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Computational methods for next generation sequencing data analysis / / edited by Ion Măndoiu, Alexander Zelikovsky
| Computational methods for next generation sequencing data analysis / / edited by Ion Măndoiu, Alexander Zelikovsky |
| Pubbl/distr/stampa | Hoboken, New Jersey : , : John Wiley & Sons, , [2016] |
| Descrizione fisica | 1 online resource (461 p.) |
| Disciplina | 611/.0181663 |
| Collana | Wiley series on bioinformatics : computational techniques and engineering |
| Soggetto topico |
Nucleotide sequence - Methodology
Nucleotide sequence - Data processing |
| ISBN |
1-119-27217-3
1-119-27216-5 1-119-27218-1 |
| Formato | Materiale a stampa  |
| Livello bibliografico | Monografia |
| Lingua di pubblicazione | eng |
| Nota di contenuto |
Cover; Title Page; Copyright; Contents; Contributors; Preface; About the Companion Website; Part I Computing and Experimental Infrastructure for NGS; Chapter 1 Cloud Computing for Next-Generation Sequencing Data Analysis; 1.1 Introduction; 1.2 Challenges for NGS Data Analysis; 1.3 Background For Cloud Computing and its Programming Models; 1.4 Cloud Computing Services for NGS Data Analysis; 1.5 Conclusions and Future Directions; References; Chapter 2 Introduction to the Analysis of Environmental Sequence Information Using Metapathways; 2.1 Introduction & Overview; 2.2 Background
2.3 Metapathways Processes2.4 Big Data Processing; 2.5 Downstream Analyses; 2.6 Conclusions; References; Chapter 3 Pooling Strategy for Massive Viral Sequencing; 3.1 Introduction; 3.2 Design of Pools for Big Viral Data; 3.3 Deconvolution of Viral Samples From Pools; 3.4 Performance of Pooling Methods on Simulated Data; 3.5 Experimental Validation of Pooling Strategy; 3.6 Conclusion; References; Chapter 4 Applications of High-Fidelity Sequencing Protocol to RNA Viruses; 4.1 Introduction; 4.2 High-Fidelity Sequencing Protocol; 4.3 Assembly of High-Fidelity Sequencing Data 4.4 Performance of VGA on Simulated Data4.5 Performance of Existing Viral Assemblers on Simulated Consensus Error-Corrected Reads; 4.6 Performance of VGA on Real Hiv Data; 4.7 Comparison of Alignment on Error-Corrected Reads; 4.8 Evaluating of Error Correction Tools Based on High-Fidelity Sequencing Reads; Acknowledgment; References; Part II Genomics and Epigenomics; Chapter 5 Scaffolding Algorithms; 5.1 Scaffolding; 5.2 State-of-The-Art Scaffolding Tools; 5.3 Recent Scaffolding Tools; 5.4 Scaffolding Software Evaluation; References; Chapter 6 Genomic Variants Detection and Genotyping 6.1 Introduction6.2 Methods for Detection and Genotyping OF SNPs and Small Indels; 6.3 Methods for Detection and Genotyping of CNVs; 6.4 Putting Everything Together; References; Chapter 7 Discovering and Genotyping Twilight Zone Deletions; 7.1 Introduction; 7.2 Notation; 7.3 Non-Twilight-Zone Deletion Discovery; 7.4 Discovering ""Twilight Zone"" Deletions: New Solutions; 7.5 Genotyping ""Twilight Zone"" Deletions; 7.6 Results; 7.7 Discussion; 7.8 Availability; Acknowledgments; References; Chapter 8 Computational Approaches for Finding Long Insertions and Deletions with NGS Data 8.1 Background8.2 Methods; 8.3 Applications; 8.4 Conclusions and Future Directions; Acknowledgment; References; Chapter 9 Computational Approaches in Next-Generation Sequencing Data Analysis for Genome-Wide DNA Methylation Studies; 9.1 Introduction; 9.2 Enrichment-Based Approaches; 9.3 Bisulfite Treatment-Based Approaches; 9.4 Conclusion; References; Chapter 10 Bisulfite-Conversion-Based Methods for DNA Methylation Sequencing Data Analysis; 10.1 Introduction; 10.2 The Problem of Mapping BS-Treated Reads; 10.3 Algorithmic Approaches to the Problem Of Mapping BS-Treated Reads 10.4 Methylation Estimation |
| Record Nr. | UNINA-9910135021603321 |
| Hoboken, New Jersey : , : John Wiley & Sons, , [2016] | ||
| Materiale a stampa | ||
| Lo trovi qui: Univ. Federico II | ||
| ||
Computational methods for next generation sequencing data analysis / / edited by Ion Măndoiu, Alexander Zelikovsky
| Computational methods for next generation sequencing data analysis / / edited by Ion Măndoiu, Alexander Zelikovsky |
