Practical bioinformatics:
Gespeichert in:
| 1. Verfasser: | |
|---|---|
| Format: | Buch |
| Sprache: | English |
| Veröffentlicht: |
New York [u.a.]
Garland Science
2013
|
| Schlagworte: | |
| Online-Zugang: | Inhaltsverzeichnis Klappentext |
| Beschreibung: | XI, 367 S., [6] Bl. Ill., graph. Darst. |
| ISBN: | 9780815344568 |
Internformat
MARC
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| 035 | |a (OCoLC)815944002 | ||
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| 245 | 1 | 0 | |a Practical bioinformatics |c Michael Agostino |
| 264 | 1 | |a New York [u.a.] |b Garland Science |c 2013 | |
| 300 | |a XI, 367 S., [6] Bl. |b Ill., graph. Darst. | ||
| 336 | |b txt |2 rdacontent | ||
| 337 | |b n |2 rdamedia | ||
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Datensatz im Suchindex
| _version_ | 1804149520729112576 |
|---|---|
| adam_text | VIII
Contents
Chapter
1
Introduction to
Bioinformatics and Sequence Analysis
1
Exercises
1.1
Introduction
1
1.2
The Growth of GenBank
2
1.3
Data, Data, Everywhere
2
Further examples of human genome
sequencing
4
Personal genome sequencing
4
Paleogenetics
4
Focused medical genomic studies
5
1.4
The Size of a Genome
5
1.5
Annotation
6
1.6
Witnessing Evolution Through
Bioinformatics
7
Recent evolutionary changes to plants
and animals
7
1.7
Large Sources of Human Sequence
Variation
7
1.8
Recent Evolutionary Changes to
Human Populations
8
1.9
DNA
Sequence in Databases
9
Genomic
DNA
assembly
10
cDNA in databases
—
where does it
come from?
12
1.10
Sequence Analysis and Data Display
14
1.11
Summary
20
Further Reading
20
Internet resources
21
Williams syndrome and oxytocin:
research with Internet tools
Chapter
2
Introduction to
Internet Resources
2.1
Introduction
2.2
The NCBI Website and
ENTREZ
2.3
PubMed
2.4
Gene Name Evolution
2.5
OMIM
2.6
Retrieving Nucleotide Sequences
2.7
Searching Patents
2.8
Public Grants Database:
NIH RePORTER
2.9
Gene Ontology
2.10
The Gene Database
2.11
UniGene
2.12
The UniGene Library Browser
2.13
Summary
23
23
23
25
27
29
30
31
33
34
36
38
43
44
Further Reading
Chapter
3
Introduction to the
BLAST Suite and BLASTN
3.1
Introduction
Why search a database?
3.2
What is BLAST?
How does BLAST work?
3.3
Your First BLAST Search
Find the query sequence in GenBank
Convert the file to another format
Performing BLASTN searches
3.4
BLAST Results
Graphic
Interpretation of the graphic
Results table
Interpretation of the table
The alignments
Other BLASTN hits from this query
Simultaneous review of the graphic,
table, and alignments
3.5
BLASTN Across Species
BLASTN of the reference sequence for
human beta hemoglobin against
nonhuman transcripts
Paralogs,
orthologs, and homologs
3.6
BLAST Output Format
3.7
Summary
Exercises
Exercise
1 :
Biofilm
analysis
Exercise
2:
RuBisCO
Further Reading
Internet resources
Chapter
4
Protein BLAST: BLASTP
4.1
Introduction
4.2
Codons
and the Genetic Code
Memorizing the genetic code
4.3
Amino
Acids
Amino
acid properties
44
44
45
47
47
47
48
48
49
49
51
52
54
54
55
55
57
57
60
63
64
64
66
68
68
68
68
70
71
71
73
73
73
76
76
77
4.4
BLASTP and the Scoring Matrix
78
Building a matrix
78
4.5
An Example BLASTP Search
80
Retrieving protein records
81
Running BLASTP
81
The results
82
The alignments
84
Distant homologies
84
4.6
Pairwise BLAST
85
4.7
Running BLASTP at the ExPASy
Website
86
Searching for pro-opiomelanocortin
using a protein sequence fragment
87
Searching for repeated domains in
alpha-1 collagen
91
4.8
Summary
94
Exercises
94
Exercise
1 :
Typing contest
94
Exercise
2:
How mammoths adapted
to cold
95
Exercise
3:
Longevity genes?
