Practical Bioinformatics

Untitled
Preface
Acknowledgments
Contents
CHAPTER 1: Introduction to Bioinformatics and Sequence Analysis
1.1 INTRODUCTION
1.2 THE GROWTH OF GenBank
1.3 DATA, DATA, EVERYWHERE
Further examples of human genome sequencing
1.4 THE SIZE OF A GENOME
1.5 ANNOTATION
1.6 WITNESSING EVOLUTION THROUGH BIOINFORMATICS
Recent evolutionary changes to plants and animals
1.7 LARGE SOURCES OF HUMAN SEQUENCE VARIATION
1.8 RECENT EVOLUTIONARY CHANGES TO HUMAN POPULATIONS
1.9 DNA SEQUENCE IN DATABASES
Genomic DNA assembly
cDNA in databases—where does it come from?
1.10 SEQUENCE ANALYSIS AND DATA DISPLAY
1.11 SUMMARY
FURTHER READING
Internet resources
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
EXERCISES
Williams syndrome and oxytocin: research with Internet tools
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
Results 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
4.4 BLASTP AND THE SCORING MATRIX
Building a matrix
4.5 AN EXAMPLE BLASTP SEARCH
Retrieving protein records
Running BLASTP
The results
The alignments
Distant homologies
4.6 PAIRWISE BLAST
4.7 RUNNING BLASTP AT THE ExPASy WEBSITE
Searching for pro-opiomelanocortin using a protein sequence fragment
Searching for repeated domains in alpha-1 collagen
4.8 SUMMARY
EXERCISES
Exercise 1: Typing contest
Exercise 2: How mammoths adapted to cold
Exercise 3: Longevity genes?
FURTHER READING
CHAPTER 5: Cross-Molecular Searches: BLASTX and TBLASTN
5.1 INTRODUCTION
5.2 MESSENGER RNA STRUCTURE
5.3 cDNA
Synthesis
cDNA in databases
ESTs
Normalized cDNA libraries
An EST record
5.4 BLASTX
Reading frames in nucleic acids
A simple BLASTX search
A more complex BLASTX
Using the annotation of sequence records
BLASTX alignments with the reverse strand
5.5 TBLASTN
A TBLASTN search
Metagenomics and TBLASTN
5.6 SUMMARY
EXERCISES
Exercise 1: Analyzing an unknown sequence
Exercise 2: Snake venom proteins
Exercise 3: Metagenomics
FURTHER READING
CHAPTER 6: Advanced Topics in BLAST
6.1 INTRODUCTION
6.2 RECIPROCAL BLAST: CONFIRMING IDENTITIES
Demonstration of a reciprocal BLASTP
6.3 ADJUSTING BLAST PARAMETERS
Gap cost
Compositional adjustments
6.4 EXON DETECTION
Exon detection with BLASTN
Look at the coordinates
Exon detection with TBLASTN
Orthologous exon searching with TBLASTN
6.5 REPETITIVE DNA
Simple sequences
Satellite DNA
Mini-satellites
LINEs and SINEs
Tandemly arrayed genes
6.6 INTERPRETING DISTANT RELATIONSHIPS
Name of the protein
Percentage identity
Alignment length and length similarity between query and hit
E value
Gaps
Conserved amino acids
6.7 SUMMARY
EXERCISES
Exercise 1: Simple sequences
Exercise 2: Reciprocal BLAST
Exercise 3: Exon identifi cation with TBLASTN
Exercise 4: Identification of orthologous exons with TBLASTN
FURTHER READING
CHAPTER 7: Bioinformatics Tools for the Laboratory
7.1 INTRODUCTION
7.2 RESTRICTION MAPPING AND GENETICENGINEERING
Restriction enzymes
Restriction enzyme mapping: the polylinker site
NEBcutter
Generating reverse strand sequences: ReverseComplement
DNA translation: the ExPASy Translate tool
7.3 FINDING OPEN READING FRAMES
The NCBI ORF Finder
