|
Chapter 1 Introduction to Bioinformatics and Sequence Analysis |
|
|
1 | (22) |
|
|
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) |
|
|
4 | (1) |
|
Focused medical genomic studies |
|
|
5 | (1) |
|
|
5 | (1) |
|
|
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) |
|
|
10 | (2) |
|
cDNA in databases---where does it come from? |
|
|
12 | (2) |
|
1.10 Sequence Analysis and Data Display |
|
|
14 | (6) |
|
|
20 | (3) |
|
|
20 | (1) |
|
|
21 | (2) |
|
Chapter 2 Introduction to Internet Resources |
|
|
23 | (24) |
|
|
23 | (1) |
|
2.2 The NCBI Website and ENTREZ |
|
|
23 | (2) |
|
|
25 | (2) |
|
|
27 | (2) |
|
|
29 | (1) |
|
2.6 Retrieving Nucleotide Sequences |
|
|
30 | (1) |
|
|
31 | (2) |
|
2.8 Public Grants Database: NIH RePORTER |
|
|
33 | (1) |
|
|
34 | (2) |
|
|
36 | (2) |
|
|
38 | (5) |
|
2.12 The UniGene Library Browser |
|
|
43 | (1) |
|
|
44 | (3) |
|
|
44 | (1) |
|
Williams syndrome and oxytocin: research with Internet tools |
|
|
44 | (1) |
|
|
45 | (2) |
|
Chapter 3 Introduction to the BLAST Suite and BLASTN |
|
|
47 | (26) |
|
|
47 | (1) |
|
|
47 | (1) |
|
|
48 | (1) |
|
|
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) |
|
|
54 | (10) |
|
|
54 | (1) |
|
Interpretation of the graphic |
|
|
55 | (1) |
|
|
55 | (2) |
|
Interpretation of the table |
|
|
57 | (1) |
|
|
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) |
|
|
68 | (1) |
|
|
68 | (5) |
|
|
68 | (1) |
|
Exercise 1 Biofilm analysis |
|
|
68 | (2) |
|
|
70 | (1) |
|
|
71 | (1) |
|
|
71 | (2) |
|
Chapter 4 Protein BLAST: BLASTP |
|
|
73 | (26) |
|
|
73 | (1) |
|
4.2 Codons and the Genetic Code |
|
|
73 | (3) |
|
Memorizing the genetic code |
|
|
76 | (1) |
|
|
76 | (2) |
|
|
77 | (1) |
|
4.4 BLASTP and the Scoring Matrix |
|
|
78 | (2) |
|
|
78 | (2) |
|
4.5 An Example BLASTP Search |
|
|
80 | (5) |
|
Retrieving protein records |
|
|
81 | (1) |
|
|
81 | (1) |
|
|
82 | (2) |
|
|
84 | (1) |
|
|
84 | (1) |
|
|
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) |
|
|
94 | (5) |
|
|
94 | (1) |
|
Exercise 1 Typing contest |
|
|
94 | (1) |
|
Exercise 2 How mammoths adapted to cold |
|
|
95 | (1) |
|
Exercise 3 Longevity genes? |
|
|
96 | (1) |
|
|
97 | (2) |
|
Chapter 5 Cross-Molecular Searches: BLASTX and TBLASTN |
|
|
99 | (28) |
|
|
99 | (1) |
|
5.2 Messenger RNA Structure |
|
|
100 | (1) |
|
|
101 | (6) |
|
|
101 | (1) |
|
|
102 | (1) |
|
|
103 | (1) |
|
Normalized cDNA libraries |
|
|
104 | (2) |
|
|
106 | (1) |
|
|
107 | (10) |
|
Reading frames in nucleic acids |
|
|
107 | (1) |
|
|
108 | (1) |
|
|
109 | (6) |
|
Using the annotation of sequence records |
|
|
115 | (2) |
|
BLASTX alignments with the reverse strand |
|
|
117 | (1) |
|
|
117 | (5) |
|
|
118 | (2) |
|
|
120 | (2) |
|
|
122 | (5) |
|
|
122 | (1) |
|
Exercise 1 Analyzing an unknown sequence |
|
|
122 | (1) |
|
Exercise 2 Snake venom proteins |
|
|
123 | (1) |
|
|
124 | (1) |
|
|
125 | (2) |
|
Chapter 6 Advanced Topics in BLAST |
|
|
127 | (30) |
|
|
127 | (1) |
|
6.2 Reciprocal BLAST: Confirming Identities |
|
|
127 | (4) |
|
Demonstration of a reciprocal BLASTP |
|
|
128 | (3) |
|
6.3 Adjusting BLAST Parameters |
|
|
131 | (3) |
|
|
131 | (2) |
|
Compositional adjustments |
|
|
133 | (1) |
|
|
134 | (10) |
|
Exon detection with BLASTN |
|
|
135 | (3) |
|
|
138 | (1) |
|
Exon detection with TBLASTN |
|
|
138 | (3) |
|
Orthologous exon searching with TBLASTN |
|
|
141 | (3) |
|
|
144 | (3) |
|
|
145 | (1) |
|
|
145 | (1) |
|
|
145 | (1) |
|
|
145 | (1) |
|
|
146 | (1) |
|
6.6 Interpreting Distant Relationships |
|
|
147 | (5) |
|
|
147 | (1) |
|
|
148 | (1) |
|
Alignment length and length similarity between query and hit |
|
|
148 | (1) |
|
|
149 | (1) |
|
|
149 | (1) |
|
|
150 | (2) |
|
|
152 | (5) |
|
|
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) |
