Preface |
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Contributors |
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xi | |
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Part I Genome Visualization and Annotation |
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1 Comparative Analysis and Visualization of Genomic Sequences Using VISTA Browser and Associated Computational Tools |
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3 | (14) |
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2 Comparative Genomic Analysis Using the UCSC Genome Browser |
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17 | (18) |
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3 Comparative Genome Analysis in the Integrated Microbial Genomes (IMG) System |
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35 | (22) |
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4 WebACT: An Online Genome Comparison Suite |
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57 | (18) |
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5 GenColors: Annotation and Comparative Genomics of Prokaryotes Made Easy |
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75 | (22) |
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6 Comparative Microbial Genome Visualization Using GenomeViz |
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97 | (12) |
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7 BugView: A Tool for Genome Visualization and Comparison |
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109 | (24) |
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8 CGAS: A Comparative Genome Annotation System |
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133 | (16) |
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Part II Sequence Alignments |
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9 BLAST QuickStart: Example-Driven Web-Based BLAST Tutorial |
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149 | (28) |
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177 | (10) |
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11 Organizing and Updating Whole Genome BLAST Searches with ReHAB |
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187 | (8) |
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12 Alignment of Genomic Sequences Using DIALIGN |
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195 | (10) |
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13 An Introduction to the Lagan Alignment Toolkit |
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205 | (16) |
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14 Aligning Multiple Whole Genomes with Mercator and MAVID |
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221 | (16) |
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15 Mulan: Multiple-Sequence Alignment to Predict Functional Elements in Genomic Sequences |
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237 | (18) |
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16 Improving Pairwise Sequence Alignment between Distantly Related Proteins |
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255 | (16) |
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Part III Identification of Conserved Sequences and Biases in Codon Usage |
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17 Discovering Sequence Motifs |
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271 | (24) |
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18 Discovery of Conserved Motifs in Promoters of Orthologous Genes in Prokaryotes |
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295 | (14) |
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19 PhyME: A Software tool for Finding Motifs in Sets of Orthologous Sequences |
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309 | (10) |
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20 Comparative Genomics-Based Orthologous Promoter Analysis Using the DoOP Database and the DoOPSearch Web Tool |
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319 | (10) |
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21 Discovery of Motifs in Promoters of Coregulated Genes |
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329 | (20) |
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22 Fastcompare: A Nonalignment Approach for Genome-Scale Discovery of DNA and mRNA Regulatory Elements Using Network-Level Conservation |
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349 | (18) |
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23 Phylogenetic Footprinting to Find Functional DNA Elements |
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367 | (14) |
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24 Detecting Regulatory Sites Using PhyloGibbs |
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381 | (22) |
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25 Using the Gibbs Motif Sampler for Phylogenetic Footprinting |
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403 | (22) |
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26 Web-Based Identification of Evolutionary Conserved DNA cis-Regulatory Elements |
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425 | (12) |
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27 Exploring Conservation of Transcription Factor Binding Sites with CON REAL |
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437 | (12) |
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28 Computational and Statistical Methodologies for ORFeome Primary Structure Analysis |
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449 | (16) |
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Part IV Identification and Structural Characterization of Noncodinc RNAs |
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29 Comparative Analysis of RNA Genes: The caRNAc Software |
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465 | (10) |
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30 Efficient Annotation of Bacterial Genomes for Small, Noncoding RNAs Using the Integrative Computational Tool sRNAPredict2 |
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475 | (14) |
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31 Methods for Multiple Alignment and Consensus Structure Prediction of RNAs Implemented in MARNA |
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489 | (14) |
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32 Prediction of Structural Noncoding RNAs With RNAz |
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503 | (24) |
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33 RNA Consensus Structure Prediction With RNAalifold |
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527 | (18) |
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Index |
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545 | |