THE
SYSTEM
.
101
8.1.2
EXPERIMENTAL
DESIGN
AND
EVALUATION
.
102
8.2
SEQUENCE-BASED
MODELS
OF
PROMOTERS
.
104
8.2.1
MARKOV
CHAIN
MODELS
.
104
8.2.2
STOCHASTIC
SEGMENT
MODELS
.
114
8.2.3
NEURAL
NETWORK
CLASSIFIER
.
123
8.2.4
LOCALIZATION
OF
PROMOTERS
WITH
SEQUENCE
MODELS
.
125
8.3
PROPERTY-PROFILE-BASED
MODELS
OF
PROMOTERS
.
131
VI
8.4
SEQUENCE/PROFILE
JOINT
MODELS
.
135
8.4.1
INTEGRATION
OF
SEQUENCE
AND
PROFILE
MODELS
.
135
8.4.2
EVALUATION
OF
THE
JOINT
MODELS
.
137
9
DISCUSSION
AND
OUTLOOK
143
9.1
PROMOTER
RECOGNITION
.
143
9.2
ANALYSIS
OF
PROMOTER
SEQUENCES
.
148
10
SUMMARY
153
A
AMBIGUOUS
NUCLEOTIDE
LETTERS
157
B
CONVERSION
OF
A
CONTEXT
TREE
INTO
AN
AUTOMATON
159
C
PARAMETERS
OF
PHYSICO-CHEMICAL
PROPERTIES
163
D
DESIGN
AND
IMPLEMENTATION
DETAILS
169
D.L
DENSITIES
FOR
SEQUENCES
.
169
D.2
DNA
SEQUENCE
HANDLING
CLASSES
.
170
D.3
FURTHER
REFERENCES
.
171
E
DVD
WITH
DATA
SETS
173
BIBLIOGRAPHY
175
VII |
| any_adam_object | 1 |
| author | Ohler, Uwe |
| author_facet | Ohler, Uwe |
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| author_sort | Ohler, Uwe |
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| classification_tum | DAT 770d CHE 820d CHE 810d BIO 110d |
| ctrlnum | (OCoLC)53376237 (DE-599)BVBBV014555822 |
| discipline | Biologie Informatik Chemie |
| format | Book |
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| genre_facet | Hochschulschrift |
| id | DE-604.BV014555822 |
| illustrated | Illustrated |
| indexdate | 2024-08-24T00:29:32Z |
| institution | BVB |
| isbn | 3897229889 |
| language | English |
| oai_aleph_id | oai:aleph.bib-bvb.de:BVB01-009898286 |
| oclc_num | 53376237 |
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| owner_facet | DE-29 DE-29T DE-91G DE-BY-TUM |
| physical | III, 186 S. Ill., graph. Darst. |
| publishDate | 2002 |
| publishDateSearch | 2002 |
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| publisher | Logos-Verl. |
| record_format | marc |
| series | Studien zur Mustererkennung |
| series2 | Studien zur Mustererkennung |
| spelling | Ohler, Uwe Verfasser aut Computational promoter recognition in eukaryotic genomic DNA from Uwe Ohler Berlin Logos-Verl. 2002 III, 186 S. Ill., graph. Darst. txt rdacontent n rdamedia nc rdacarrier Studien zur Mustererkennung 7 Zugl.: Erlangen, Nürnberg, Univ., Diss., 2002. - Zsfassung in dt. Sprache Eukaryoten (DE-588)4070991-7 gnd rswk-swf Computerunterstütztes Verfahren (DE-588)4139030-1 gnd rswk-swf DNS-Sequenz (DE-588)4150352-1 gnd rswk-swf Promotor Genetik (DE-588)4263977-3 gnd rswk-swf Mustererkennung (DE-588)4040936-3 gnd rswk-swf (DE-588)4113937-9 Hochschulschrift gnd-content Eukaryoten (DE-588)4070991-7 s DNS-Sequenz (DE-588)4150352-1 s Promotor Genetik (DE-588)4263977-3 s Mustererkennung (DE-588)4040936-3 s Computerunterstütztes Verfahren (DE-588)4139030-1 s DE-604 Studien zur Mustererkennung 7 (DE-604)BV013645858 7 DNB Datenaustausch application/pdf http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=009898286&sequence=000001&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA Inhaltsverzeichnis |
| spellingShingle | Ohler, Uwe Computational promoter recognition in eukaryotic genomic DNA Studien zur Mustererkennung Eukaryoten (DE-588)4070991-7 gnd Computerunterstütztes Verfahren (DE-588)4139030-1 gnd DNS-Sequenz (DE-588)4150352-1 gnd Promotor Genetik (DE-588)4263977-3 gnd Mustererkennung (DE-588)4040936-3 gnd |
| subject_GND | (DE-588)4070991-7 (DE-588)4139030-1 (DE-588)4150352-1 (DE-588)4263977-3 (DE-588)4040936-3 (DE-588)4113937-9 |
| title | Computational promoter recognition in eukaryotic genomic DNA |
| title_auth | Computational promoter recognition in eukaryotic genomic DNA |
| title_exact_search | Computational promoter recognition in eukaryotic genomic DNA |
| title_full | Computational promoter recognition in eukaryotic genomic DNA from Uwe Ohler |
| title_fullStr | Computational promoter recognition in eukaryotic genomic DNA from Uwe Ohler |
| title_full_unstemmed | Computational promoter recognition in eukaryotic genomic DNA from Uwe Ohler |
| title_short | Computational promoter recognition in eukaryotic genomic DNA |
| title_sort | computational promoter recognition in eukaryotic genomic dna |
| topic | Eukaryoten (DE-588)4070991-7 gnd Computerunterstütztes Verfahren (DE-588)4139030-1 gnd DNS-Sequenz (DE-588)4150352-1 gnd Promotor Genetik (DE-588)4263977-3 gnd Mustererkennung (DE-588)4040936-3 gnd |
| topic_facet | Eukaryoten Computerunterstütztes Verfahren DNS-Sequenz Promotor Genetik Mustererkennung Hochschulschrift |
| url | http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=009898286&sequence=000001&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA |
| volume_link | (DE-604)BV013645858 |
| work_keys_str_mv | AT ohleruwe computationalpromoterrecognitionineukaryoticgenomicdna |