Annotation of non-coding RNAs and examination of Next Generation Sequencing data of pathogenic organisms:
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| 1. Verfasser: | |
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| Format: | Abschlussarbeit Buch |
| Sprache: | English |
| Veröffentlicht: |
Jena
11.06.2018
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| Online-Zugang: | Inhaltsverzeichnis Inhaltsverzeichnis |
| Beschreibung: | xv, 130 Seiten Illustrationen 30 cm |
Internformat
MARC
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| 100 | 1 | |a Riege, Konstantin |d 1988- |e Verfasser |0 (DE-588)1180785924 |4 aut | |
| 245 | 1 | 0 | |a Annotation of non-coding RNAs and examination of Next Generation Sequencing data of pathogenic organisms |c von Diplom Bioinformatiker Konstantin Riege |
| 264 | 1 | |a Jena |c 11.06.2018 | |
| 300 | |a xv, 130 Seiten |b Illustrationen |c 30 cm | ||
| 336 | |b txt |2 rdacontent | ||
| 337 | |b n |2 rdamedia | ||
| 338 | |b nc |2 rdacarrier | ||
| 502 | |b Dissertation |c Friedrich-Schiller-Universität Jena |d 2019 | ||
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| 999 | |a oai:aleph.bib-bvb.de:BVB01-031423342 | ||
Datensatz im Suchindex
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| adam_text | CONTENTS
AUTHOR
*
S
PUBLICATIONS
VII
LIST
OF
FIGURES
IX
LIST
OF
TABLES
XV
1
INTRODUCTION
1
1.1
NON-CODING
GENES
.................................................................................................
2
1.1.1
CIS-ACTING
NCRNAS
..................................................................................
3
1.1.1.1
RNAI,
MIRNAS
AND
PIRNAS
..................................................
4
1.1.1.2
RIBOSWITCHES
.............................................................................
4
1.1.1.3
SELF-SPLICING
RIBOZYMES
...........................................................
5
1.1.2
TRANS-ACTING
NCRNAS
............................................................................
6
1.1.2.1
SMALL
NUCLEAR
RNAS
.................................................................
6
1.1.2.2
HOUSEKEEPING
NCRNAS
..............................................................
7
1.1.3
EUKARYOTIC
NCRNAS
...............................................................................
8
1.1.4
PROKARYOTIC
NCRNAS
...............................................................................
9
1.1.5
GENUS
SPECIFIC
NCRNAS
.........................................................................
10
1.2
NEXT
GENERATION
SEQUENCING
...............................................................................
10
1.2.1
RNA
LIBRARY
PREPARATION
......................................................................
11
1.2.2
CONCEPTS
FOR
RNA-SEQ
PREPROCESSING
....................................................
13
1.2.3
CONCEPTS
FOR
RNA-SEQ
DRIVEN
DIFFERENTIAL
GENE
EXPRESSION
ANALYSIS
.
14
1.2.4
CONCEPTS
OF
NCRNA
ANNOTATION
BY
DRNA-SEQ
.....................................
15
1.3
PATHOGENIC
RELEVANCE
OF
GENE
ANNOTATION
AND
TRANSCRIPTOME
ANALYSIS
....
16
2
METHODS
19
2.1
HOMOLOGY
BASED
GENE
PREDICTION
.......................................................................
19
2.1.1
TEXT
BASED
SEARCH
......................................................................................
20
2.1.2
HIDDEN
MARKOV
MODEL
BASED
SEARCH
........................................................
22
2.1.3
COVARIANCE
MODEL
BASED
SEARCH
..................................................................
24
2.2
DE
NOVO
GENE
PREDICTION
..........................................................................................
26
2.2.1
SECONDARY
STRUCTURE
BASED
SEARCH
..............................................................
26
2.2.2
MOTIF
BASED
SEARCH
...................................................................................
27
2.2.3
MACHINE
LEARNING
..........................................................................................
28
2.2.4
R
N
A
-
SEQUENCING
..........................................................................................
28
2.2.4.1
TRANSCRIPT
ASSEMBLY
....................................................................
28
2.2.4.2
EXPRESSION
PATTERN
.......................................................................
29
2.2.4.3
EXPRESSION
QUANTIFICATION
AND
NORMALIZATION
.........................
29
2.3
PHYLOGENY
RECONSTRUCTION
.......................................................................................
31
3
GORAP:
A
GENOME-WIDE
NCRNA
ANNOTATION
PIPELINE
35
3.1
WORKFLOW
AND
IMPLEMENTATIONS
..............................................................................
36
3.1.1
INFERNAL
.........................................................................................................
38
3.1.2
BLAST
.........................................................................................................
38
3.1.3
TRNASCAN-SE
................................................................................................
39
3.1.4
RNAMMER
...................................................................................................
40
3.1.5
BAR
MAP
.........................................................................................................
40
3.1.6
BCHECK
............................................................................................................
40
3.1.7
CRT
...............................................................................................................
41
3.2
FILTER
......................................................................
42
3.2.1
BITSCORE
AND
TAXONOMY
BASED
FILTER
..............................................................
42
3.2.2
SECONDARY
STRUCTURE
BASED
FILTER
....................................................................
43
3.2.3
SEQUENCE
CONSTRAINS
AND
CONSERVATION
BASED
FILTER
.....................................
43
3.2.4
OVERLAP
BASED
FILTER
....................................................................................