96
Further Reading
97
Chapter
5
Cross-Molecular
Searches: BLASTX and TBLASTN
99
5.1
Introduction
99
5.2
Messenger
RNA
Structure
100
5.3
cDNA
101
Synthesis
101
cDNA in databases
102
ESTs
103
Normalized cDNA libraries
104
An
EST
record
106
5.4
BLASTX
107
Reading frames in nucleic acids
107
A simple BLASTX search
108
A more complex BLASTX
109
Using the annotation of sequence
records
115
BLASTX alignments with the reverse
strand
117
5.5
TBLASTN
117
A TBLASTN search
118
Metagenomics and TBLASTN
120
5.6
Summary
122
Exercises
122
Exercise
1 :
Analyzing an unknown
sequence
122
Exercise
2:
Snake venom proteins
123
Exercise
3:
Metagenomics
124
Further Reading
125
Contents
ix
Chapter
6
Advanced Topics
in BLAST
127
6.1
Introduction
127
6.2
Reciprocal BLAST: Confirming
Identities
127
Demonstration of a reciprocal BLASTP
128
6.3
Adjusting BLAST Parameters
131
Gap cost
131
Compositional adjustments
133
6.4
Exon Detection
134
Exon detection with BLASTN
135
Look at the coordinates
138
Exon detection with TBLASTN
138
Orthologous exon searching with
TBLASTN
141
6.5
Repetitive
DNA
144
Simple sequences
145
Satellite
DNA
145
Mini-satellites
145
LINEs and SINEs
145
Tandemly arrayed genes
146
6.6
Interpreting Distant Relationships
147
Name of the protein
147
Percentage identity
148
Alignment length and length similarity
between query and hit
148
E
value
149
Gaps
149
Conserved
amino
acids
150
6.7
Summary
152
Exercises
152
Exercise
1 :
Simple sequences
152
Exercise
2:
Reciprocal BLAST
153
Exercise
3:
Exon identification with
TBLASTN
153
Exercise
4:
Identification of orthologous
exons with TBLASTN
154
Further Readinq
155
Chapter
7
Bioinformatics Tools
for the Laboratory
157
7.1
Introduction
157
7.2
Restriction Mapping and Genetic
Engineering
158
Restriction enzymes
158
Restriction enzyme mapping:
the
polylinker
site
160
NEBcutter
160
Generating reverse strand sequences:
Reverse Complement
162
DNA
translation: the ExPASy
Translate tool
162
Contents
7.3
7.4
7.S
Finding Open Reading Frames
163
The NCBI
ORF
Finder
163
PCR and Primer Design Tools
165
РгітегЗ
166
Primer-BLAST
169
Measuring
DNA
and Protein
Composition
170
DNA
Stats
170
Composition/Molecular Weight
Calculation Form
7.6
7.7
7.8
Asking Very Specific Questions:
The Sequence Retrieval System
(SRS)
DotPlot
DotPlot of alternative transcripts
DotPlots of orthologous genes
Summary
Exercises
Spider silk: a workflow of analysis
Further Reading
Chapter
8
Protein Analysis
8.1
Introduction
8.2
Finding Functional Patterns
A repeating pattern within a zinc finger
8.3
Annotating an Unknown Sequence
A zinc protease pattern
The ADAM_MEPRO profile
8.4
Looking at Three-dimensional
Protein Structures
Jmol: a protein structure viewer
Exploring and understanding a structure
jmol scripting
8.5
ProPhylER
The Interface view
The CrystalPainter view
8.6
The Impact of Sequence on
Structure
8.7
Building Blocks: A Multiple Domain
Protein
8.8
Post-translational Modification
Secretion signals
Prediction of protein glycosylation sites
8.9
Transmembrane
Domain Detection
8.10
Summary
Exercises
Aquaporin-5
Further Reading
Internet resources
171
172
174
175
176
179
179
179
181
183
183
183
184
187
188
188
190
192
193
194
195
196
198
201
204
204
206
208
208
211
211
211
213
214
Chapter
9
Explorations of Short
Nucleotide Sequences
215
9.1
Introduction
215
9.2
Transcription Factor Binding Sites
216
Transfac
216
Identifying other binding sites for the
estrogen receptor
219
Predicting transcription factor
binding sites
220
An experiment with MATCH
221
An experiment with PATCH
224
9.3
Translation Initiation:
The
Kozak
Sequence
226
9.4
Viewing Whole Genes
228
9.5
Exon Splicing
231
Renin: a striking example of a
small exon
234
Another striking splice: human ISG15
ubiquitin-like modifier
235
Alternative splicing
236
Human plectin: alternative splicing at
the 5P end
237
Consensus splice junctions, translated
238
9.6
Polyadenylation Signals
239
9.7
Summary
240
Exercises
242
Inhibitor of Kappa light polypeptide
gene enhancer in B-cells (IKBKAP)
242
Further Reading
243
Chapter
10
MicroRNAs
and Pathway Analysis
10.1
Introduction
miRNA Function
miRNA Nomenclature
10.2
10.3
10.4
10.5
10.6
10.7
10.8
245
245
245
247
miRNA Families and Conservation
247
Structure and Processing of miRNAs
248
miRBase: The Repository for miRNAs
250
Numbers and Locations
251
Linking miRNA Analysis to a
Biochemical Pathway:
Gastric Cancer
251
10.9
KEGG: Biological Networks at
Your Fingertips
253
miRNAs in the cell cycle pathway
255
10.10
TarBase: Experimentally Verified
miRNA Inhibition
256