|
|
155 | (2) |
|
Chapter 7 Bioinformatics Tools for the Laboratory |
|
|
157 | (26) |
|
|
157 | (1) |
|
7.2 Restriction Mapping and Genetic Engineering |
|
|
158 | (5) |
|
|
158 | (2) |
|
Restriction enzyme mapping: the polylinker site |
|
|
160 | (1) |
|
|
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) |
|
|
163 | (2) |
|
7.4 PCR and Primer Design Tools |
|
|
165 | (5) |
|
|
166 | (3) |
|
|
169 | (1) |
|
7.5 Measuring DNA and Protein Composition |
|
|
170 | (2) |
|
|
170 | (1) |
|
Composition/Molecular Weight Calculation Form |
|
|
171 | (1) |
|
7.6 Asking Very Specific Questions: The Sequence Retrieval System (SRS) |
|
|
172 | (2) |
|
|
174 | (5) |
|
DotPlot of alternative transcripts |
|
|
175 | (1) |
|
DotPlots of orthologous genes |
|
|
176 | (3) |
|
|
179 | (4) |
|
|
179 | (1) |
|
Spider silk: a workflow of analysis |
|
|
179 | (2) |
|
|
181 | (2) |
|
Chapter 8 Protein Analysis |
|
|
183 | (32) |
|
|
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) |
|
|
188 | (1) |
|
|
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) |
|
|
194 | (1) |
|
|
195 | (6) |
|
|
196 | (2) |
|
|
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) |
|
|
206 | (2) |
|
Prediction of protein glycosylation sites |
|
|
208 | (1) |
|
8.9 Transmembrane Domain Detection |
|
|
208 | (3) |
|
|
211 | (4) |
|
|
211 | (1) |
|
|
211 | (2) |
|
|
213 | (1) |
|
|
214 | (1) |
|
Chapter 9 Explorations of Short Nucleotide Sequences |
|
|
215 | (30) |
|
|
215 | (1) |
|
9.2 Transcription Factor Binding Sites |
|
|
216 | (10) |
|
|
216 | (3) |
|
Identifying other binding sites for the estrogen receptor |
|
|
219 | (1) |
|
Predicting transcription factor binding sites |
|
|
220 | (1) |
|
|
221 | (3) |
|
|
224 | (2) |
|
9.3 Translation Initiation: The Kozak Sequence |
|
|
226 | (2) |
|
|
228 | (3) |
|
|
231 | (8) |
|
Renin: a striking example of a small exon |
|
|
234 | (1) |
|
Another striking splice: human ISG15 ubiquitin-like modifier |
|
|
235 | (1) |
|
|
236 | (1) |
|
Human plectin: alternative splicing at the 5P end |
|
|
237 | (1) |
|
Consensus splice junctions, translated |
|
|
238 | (1) |
|
9.6 Polyadenylation Signals |
|
|
239 | (1) |
|
|
240 | (5) |
|
|
242 | (1) |
|
Inhibitor of Kappa light polypeptide gene enhancer in B-cells (IKBKAP) |
|
|
242 | (1) |
|
|
243 | (2) |
|
Chapter 10 MicroRNAs and Pathway Analysis |
|
|
245 | (26) |
|
|
245 | (1) |
|
|
245 | (2) |
|
|
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) |
|
|
267 | (4) |
|
|
267 | (1) |
|
|
267 | (2) |
|
|
269 | (2) |
|
Chapter 11 Multiple Sequence Alignments |
|
|
271 | (28) |
|
|
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) |
|
|
277 | (3) |
|
|
280 | (2) |
|
DNA versus protein identities |
|
|
282 | (1) |
|
11.5 Modifying ClustalW Parameters |
|
|
282 | (4) |
|
|
282 | (1) |
|
|
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) |
|
|
294 | (2) |
|
Editing with a word processor |
|
|
296 | (1) |
|
|
296 | (3) |
|
|
296 | (1) |
|
|
296 | (1) |
|
|
297 | (2) |
|
Chapter 12 Browsing the Genome |
|
|
299 | (30) |
|
|
299 | (1) |
|
|
299 | (4) |
|
Human chromosome statistics |
|
|
300 | (2) |
|
Chromosome details and comparisons |
|
|
302 | (1) |
|
|
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) |
|
|
324 | (1) |
|
|
325 | (4) |
|
|
325 | (1) |
|
|
325 | (2) |
|
|
327 | (2) |
|
Appendix 1 Formatting Your Report |
|
|
329 | (8) |
|
|
329 | (1) |
|
A1.2 Font Choice and Pasting Issues |
|
|
329 | (2) |
|
|
331 | (2) |
|
|
332 | (1) |
|
|
333 | (1) |
|
|
334 | (1) |
|
Selecting a column of text |
|
|
334 | (1) |
|
|
334 | (3) |
|
Appendix 2 Running NCBI BLAST in "batch" Mode |
|
|
337 | (3) |
Abbreviations |
|
340 | (1) |
Glossary |
|
341 | (3) |
Web Resources |
|
344 | (3) |
Index |
|
347 | |