Muutke küpsiste eelistusi

Practical Bioinformatics [Pehme köide]

(Merrimack College, USA and Pfizer Inc., USA)
  • Formaat: Paperback / softback, 392 pages, kõrgus x laius: 276x219 mm, kaal: 1080 g, 20 Line drawings, black and white; 10 Halftones, color; 296 Illustrations, black and white
  • Ilmumisaeg: 26-Sep-2012
  • Kirjastus: CRC Press Inc
  • ISBN-10: 0815344562
  • ISBN-13: 9780815344568
Teised raamatud teemal:
  • Formaat: Paperback / softback, 392 pages, kõrgus x laius: 276x219 mm, kaal: 1080 g, 20 Line drawings, black and white; 10 Halftones, color; 296 Illustrations, black and white
  • Ilmumisaeg: 26-Sep-2012
  • Kirjastus: CRC Press Inc
  • ISBN-10: 0815344562
  • ISBN-13: 9780815344568
Teised raamatud teemal:
Practical Bioinformatics is specifically designed for biology majors, with a heavy emphasis on the steps required to perform bioinformatics analysis to answer biological questions. It is written for courses that have a practical, hands-on element and contains many exercises (for example, database searches, protein analysis, data interpretation) to complement the straightforward and practical topics. The chapters are focused on DNA, RNA, and protein sequence analysisfrequently performed subsets of the field of bioinformaticstaking the reader through the commonly asked question what can I learn about this sequence?

A special note to established scientists: new genomic sequences are being published at an accelerating pace. Although new technology has led to unprecedented accuracy of the sequence, incomplete and challenging assemblies along with imperfect predictive methods are still generating gene models that require verification. With the sequence analysis skills learned from this book, features such as missing exons and incorrect termini can be easily recognized and more accurate gene models can be constructed.

Arvustused

This is one of the most well written and well organized books on bioinformatics that I have come across. The chapters and concepts are arranged in order of complexity and the writing is easy to understand. This is an excellent introductory book for bioinformatics, yet it contains enough detail to help both a serious researcher as well as a beginner in the field. Science Books & Film

"This textbook would be useful to any biologist, as its chapters span RNA sequencing to protein analysis to miRNA target prediction. It is hard to think of a database currently available online on which this text does not include a detailed tutorial....it made bioinformatics appealing to learn about, as some pages contained highlighted boxes of interesting facts about the history of sequencing, biology, or various discoveries....Practical Bioinformatics will be invaluable to the general researcher or student..." -Yale Journal of Biology and Medicine

"The book is well laid out, focusing initially on finding and manipulating single DNA or protein sequences from a number of different databases....Anyone who deals with biochemical data would find this work of great value. Even an absolute novice to bioinformatics would, with a little practice, be able to retrieve and manage data." -The Biologist

"This is exactly the kind of text that I have been looking for to support my bioinformatics teaching To minimise the entry barrier for using bioinformatics, the author uses only free Web-based toolsThere is really good coverage of the many flavours of BLAST, multiple sequence alignments and common tools for DNA and protein sequence analysis, with clear and interesting worked examples and critical analysis of outputs." - Microbiology Today

"This well-written book, replete with helpful illustrations, provides a valuable introduction to the field of bioinformatics....It also will be extremely useful for scientists whose biological training predated the Internet or for scientists in related disciplines who develop an interest in bioinformatics....This book is truly practical in that one can read it independently, performing the exercises on ones own computerWell written and easy to follow, this book provides an excellent foundation for anyone interested in the analysis of nucleotide or amino acid sequences. It is well suited for the undergraduate classroom, as well as for those scientists new to the field of bioinformatics." - Doody

