| Preface |
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xi | |
| Acknowledgements |
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xiv | |
| Design and conventions of this book |
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xvi | |
| 1 Introduction: working with the molecules of life in the computer |
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1 | (18) |
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Life on Earth and evolution |
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2 | (2) |
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The machinery of genetic information: more about DNA |
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4 | (3) |
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7 | (1) |
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Genes at work: transcription and translation |
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8 | (3) |
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Organization of the human genome |
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11 | (1) |
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Inferring products of DNA replication |
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12 | (2) |
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Inferring RNA products of transcription |
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14 | (1) |
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Inferring protein products of translation |
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14 | (3) |
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17 | (2) |
| 2 Gene technology: cutting DNA |
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19 | (12) |
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Early days of restriction enzymes |
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20 | (1) |
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Properties of restriction enzymes |
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21 | (2) |
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23 | (1) |
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Identifying restriction enzyme sites with Perl |
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24 | (5) |
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29 | (2) |
| 3 Gene technology: knocking genes down |
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31 | (13) |
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Interfering with gene expression |
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31 | (1) |
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32 | (2) |
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RNAi: functions and applications |
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34 | (1) |
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Silencing RNAs and design principles |
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35 | (2) |
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Identifying siRNA candidates |
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37 | (5) |
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42 | (2) |
| 4 Gene technology: amplifying DNA |
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44 | (11) |
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44 | (2) |
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46 | (1) |
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46 | (2) |
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48 | (3) |
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Good manners during Perl programming |
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51 | (3) |
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54 | (1) |
| 5 Human disease: when DNA sequences are toxic |
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55 | (11) |
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Inherited disease and changes in DNA |
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55 | (2) |
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Huntington's disease and CAG repeat expansion |
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57 | (2) |
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Identifying mRNAs with CAG repeats |
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59 | (6) |
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65 | (1) |
| 6 Human disease: iron imbalance and the iron responsive element |
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66 | (8) |
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An inherited disease affecting the iron-binding protein ferritin |
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66 | (1) |
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Many proteins of iron metabolism are regulated at the level of translation |
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66 | (2) |
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Structure of the iron responsive element |
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68 | (1) |
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Identifying the iron responsive element |
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69 | (3) |
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72 | (2) |
| 7 Human disease: cancer as a result of aberrant proteins |
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74 | (18) |
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Cancer as a genetic disease |
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74 | (1) |
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75 | (1) |
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Chromosome rearrangements and the Philadelphia chromosome |
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76 | (1) |
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77 | (4) |
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81 | (2) |
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Using BLAST to examine the BCR-ABL fusion protein |
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83 | (7) |
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90 | (2) |
| 8 Evolution: what makes us human? |
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92 | (13) |
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Genetic differences between humans and chimpanzees |
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92 | (1) |
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A protein related to human speech |
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93 | (1) |
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94 | (1) |
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Comparing FOXP2 in different animals |
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95 | (6) |
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Changes in FOXP2 specific to humans |
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101 | (1) |
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102 | (3) |
| 9 Evolution: resolving a criminal case |
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105 | (16) |
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105 | (1) |
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Methods of molecular phylogeny |
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106 | (7) |
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Examination of the criminal case |
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113 | (7) |
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120 | (1) |
| 10 Evolution: the sad case of the Tasmanian tiger |
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121 | (16) |
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121 | (1) |
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122 | (1) |
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123 | (2) |
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125 | (1) |
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Inferring the phylogeny of marsupials |
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126 | (3) |
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129 | (6) |
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135 | (2) |
| 11 A function to every gene: termites, metagenomics and learning about the function of a sequence |
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137 | (13) |
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Assigning function based on sequence similarity |
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137 | (1) |
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138 | (1) |
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139 | (1) |
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Termites and cellulose digestion |
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140 | (1) |
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Assigning function to termite sequences |
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141 | (6) |
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147 | (3) |
| 12 A function to every gene: royal blood and order in the sequence universe |
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150 | (14) |
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150 | (1) |
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151 | (2) |
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Protein domain architecture |
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153 | (1) |
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Bioinformatics of protein domains |
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154 | (2) |
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Bioinformatic analysis of blood-clotting proteins |
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156 | (4) |
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Evolution of blood clotting |
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160 | (2) |
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162 | (2) |
| 13 A function to every gene: a slimy molecule |
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164 | (9) |
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Extensive sugar decoration |
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164 | (1) |
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165 | (3) |
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Computational identification of mucin domains |
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168 | (3) |
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171 | (2) |
| 14 Information resources: learning about flu viruses |
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173 | (25) |
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Short history of sequence databases |
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173 | (2) |
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Features of nucleotide sequence databases |
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175 | (2) |
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177 | (1) |
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Protein sequence and structure data |
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178 | (2) |
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Exploring databases at the NCBI |
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180 | (1) |
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181 | (1) |
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182 | (3) |
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The Entrez Programming Utilities |
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185 | (1) |
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Parameters supplied to eUtils: scripts and construction of URLs |
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185 | (2) |
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187 | (1) |
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188 | (4) |
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Further analysis of influenza viruses: extracting and filtering information with Perl and Unix tools |
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192 | (3) |
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195 | (1) |
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196 | (1) |
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NCBI documentation resources |
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196 | (2) |
| 15 Finding genes: going ashore at CpG islands |
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198 | (10) |
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Transcription and its regulation |
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198 | (1) |
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DNA sequences that influence transcription |
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199 | (1) |
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200 | (2) |
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202 | (4) |
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206 | (2) |
| 16 Finding genes: in the world of snurps |
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208 | (14) |
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Methods of gene prediction |
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208 | (1) |
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209 | (4) |
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213 | (3) |
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216 | (3) |
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219 | (3) |
| 17 Finding genes: hunting for the distant RNA relatives |
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222 | (19) |
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222 | (1) |
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Properties of RNA and computational RNA finding |
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223 | (4) |
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An RNA involved in protein transport |
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227 | (1) |
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The organelles and their evolution |
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227 | (2) |
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The quest for chloroplast RNAs |
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229 | (2) |
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Automating tasks with Unix and Perl |
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231 | (7) |
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238 | (3) |
| 18 Personal genomes: the differences between you and me |
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241 | (11) |
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241 | (1) |
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Individual variation and SNPs |
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242 | (2) |
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244 | (6) |
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250 | (2) |
| 19 Personal genomes: what's in my genome? |
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252 | (14) |
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252 | (1) |
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An SNP dataset of South African individuals |
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253 | (3) |
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What SNPs are unique to the Bushmen? |
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256 | (1) |
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What SNPs are in coding regions? |
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257 | (3) |
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260 | (3) |
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Constructing your own modules |
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263 | (1) |
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264 | (2) |
| 20 Personal genomes: details of family genetics |
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266 | (12) |
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Basic principles of genetic inheritance |
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266 | (3) |
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Analysis of a family quartet |
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269 | (3) |
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Where are the crossing-over sites? |
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272 | (5) |
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277 | (1) |
| Appendix I: Brief Unix reference |
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278 | (11) |
| Appendix II: A selection of biological sequence analysis software |
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289 | (11) |
| Appendix III: A short Perl reference |
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300 | (23) |
| Appendix IV: A brief introduction to R |
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323 | (7) |
| Index |
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330 | |
Lisainfo e-raamatute kohta