7.4 PCR AND PRIMER DESIGN TOOLS
Primer3
Primer-BLAST
7.5 MEASURING DNA AND PROTEINCOMPOSITION
DNA Stats
Composition/Molecular Weight Calculation Form
7.6 ASKING VERY SPECIFIC QUESTIONS:THE SEQUENCE RETRIEVAL SYSTEM (SRS)
7.7 DotPlot
DotPlot of alternative transcripts
DotPlots of orthologous genes
7.8 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 fi nger
8.3 ANNOTATING AN UNKNOWN SEQUENCE
A zinc protease pattern
The ADAM_MEPRO profi le
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 DOMAINPROTEIN
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
CHAPTER 9: Explorations of Short Nucleotide Sequences
9.1 INTRODUCTION
9.2 TRANSCRIPTION FACTOR BINDING SITES
Transfac
Identifying other binding sites for the estrogen receptor
Predicting transcription factor binding sites
An experiment with MATCH
An experiment with PATCH
9.3 TRANSLATION INITIATION:THE KOZAK SEQUENCE
9.4 VIEWING WHOLE GENES
9.5 EXON SPLICING
Renin: a striking example of a small exon
Another striking splice: human ISG15 ubiquitin-like modifier
Alternative splicing
Human plectin: alternative splicing at the 5P end
Consensus splice junctions, translated
9.6 POLYADENYLATION SIGNALS
9.7 SUMMARY
EXERCISES
Inhibitor of Kappa light polypeptide gene enhancer in B-cells (IKBKAP)
FURTHER READING
CHAPTER 10: MicroRNAs and Pathway Analysis
10.1 INTRODUCTION
10.2 miRNA FUNCTION
10.3 miRNA NOMENCLATURE
10.4 miRNA FAMILIES AND CONSERVATION
10.5 STRUCTURE AND PROCESSING OF miRNAs
10.6 miRBase: THE REPOSITORY FOR miRNAs
10.7 NUMBERS AND LOCATIONS
10.8 LINKING miRNA ANALYSIS TO ABIOCHEMICAL PATHWAY: GASTRIC CANCER
10.9 KEGG: BIOLOGICAL NETWORKS ATYOUR FINGERTIPS
miRNAs in the cell cycle pathway
10.10 TarBase: EXPERIMENTALLY VERIFIED miRNA INHIBITION
Verified miRNA-driven translation repression
10.11 TargetScan: miRNA TARGET SITEPREDICTION
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
GDF8
FURTHER READING
CHAPTER 11: Multiple Sequence Alignments
11.1 INTRODUCTION
11.2 MULTIPLE SEQUENCE ALIGNMENTSTHROUGH NCBI BLAST
11.3 ClustalW FROM THE ExPASy WEBSITE
11.4 ClustalW AT THE EMBL-EBI SERVER
MARK1 kinase
MAPK15 kinase
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
CHAPTER 12: Browsing the Genome
12.1 INTRODUCTION
12.2 CHROMOSOMES
Human chromosome statistics
Chromosome details and comparisons
12.3 SYNTENY
Synteny of the sex chromosomes
12.4 THE UCSC GENOME BROWSER
OPN5: a sample gene to browse
Simple view changes in the UCSC Genome Browser
Confi guring the UCSC Genome Browser window
Searching genomes and adding tracks through BLAT
Viewing the Multiz alignments
Zooming out: seeing the big picture
Very large genes: dystrophin and titin
Gene density
Interspecies comparison of genomes
The beta globin locus
12.5 SUMMARY
EXERCISES
Olfactory genes
FURTHER READING
APPENDIX 1: Formatting Your Report
A1.1 INTRODUCTION
A1.2 FONT CHOICE AND PASTING ISSUES
A1.3 FIND AND REPLACE
Changing file format
A1.4 HYPERTEXT
Creating hypertext
Selecting a column of text
A1.5 SUMMARY
APPENDIX 2: Running NCBI BLAST in “batch” Mode
ABBREVIATIONS
GLOSSARY
WEB RESOURCES
INDEX
Color Versions of Selected Figures