Verified miRNA-driven translation
repression
256
10.11
TargetScan: miRNA
Target
Site
Prediction
TargetScan predictions for cell cycle
transcripts
10.12
Expanding miRNA Regulation of
the Cell Cycle Using TarBase
and TargetScan
10.13
Making Sense of miRNAs and
Their Many Predicted Targets
10.14
miRNAs Associated With Diseases
10.15
Summary
Exercises
CDF8
Further Reading
Chapter
11
Multiple Sequence
Alignments
11.1
Introduction
11.2
Multiple Sequence Alignments
Through NCBI BLAST
11.3
ClustalW from the ExPASy Website
11.4
ClustalW at the EMBL-EBI Server
MARK1 kinase
MAPK15kinase
DNA
versus protein identities
11.5
Modifying ClustalW Parameters
Gap-opening penalty
The clustering method
11.6
Comparing ClustalW, MUSCLE,
and COBALT
11.7 Isoform
Alignment Problem:
Internal Splicing
11.8
Aligning Paralog Domains
11.9
Manually Editing a Multiple
Sequence Alignment
Jalview
Editing with a word processor
11.10
Summary
Exercises
FOXP2
Further Reading
Contents
xi
12.3
Synteny
303
258
Synteny
of the sex chromosomes
304
12.4
The UCSC Genome Browser
304
260
OPN5: a sample gene to browse
305
Simple view changes in the UCSC
УЛЧ
Genome Browser
308
Configuring the UCSC Genome Browser
window
310
265
Searching genomes and adding tracks
266
through
BLAT
312
267
Viewing the Multiz alignments
314
267
Zooming out: seeing the big picture
316
267
Very large genes: dystrophin and titin
318
269
Gene density
320
Interspecies
comparison of genomes
323
The beta globin locus
324
12.5
Summary
325
271
Exercises
325
Olfactory genes
325
Further Reading
327
271
274
276
Appendix
1
Formatting Your
277
Report
329
280
A1.1 Introduction
329
282
Al
.2
Font Choice and Pasting Issues
329
282
A1.3 Find and Replace
331
282
Changing file format
332
283
Al
.4
Hypertext
333
Creating hypertext
334
286
Selecting a column of text
334
Al
.5
Summary
334
288
292
Appendix
2
Running NCBI BLAST
294
294
in batch Mode
337
296
296
Abbreviations
340
296
Glossary
341
296
297
Web Resources
344
Index
347
Chapter
12
Browsing the Genome
299
12.1
Introduction
299
12.2
Chromosomes
299
Human chromosome statistics
300
Chromosome details and comparisons
302
Written for biology and biochemistry students.
Practical Bioinformatics is designed to be used as
a first text on bioinformatics sequence analysis in
courses that have a practical hands-on element.
The book is focused on the analysis of
DNA, RNA,
and protein sequences, and contains many exercises
to complement the biological examples used to
illustrate concepts. No software installation or
programming skills are required for the exercises,
just a connection to the web.
Online resources for qualified instructors:
•
Artwork
m JPEG
and PowerPoint formats
•
Solutions ro cfuestions
|
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| institution | BVB |
| isbn | 9780815344568 |
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| spelling | Agostino, Michael J. Verfasser aut Practical bioinformatics Michael Agostino New York [u.a.] Garland Science 2013 XI, 367 S., [6] Bl. Ill., graph. Darst. txt rdacontent n rdamedia nc rdacarrier Bioinformatik (DE-588)4611085-9 gnd rswk-swf (DE-588)4123623-3 Lehrbuch gnd-content Bioinformatik (DE-588)4611085-9 s b DE-604 Digitalisierung UB Regensburg application/pdf http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=025304766&sequence=000003&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA Inhaltsverzeichnis Digitalisierung UB Regensburg application/pdf http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=025304766&sequence=000004&line_number=0002&func_code=DB_RECORDS&service_type=MEDIA Klappentext |
| spellingShingle | Agostino, Michael J. Practical bioinformatics Bioinformatik (DE-588)4611085-9 gnd |
| subject_GND | (DE-588)4611085-9 (DE-588)4123623-3 |
| title | Practical bioinformatics |
| title_auth | Practical bioinformatics |
| title_exact_search | Practical bioinformatics |
| title_full | Practical bioinformatics Michael Agostino |
| title_fullStr | Practical bioinformatics Michael Agostino |
| title_full_unstemmed | Practical bioinformatics Michael Agostino |
| title_short | Practical bioinformatics |
| title_sort | practical bioinformatics |
| topic | Bioinformatik (DE-588)4611085-9 gnd |
| topic_facet | Bioinformatik Lehrbuch |
| url | http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=025304766&sequence=000003&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=025304766&sequence=000004&line_number=0002&func_code=DB_RECORDS&service_type=MEDIA |
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