Chapter 1 Introduction to Bioinformatics and Sequence Analysis
1(22)
1.1 Introduction
1(1)
1.2 The Growth of GenBank
2(1)
1.3 Data, Data, Everywhere
2(3)
Further examples of human genome sequencing
4(1)
Personal genome sequencing
4(1)
Paleogenetics
4(1)
Focused medical genomic studies
5(1)
1.4 The Size of a Genome
5(1)
1.5 Annotation
6(1)
1.6 Witnessing Evolution Through Bioinformatics
7(1)
Recent evolutionary changes to plants and animals
7(1)
1.7 Large Sources of Human Sequence Variation
7(1)
1.8 Recent Evolutionary Changes to Human Populations
8(1)
1.9 DNA Sequence in Databases
9(5)
Genomic DNA assembly
10(2)
cDNA in databases---where does it come from?
12(2)
1.10 Sequence Analysis and Data Display
14(6)
1.11 Summary
20(3)
Further Reading
20(1)
Internet resources
21(2)
Chapter 2 Introduction to Internet Resources
23(24)
2.1 Introduction
23(1)
2.2 The NCBI Website and ENTREZ
23(2)
2.3 PubMed
25(2)
2.4 Gene Name Evolution
27(2)
2.5 OMIM
29(1)
2.6 Retrieving Nucleotide Sequences
30(1)
2.7 Searching Patents
31(2)
2.8 Public Grants Database: NIH RePORTER
33(1)
2.9 Gene Ontology
34(2)
2.10 The Gene Database
36(2)
2.11 UniGene
38(5)
2.12 The UniGene Library Browser
43(1)
2.13 Summary
44(3)
Exercises
44(1)
Williams syndrome and oxytocin: research with Internet tools
44(1)
Further Reading
45(2)
Chapter 3 Introduction to the BLAST Suite and BLASTN
47(26)
3.1 Introduction
47(1)
Why search a database?
47(1)
3.2 What is BLAST?
48(1)
How does BLAST work?
48(1)
3.3 Your First BLAST Search
49(5)
Find the query sequence in GenBank
49(2)
Convert the file to another format
51(1)
Performing BLASTN searches
52(2)
3.4 BLAST Results
54(10)
Graphic
54(1)
Interpretation of the graphic
55(1)
Results table
55(2)
Interpretation of the table
57(1)
The alignments
57(3)
Other BLASTN hits from this query
60(3)
Simultaneous review of the graphic, table, and alignments
63(1)
3.5 BLASTN Across Species
64(4)
Blastn of the reference sequence for human beta hemoglobin against nonhuman transcripts
64(2)
Paralogs, orthologs, and homologs
66(2)
3.6 BLAST Output Format
68(1)
3.7 Summary
68(5)
Exercises
68(1)
Exercise 1 Biofilm analysis
68(2)
Exercise 2 RuBisCO
70(1)
Further Reading
71(1)
Internet resources
71(2)
Chapter 4 Protein BLAST: BLASTP
73(26)
4.1 Introduction
73(1)
4.2 Codons and the Genetic Code
73(3)
Memorizing the genetic code
76(1)
4.3 Amino Acids
76(2)
Amino acid properties
77(1)
4.4 BLASTP and the Scoring Matrix
78(2)
Building a matrix
78(2)
4.5 An Example BLASTP Search
80(5)
Retrieving protein records
81(1)
Running BLASTP
81(1)
The results
82(2)
The alignments
84(1)
Distant homologies
84(1)
4.6 Pairwise BLAST
85(1)
4.7 Running BLASTP at the ExPASy Website
86(8)
Searching for pro-opiomelanocortin using a protein sequence fragment
87(4)
Searching for repeated domains in alpha-1 collagen
91(3)
4.8 Summary
94(5)
Exercises
94(1)
Exercise 1 Typing contest
94(1)
Exercise 2 How mammoths adapted to cold
95(1)
Exercise 3 Longevity genes?
96(1)
Further Reading
97(2)
Chapter 5 Cross-Molecular Searches: BLASTX and TBLASTN
99(28)
5.1 Introduction
99(1)
5.2 Messenger RNA Structure
100(1)
5.3 cDNA
101(6)
Synthesis
101(1)
cDNA in databases
102(1)
ESTs
103(1)
Normalized cDNA libraries
104(2)
An EST record
106(1)
5.4 BLASTX
107(10)
Reading frames in nucleic acids
107(1)
A simple BLASTX search
108(1)
A more complex BLASTX
109(6)
Using the annotation of sequence records
115(2)