| Pubbl/distr/stampa | Hoboken, New Jersey : , : John Wiley & Sons, , [2016] |
| Descrizione fisica | 1 online resource (461 p.) |
| Disciplina | 611/.0181663 |
| Collana | Wiley series on bioinformatics : computational techniques and engineering |
| Soggetto topico |
Nucleotide sequence - Methodology
Nucleotide sequence - Data processing |
| ISBN |
1-119-27217-3
1-119-27216-5 1-119-27218-1 |
| Formato | Materiale a stampa |
| Livello bibliografico | Monografia |
| Lingua di pubblicazione | eng |
| Nota di contenuto |
Cover; Title Page; Copyright; Contents; Contributors; Preface; About the Companion Website; Part I Computing and Experimental Infrastructure for NGS; Chapter 1 Cloud Computing for Next-Generation Sequencing Data Analysis; 1.1 Introduction; 1.2 Challenges for NGS Data Analysis; 1.3 Background For Cloud Computing and its Programming Models; 1.4 Cloud Computing Services for NGS Data Analysis; 1.5 Conclusions and Future Directions; References; Chapter 2 Introduction to the Analysis of Environmental Sequence Information Using Metapathways; 2.1 Introduction & Overview; 2.2 Background
2.3 Metapathways Processes2.4 Big Data Processing; 2.5 Downstream Analyses; 2.6 Conclusions; References; Chapter 3 Pooling Strategy for Massive Viral Sequencing; 3.1 Introduction; 3.2 Design of Pools for Big Viral Data; 3.3 Deconvolution of Viral Samples From Pools; 3.4 Performance of Pooling Methods on Simulated Data; 3.5 Experimental Validation of Pooling Strategy; 3.6 Conclusion; References; Chapter 4 Applications of High-Fidelity Sequencing Protocol to RNA Viruses; 4.1 Introduction; 4.2 High-Fidelity Sequencing Protocol; 4.3 Assembly of High-Fidelity Sequencing Data 4.4 Performance of VGA on Simulated Data4.5 Performance of Existing Viral Assemblers on Simulated Consensus Error-Corrected Reads; 4.6 Performance of VGA on Real Hiv Data; 4.7 Comparison of Alignment on Error-Corrected Reads; 4.8 Evaluating of Error Correction Tools Based on High-Fidelity Sequencing Reads; Acknowledgment; References; Part II Genomics and Epigenomics; Chapter 5 Scaffolding Algorithms; 5.1 Scaffolding; 5.2 State-of-The-Art Scaffolding Tools; 5.3 Recent Scaffolding Tools; 5.4 Scaffolding Software Evaluation; References; Chapter 6 Genomic Variants Detection and Genotyping 6.1 Introduction6.2 Methods for Detection and Genotyping OF SNPs and Small Indels; 6.3 Methods for Detection and Genotyping of CNVs; 6.4 Putting Everything Together; References; Chapter 7 Discovering and Genotyping Twilight Zone Deletions; 7.1 Introduction; 7.2 Notation; 7.3 Non-Twilight-Zone Deletion Discovery; 7.4 Discovering ""Twilight Zone"" Deletions: New Solutions; 7.5 Genotyping ""Twilight Zone"" Deletions; 7.6 Results; 7.7 Discussion; 7.8 Availability; Acknowledgments; References; Chapter 8 Computational Approaches for Finding Long Insertions and Deletions with NGS Data 8.1 Background8.2 Methods; 8.3 Applications; 8.4 Conclusions and Future Directions; Acknowledgment; References; Chapter 9 Computational Approaches in Next-Generation Sequencing Data Analysis for Genome-Wide DNA Methylation Studies; 9.1 Introduction; 9.2 Enrichment-Based Approaches; 9.3 Bisulfite Treatment-Based Approaches; 9.4 Conclusion; References; Chapter 10 Bisulfite-Conversion-Based Methods for DNA Methylation Sequencing Data Analysis; 10.1 Introduction; 10.2 The Problem of Mapping BS-Treated Reads; 10.3 Algorithmic Approaches to the Problem Of Mapping BS-Treated Reads 10.4 Methylation Estimation |
| Record Nr. | UNINA-9910812209403321 |
| Hoboken, New Jersey : , : John Wiley & Sons, , [2016] | ||
| Materiale a stampa | ||
| Lo trovi qui: Univ. Federico II | ||
| ||
Database annotation in molecular biology / / editor, Arthur M. Lesk
| Database annotation in molecular biology / / editor, Arthur M. Lesk |
| Pubbl/distr/stampa | Chichester, West Sussex ; ; Hoboken, NJ, : John Wiley, c2005 |
| Descrizione fisica | 1 online resource (267 p.) |
| Disciplina | 572.8 |
| Altri autori (Persone) | LeskArthur M |
| Soggetto topico |
Bioinformatics
Nucleotide sequence - Data processing Amino acid sequence - Data processing |
| ISBN |
1-280-23872-0
9786610238729 0-470-01242-0 0-470-85685-8 |
