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Title Computational methods for understanding bacterial and archaeal genomes / editors, Ying Xu, J. Peter Gogarten
Published London : Imperial College Press ; Hackensack, NJ : Distributed by World Scientific Publishing, [2008]
©2008
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Description 1 online resource (xix, 473 pages) : illustrations (some color)
Series Series on advances in bioinformatics and computational biology, 1751-6404 ; v. 7
Series on advances in bioinformatics and computational biology ; v. 7
Contents Preface; CONTENTS; List of Contributors; Acknowledgments; 1. General Characteristics of Prokaryotic Genomes Jan Mr ́azek and Anne O. Summers; 1. Introduction; 1.1. The Replicon Concept and Classification of Replicons; 1.2. Physical Organization of Replicons in the Cell; 2. Overall Properties of Prokaryotic Chromosomes; 2.1. Size and Gene Content; 2.2. Why Are Prokaryotic Chromosomes Small?; 2.3. G+C Content; 2.4. Oligonucleotide Composition and Genome Signature; 2.5. Amino Acid Composition and Adaptation to Growth at High Temperatures; 3. Heterogeneity of Prokaryotic Chromosomes
15. Discussion16. Further Reading; Acknowledgments; 3. Evolution of the Genetic Code: Computational Methods and Inferences Greg Fournier; 1. Introduction; 1.1. The Amino Acids; 1.2. Codon Designations; 1.3. Transfer RNA; 1.4. Aminoacyl-tRNA Synthetases; 2. Major Methods and Algorithms: Variations of the Genetic Code; 2.1. Non-canonical Codes; 2.2. Selenocysteine; 2.3. Pyrrolysine; 2.4. The Sep System; 2.5. Asparagine and Glutamine; 2.6. Evolutionary Considerations; 2.7. Nanoarchaeal tRNA; 3. Major Methods and Algorithms: Models of Genetic Code Evolution; 3.1. Overview
2. Genes in Prokaryotic Genomes and Their Computational Prediction Rajeev K. Azad1. Introduction; 2. Inhomogeneous Markov Models; 2.1. The GeneMark Program; 3. Interpolated Markov Models; 3.1. The Glimmer Program; 3.2. Using Deleted Interpolation in Gene Prediction; 4. Hidden Markov Models; 4.1. The Forward-Backward Algorithm; 4.2. The Viterbi Algorithm; 4.3. HMM Training; 4.4. The ECOPARSE Program; 4.5. The GeneHacker Program; 4.6. HMM Versions of the GeneMark Program; 5. Fourier Transform Methods; 5.1. The GeneScan Program; 5.2. The Lengthen-Shu.e Program; 6. Self-Organizing Maps
3.1. Intrachromosomal Variance of Nucleotide and Oligonucleotide Composition3.2. Synonymous Codon Usage; 3.3. Identification of Genomic Islands and Lateral Gene Transfer Events; 3.4. G-C Skew; 4. Repeats in Prokaryotic Genomes; 4.1. Large Repeats and Duplications; 4.2. Transposons and Insertion Sequences; 4.3. Integrons; 4.4. Chimeric Mobile Elements: Conjugative Transposons, ICEs, Plasmid-Prophages, Transposon-Prophages, Genomic Islands, and Genetic Litter; 4.5. Retrons; 4.6. Short Dispersed Repeats; 4.7. Simple Sequence Repeats; 4.8. CRISPR Repeats; 5. Further Reading; Acknowledgments
6.1. The RescueNet Program7. Directed Acyclic Graphs; 7.1. The FrameD Program; 8. Linear Discriminant Function; 8.1. The ZCURVE Program; 9. Unsupervised Model Training: The Self-Learning Algorithms; 9.1. The GeneMark-Genesis Program; 9.2. The GeneMarkS Program; 9.3. The MED Program; 10. Using Similarity Search in Gene Prediction; 10.1. The ORPHEUS Program; 10.2. The CRITICA Program; 10.3. The BDGF Program; 10.4. The EasyGene Program; 10.5. The GISMO Program; 11. Gene Start Prediction; 12. Resolving Overlapping Genes; 13. Non-coding RNA Gene Prediction; 14. Assessing Gene Prediction Programs
Summary Over 500 prokaryotic genomes have been sequenced to date, and thousands more have been planned for the next few years. While these genomic sequence data provide unprecedented opportunities for biologists to study the world of prokaryotes, they also raise extremely challenging issues such as how to decode the rich information encoded in these genomes. This comprehensive volume includes a collection of cohesively written chapters on prokaryotic genomes, their organization and evolution, the information they encode, and the computational approaches needed to derive such information. A comparative
Bibliography Includes bibliographical references (pages 397-466) and index
Notes Print version record
Subject Bacterial genomes -- Data processing -- Textbooks.
Computational biology -- Textbooks.
Microbial genetics -- Data processing -- Textbooks.
Prokaryotes -- Textbooks.
Computational Biology -- methods.
Genetics, Microbial.
Genome, Archaeal.
Genome, Bacterial.
Genre/Form Textbooks.
Form Electronic book
Author Gogarten, J. Peter.
Xu, Ying, 1960-
ISBN 1860949835 (electronic bk.)
9781860949838 (electronic bk.)