BLASTX alignments with the reverse strand
117(1)
5.5 TBLASTN
117(5)
A TBLASTN search
118(2)
Metagenomics and TBLASTN
120(2)
5.6 Summary
122(5)
Exercises
122(1)
Exercise 1 Analyzing an unknown sequence
122(1)
Exercise 2 Snake venom proteins
123(1)
Exercise 3 Metagenomics
124(1)
Further Reading
125(2)
Chapter 6 Advanced Topics in BLAST
127(30)
6.1 Introduction
127(1)
6.2 Reciprocal BLAST: Confirming Identities
127(4)
Demonstration of a reciprocal BLASTP
128(3)
6.3 Adjusting BLAST Parameters
131(3)
Gap cost
131(2)
Compositional adjustments
133(1)
6.4 Exon Detection
134(10)
Exon detection with BLASTN
135(3)
Look at the coordinates
138(1)
Exon detection with TBLASTN
138(3)
Orthologous exon searching with TBLASTN
141(3)
6.5 Repetitive DNA
144(3)
Simple sequences
145(1)
Satellite DNA
145(1)
Mini-satellites
145(1)
LINEs and SINEs
145(1)
Tandemly arrayed genes
146(1)
6.6 Interpreting Distant Relationships
147(5)
Name of the protein
147(1)
Percentage identity
148(1)
Alignment length and length similarity between query and hit
148(1)
E value
149(1)
Gaps
149(1)
Conserved amino acids
150(2)
6.7 Summary
152(5)
Exercises
152(1)
Exercise 1 Simple sequences
152(1)
Exercise 2 Reciprocal BLAST
153(1)
Exercise 3 Exon identification with TBLASTN
153(1)
Exercise 4 Identification of orthologous exons with TBLASTN
154(1)
Further Reading
155(2)
Chapter 7 Bioinformatics Tools for the Laboratory
157(26)
7.1 Introduction
157(1)
7.2 Restriction Mapping and Genetic Engineering
158(5)
Restriction enzymes
158(2)
Restriction enzyme mapping: the polylinker site
160(1)
NEBcutter
160(2)
Generating reverse strand sequences: Reverse Complement
162(1)
DNA translation: the ExPASy Translate tool
162(1)
7.3 Finding Open Reading Frames
163(2)
The NCBI ORF Finder
163(2)
7.4 PCR and Primer Design Tools
165(5)
Primer3
166(3)
Primer-BLAST
169(1)
7.5 Measuring DNA and Protein Composition
170(2)
DNA Stats
170(1)
Composition/Molecular Weight Calculation Form
171(1)
7.6 Asking Very Specific Questions: The Sequence Retrieval System (SRS)
172(2)
7.7 DotPlot
174(5)
DotPlot of alternative transcripts
175(1)
DotPlots of orthologous genes
176(3)
7.8 Summary
179(4)
Exercises
179(1)
Spider silk: a workflow of analysis
179(2)
Further Reading
181(2)
Chapter 8 Protein Analysis
183(32)
8.1 Introduction
183(1)
8.2 Finding Functional Patterns
183(4)
A repeating pattern within a zinc finger
184(3)
8.3 Annotating an Unknown Sequence
187(3)
A zinc protease pattern
188(1)
The ADAM_MEPRO profile
188(2)
8.4 Looking at Three-dimensional Protein Structures
190(5)
Jmol: a protein structure viewer
192(1)
Exploring and understanding a structure
193(1)
Jmol scripting
194(1)
8.5 ProPhyIER
195(6)
The Interface view
196(2)
The CrystalPainter view
198(3)
8.6 The Impact of Sequence on Structure
201(3)
8.7 Building Blocks: A Multiple Domain Protein
204(1)
8.8 Post-translational Modification
204(4)
Secretion signals
206(2)
Prediction of protein glycosylation sites
208(1)
8.9 Transmembrane Domain Detection
208(3)
8.10 Summary
211(4)
Exercises
211(1)
Aquaporin-5
211(2)
Further Reading
213(1)
Internet resources
214(1)
Chapter 9 Explorations of Short Nucleotide Sequences
215(30)
9.1 Introduction
215(1)
9.2 Transcription Factor Binding Sites
216(10)
Transfac
216(3)
Identifying other binding sites for the estrogen receptor
219(1)
Predicting transcription factor binding sites
220(1)
An experiment with MATCH
221(3)
An experiment with PATCH
