The Resource Computational methods for understanding bacterial and archaeal genomes, editors, Ying Xu, J. Peter Gogarten
Computational methods for understanding bacterial and archaeal genomes, editors, Ying Xu, J. Peter Gogarten
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The item Computational methods for understanding bacterial and archaeal genomes, editors, Ying Xu, J. Peter Gogarten represents a specific, individual, material embodiment of a distinct intellectual or artistic creation found in University of Missouri-St. Louis Libraries.This item is available to borrow from 1 library branch.
Resource Information
The item Computational methods for understanding bacterial and archaeal genomes, editors, Ying Xu, J. Peter Gogarten represents a specific, individual, material embodiment of a distinct intellectual or artistic creation found in University of Missouri-St. Louis Libraries.
This item is available to borrow from 1 library branch.
- 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
- Language
- eng
- Extent
- 1 online resource (xix, 473 pages)
- 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
- 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
- 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
- 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
- 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
- Isbn
- 9781860949838
- Label
- Computational methods for understanding bacterial and archaeal genomes
- Title
- Computational methods for understanding bacterial and archaeal genomes
- Statement of responsibility
- editors, Ying Xu, J. Peter Gogarten
- Subject
-
- Bacterial genomes -- Data processing -- Textbooks
- Biochemistry
- Computational Biology -- methods
- Computational biology
- Computational biology -- Textbooks
- Computer science
- Electronic books
- Genetics (non-medical)
- Genetics, Microbial
- Genome, Archaeal
- Genome, Bacterial
- Microbial genetics -- Data processing -- Textbooks
- Prokaryotes
- Prokaryotes -- Textbooks
- SCIENCE -- Life Sciences | Genetics & Genomics
- Science
- Textbooks
- Language
- eng
- 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
- Cataloging source
- N$T
- Dewey number
- 572.860285
- Illustrations
- illustrations
- Index
- index present
- LC call number
- QH434
- LC item number
- .C66 2008eb
- Literary form
- non fiction
- NAL call number
- QH434
- NAL item number
- .C66 2008
- Nature of contents
-
- dictionaries
- bibliography
- NLM call number
- QW 51 C738 2008
- http://library.link/vocab/relatedWorkOrContributorDate
- 1960-
- http://library.link/vocab/relatedWorkOrContributorName
-
- Xu, Ying
- Gogarten, J. Peter
- Series statement
- Series on advances in bioinformatics and computational biology,
- Series volume
- v. 7
- http://library.link/vocab/subjectName
-
- Microbial genetics
- Bacterial genomes
- Prokaryotes
- Computational biology
- Genome, Bacterial
- Genome, Archaeal
- Genetics, Microbial
- Computational Biology
- SCIENCE
- Computational biology
- Prokaryotes
- Biochemistry
- Computer science
- Genetics (non-medical)
- Science
- Label
- Computational methods for understanding bacterial and archaeal genomes, editors, Ying Xu, J. Peter Gogarten
- Antecedent source
- unknown
- Bibliography note
- Includes bibliographical references (pages 397-466) and index
- Carrier category
- online resource
- Carrier category code
-
- cr
- Carrier MARC source
- rdacarrier
- Color
- multicolored
- Content category
- text
- Content type code
-
- txt
- Content type MARC source
- rdacontent
- 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
- 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
- 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
- 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
- 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
- Control code
- 828425182
- Dimensions
- unknown
- Extent
- 1 online resource (xix, 473 pages)
- File format
- unknown
- Form of item
- online
- Isbn
- 9781860949838
- Level of compression
- unknown
- Media category
- computer
- Media MARC source
- rdamedia
- Media type code
-
- c
- Other physical details
- illustrations (some color)
- Quality assurance targets
- not applicable
- Reformatting quality
- unknown
- Sound
- unknown sound
- Specific material designation
- remote
- System control number
- (OCoLC)828425182
- Label
- Computational methods for understanding bacterial and archaeal genomes, editors, Ying Xu, J. Peter Gogarten
- Antecedent source
- unknown
- Bibliography note
- Includes bibliographical references (pages 397-466) and index
- Carrier category
- online resource
- Carrier category code
-
- cr
- Carrier MARC source
- rdacarrier
- Color
- multicolored
- Content category
- text
- Content type code
-
- txt
- Content type MARC source
- rdacontent
- 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
- 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
- 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
- 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
- 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
- Control code
- 828425182
- Dimensions
- unknown
- Extent
- 1 online resource (xix, 473 pages)
- File format
- unknown
- Form of item
- online
- Isbn
- 9781860949838
- Level of compression
- unknown
- Media category
- computer
- Media MARC source
- rdamedia
- Media type code
-
- c
- Other physical details
- illustrations (some color)
- Quality assurance targets
- not applicable
- Reformatting quality
- unknown
- Sound
- unknown sound
- Specific material designation
- remote
- System control number
- (OCoLC)828425182
Subject
- Bacterial genomes -- Data processing -- Textbooks
- Biochemistry
- Computational Biology -- methods
- Computational biology
- Computational biology -- Textbooks
- Computer science
- Electronic books
- Genetics (non-medical)
- Genetics, Microbial
- Genome, Archaeal
- Genome, Bacterial
- Microbial genetics -- Data processing -- Textbooks
- Prokaryotes
- Prokaryotes -- Textbooks
- SCIENCE -- Life Sciences | Genetics & Genomics
- Science
- Textbooks
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<div class="citation" vocab="http://schema.org/"><i class="fa fa-external-link-square fa-fw"></i> Data from <span resource="http://link.umsl.edu/portal/Computational-methods-for-understanding-bacterial/LzNoPR9wDTw/" typeof="Book http://bibfra.me/vocab/lite/Item"><span property="name http://bibfra.me/vocab/lite/label"><a href="http://link.umsl.edu/portal/Computational-methods-for-understanding-bacterial/LzNoPR9wDTw/">Computational methods for understanding bacterial and archaeal genomes, editors, Ying Xu, J. Peter Gogarten</a></span> - <span property="potentialAction" typeOf="OrganizeAction"><span property="agent" typeof="LibrarySystem http://library.link/vocab/LibrarySystem" resource="http://link.umsl.edu/"><span property="name http://bibfra.me/vocab/lite/label"><a property="url" href="http://link.umsl.edu/">University of Missouri-St. Louis Libraries</a></span></span></span></span></div>