44
3.3
DE
NOVO
GENE
PREDICTION
INTEGRATING
RNA-SEQ
.....................................................
45
3.4
PHYLOGENY
RECONSTRUCTION
.......................................................................................
45
3.5
EVALUATION
..................................................................................................................
46
4
FURTHER
RESULTS
AND
DISCUSSION
51
4.1
SPECIES
SPECIFIC
ANNOTATION
USING
GORAP
.................................................................
51
4.1.1
CHLAMYDIA
...................................................................................................
51
4.1.2
AQUIFICALES
...................................................................................................
53
4.1.3
PROTOSTELIA
...................................................................................................
57
4.1.4
LICHTHEIMIA
AND
BASAL
FUNGI
.........................................................................
60
4.1.5
CANDIDA
GLABRATA
..........................................................................................
63
4.1.6
ASPERGILLUS
FUMIGATUS
POWERED
BY
SMALLRNA-SEQ
.............................
66
4.2
RNONIE
POWERED
INFERENCE
OF
PHYLOGENY
..........................................................
70
4.2.1
CHLAMY
DIALES
.......................................................................................
71
4.2.2
AQUIFICALES
..................................................................................................
72
4.2.3
LICHTHEIMIA
AND
BASAL
FUNGI
...............................................................
73
4.2.4
PROTOSTELIA
..................................................................................................
74
4.2.5
FUNGI
KINGDOM
....................................................................................
75
4.3
EXPLORATION
OF
TRANSCRIPTOMIC
LANDSCAPES
77
4.3.1
EXPLORING
THE
MOLECULAR
BASIS
FOR
PATHOGENICITY
OF
LICHTHEIMIA
...
77
4.3.2
ROLES
OF
HUMAN
INCRNAS
DURING
IMMUNOMODULATION
BY
VITAMINS
.
.
83
5
ACKNOWLEDGMENTS
101
BIBLIOGRAPHY
103
|
| any_adam_object | 1 |
| author | Riege, Konstantin 1988- |
| author_GND | (DE-588)1180785924 |
| author_facet | Riege, Konstantin 1988- |
| author_role | aut |
| author_sort | Riege, Konstantin 1988- |
| author_variant | k r kr |
| building | Verbundindex |
| bvnumber | BV046041656 |
| ctrlnum | (OCoLC)1108330450 (DE-599)DNB1183003358 |
| discipline | Biologie |
| format | Thesis Book |
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| genre_facet | Hochschulschrift |
| id | DE-604.BV046041656 |
| illustrated | Illustrated |
| indexdate | 2024-07-10T08:33:35Z |
| institution | BVB |
| language | English |
| oai_aleph_id | oai:aleph.bib-bvb.de:BVB01-031423342 |
| oclc_num | 1108330450 |
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| physical | xv, 130 Seiten Illustrationen 30 cm |
| publishDate | 2018 |
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| spelling | Riege, Konstantin 1988- Verfasser (DE-588)1180785924 aut Annotation of non-coding RNAs and examination of Next Generation Sequencing data of pathogenic organisms von Diplom Bioinformatiker Konstantin Riege Jena 11.06.2018 xv, 130 Seiten Illustrationen 30 cm txt rdacontent n rdamedia nc rdacarrier Dissertation Friedrich-Schiller-Universität Jena 2019 Non-coding RNA (DE-588)7650051-2 gnd rswk-swf (DE-588)4113937-9 Hochschulschrift gnd-content Non-coding RNA (DE-588)7650051-2 s DE-604 B:DE-101 application/pdf http://d-nb.info/1183003358/04 Inhaltsverzeichnis DNB Datenaustausch application/pdf http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=031423342&sequence=000001&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA Inhaltsverzeichnis |
| spellingShingle | Riege, Konstantin 1988- Annotation of non-coding RNAs and examination of Next Generation Sequencing data of pathogenic organisms Non-coding RNA (DE-588)7650051-2 gnd |
| subject_GND | (DE-588)7650051-2 (DE-588)4113937-9 |
| title | Annotation of non-coding RNAs and examination of Next Generation Sequencing data of pathogenic organisms |
| title_auth | Annotation of non-coding RNAs and examination of Next Generation Sequencing data of pathogenic organisms |
| title_exact_search | Annotation of non-coding RNAs and examination of Next Generation Sequencing data of pathogenic organisms |
| title_full | Annotation of non-coding RNAs and examination of Next Generation Sequencing data of pathogenic organisms von Diplom Bioinformatiker Konstantin Riege |
| title_fullStr | Annotation of non-coding RNAs and examination of Next Generation Sequencing data of pathogenic organisms von Diplom Bioinformatiker Konstantin Riege |
| title_full_unstemmed | Annotation of non-coding RNAs and examination of Next Generation Sequencing data of pathogenic organisms von Diplom Bioinformatiker Konstantin Riege |
| title_short | Annotation of non-coding RNAs and examination of Next Generation Sequencing data of pathogenic organisms |
| title_sort | annotation of non coding rnas and examination of next generation sequencing data of pathogenic organisms |
| topic | Non-coding RNA (DE-588)7650051-2 gnd |
| topic_facet | Non-coding RNA Hochschulschrift |
| url | http://d-nb.info/1183003358/04 http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=031423342&sequence=000001&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA |
| work_keys_str_mv | AT riegekonstantin annotationofnoncodingrnasandexaminationofnextgenerationsequencingdataofpathogenicorganisms |
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