224(2)
9.3 Translation Initiation: The Kozak Sequence
226(2)
9.4 Viewing Whole Genes
228(3)
9.5 Exon Splicing
231(8)
Renin: a striking example of a small exon
234(1)
Another striking splice: human ISG15 ubiquitin-like modifier
235(1)
Alternative splicing
236(1)
Human plectin: alternative splicing at the 5P end
237(1)
Consensus splice junctions, translated
238(1)
9.6 Polyadenylation Signals
239(1)
9.7 Summary
240(5)
Exercises
242(1)
Inhibitor of Kappa light polypeptide gene enhancer in B-cells (IKBKAP)
242(1)
Further Reading
243(2)
Chapter 10 MicroRNAs and Pathway Analysis
245(26)
10.1 Introduction
245(1)
10.2 miRNA Function
245(2)
10.3 miRNA Nomenclature
247(1)
10.4 miRNA Families and Conservation
247(1)
10.5 Structure and Processing of miRNAs
248(2)
10.6 miRBase: The Repository for miRNAs
250(1)
10.7 Numbers and Locations
251(1)
10.8 Linking miRNA Analysis to a Biochemical Pathway: Gastric Cancer
251(2)
10.9 KEGG: Biological Networks at Your Fingertips
253(3)
miRNAs in the cell cycle pathway
255(1)
10.10 TarBase: Experimentally Verified miRNA Inhibition
256(2)
Verified miRNA-driven translation repression
256(2)
10.11 TargetScan: miRNA Target Site Prediction
258(5)
TargetScan predictions for cell cycle transcripts
260(3)
10.12 Expanding miRNA Regulation of the Cell Cycle Using TarBase and TargetScan
263(2)
10.13 Making Sense of miRNAs and Their Many Predicted Targets
265(1)
10.14 miRNAs Associated With Diseases
266(1)
10.15 Summary
267(4)
Exercises
267(1)
GDF8
267(2)
Further Reading
269(2)
Chapter 11 Multiple Sequence Alignments
271(28)
11.1 Introduction
271(1)
11.2 Multiple Sequence Alignments Through NCBI BLAST
271(3)
11.3 ClustalW from the ExPASy Website
274(2)
11.4 ClustalW at the EMBL-EBI Server
276(6)
MARK1 kinase
277(3)
MAPK15 kinase
280(2)
DNA versus protein identities
282(1)
11.5 Modifying ClustalW Parameters
282(4)
Gap-opening penalty
282(1)
The clustering method
283(3)
11.6 Comparing ClustalW, MUSCLE, and COBALT
286(2)
11.7 Isoform Alignment Problem: Internal Splicing
288(4)
11.8 Aligning Paralog Domains
292(2)
11.9 Manually Editing a Multiple Sequence Alignment
294(2)
Jalview
294(2)
Editing with a word processor
296(1)
11.10 Summary
296(3)
Exercises
296(1)
FOXP2
296(1)
Further Reading
297(2)
Chapter 12 Browsing the Genome
299(30)
12.1 Introduction
299(1)
12.2 Chromosomes
299(4)
Human chromosome statistics
300(2)
Chromosome details and comparisons
302(1)
12.3 Synteny
303(1)
Synteny of the sex chromosomes
304(1)
12.4 The UCSC Genome Browser
304(21)
OPN5: a sample gene to browse
305(3)
Simple view changes in the UCSC Genome Browser
308(2)
Configuring the UCSC Genome Browser window
310(2)
Searching genomes and adding tracks through BLAT
312(2)
Viewing the Multiz alignments
314(2)
Zooming out: seeing the big picture
316(4)
Very large genes: dystrophin and titin Gene density
320(3)
Interspecies comparison of genomes
323(1)
The beta globin locus
324(1)
12.5 Summary
325(4)
Exercises
325(1)
Olfactory genes
325(2)
Further Reading
327(2)
Appendix 1 Formatting Your Report
329(8)
A1.1 Introduction
329(1)
A1.2 Font Choice and Pasting Issues
329(2)
A1.3 Find and Replace
331(2)
Changing file format
332(1)
A1.4 Hypertext
333(1)
Creating hypertext
334(1)
Selecting a column of text
334(1)
A1.5 Summary
334(3)
Appendix 2 Running NCBI BLAST in "batch" Mode
337(3)
Abbreviations 340(1)
Glossary 341(3)
Web Resources 344(3)
Index 347
Michael Agostino