| Formato | Materiale a stampa |
| Livello bibliografico | Monografia |
| Lingua di pubblicazione | eng |
| Nota di contenuto |
Database Annotation in Molecular Biology; Contents; Preface; List of Contributors; 1 Annotation and Databases: Status and Prospects; 1.1 Introduction; 1.2 Annotation of Genomic Data; 1.3 Databases: Concepts and Definitions; 1.4 Access to Annotation Databases; Glossary; References; I THE DATABANKS; 2 Survey of Sequence Databases: Archival Projects; 2.1 Introduction; 2.2 Nucleotide Sequence Databases; 2.3 Swiss-Prot; 2.4 TrEMBL; 2.5 PIR; 2.6 UniProt; References; 3 Survey of Sequence Databases: Derived Databases; 3.1 Introduction; 3.2 Protein and Gene Family Databases; 3.3 Discussion; References
4 Databanks of Macromolecular Structure4.1 Introduction; 4.2 Background; 4.3 Archival Structural Databases Now; 4.4 Contextual Databases; 4.5 Derived Structural Data Databases; 4.6 Summary and View of the Future; References; 5 Gene Expression Databases; 5.1 Introduction; 5.2 What Do We Mean by Microarray Gene Expression Data?; 5.3 Data Complexity; 5.4 Minimum Information About a Microarray Experiment (MIAME); 5.5 Journals and MIAME; 5.6 Storage and Exchange Formats: MAGE-OM and MAGE-ML; 5.7 ArrayExpress; 5.8 Annotation Tools; 5.9 Curation; 5.10 Standardization and Semantics 5.11 Public Microarray Databases5.12 ArrayExpress, an Example of a Public Repository; 5.13 Submissions to ArrayExpress; 5.14 MIAMExpress and Other MIAME Compliant Annotation Systems; 5.15 Databases of Protein Expression Patterns; 5.16 The Gene Expression Database (GXD); 5.17 Conclusion; References; II THE BASIS OF ANNOTATION; 6 Taxonomy: a Moving Target for Sequence Data; 6.1 Introduction; 6.2 Nomenclature; 6.3 Operational Definitions; 6.4 Searching for the Taxonomic Gold Standard; 6.5 Conclusions; References; 7 Genomics and Proteomics: Design and Sources of Annotation 7.1 Beyond the Sequence: the Challenge of Complete Genome Analysis7.2 Extracting the Genes; 7.3 Organism Specific Peculiarities; 7.4 Topology of Genomes; 7.5 Gene Extraction Pipelines; 7.6 Added Value and Knowledge; 7.7 Beyond the Parts List; References; 8 Annotation of Protein Sequences; 8.1 Introduction; 8.2 What is Annotation?; 8.3 UniProt: Universal Protein Resource; 8.4 Protein Family Classification; 8.5 InterPro: Integrated Resource of Protein Families, Domains and Sites; 8.6 PIR Protein Families and Superfamilies; 8.7 Ontologies 8.8 Protein Names, Source Information and Unique Identifiers8.9 Common Identification Errors; 8.10 Evidence Attribution; 8.11 Position Specific Annotations; 8.12 Rule-based Annotation; 8.13 Conclusions; Acknowledgements; References; 9 Issues in the Annotation of Protein Structures; 9.1 Data Harvesting; 9.2 Identification of the Biologically Relevant Assembly; 9.3 Taxonomy; 9.4 Sequence Recognition and Cross-reference; 9.5 Recognition of Secondary Structure Elements; 9.6 Validation of Structures; 9.7 Residue Identification; 9.8 Hetgroup Identification; 9.9 Solvent Handling 9.10 Miscellaneous Annotation Issues |
| Record Nr. | UNINA-9910143748003321 |
| Chichester, West Sussex ; ; Hoboken, NJ, : John Wiley, c2005 | ||
| Materiale a stampa | ||
| Lo trovi qui: Univ. Federico II | ||
| ||
Next generation sequencing technologies in medical genetics / / C. Alexander Valencia [and four others]
| Next generation sequencing technologies in medical genetics / / C. Alexander Valencia [and four others] |
| Autore | Valencia C. Alexander |
| Edizione | [1st ed. 2013.] |
| Pubbl/distr/stampa | New York : , : Springer, , 2013 |
| Descrizione fisica | 1 online resource (xii, 94 pages) : color illustrations |
| Disciplina | 611.01816 |
| Collana | SpringerBriefs in Genetics |
| Soggetto topico |
Nucleotide sequence - Data processing
Medical genetics - Technique |
| ISBN | 1-4614-9032-4 |
| Formato | Materiale a stampa |
| Livello bibliografico | Monografia |
| Lingua di pubblicazione | eng |
| Nota di contenuto | Sanger sequencing principles, history and landmarks -- A survey of next-generation sequencing technologies -- A review of DNA enrichment technologies -- Application of next-generation sequencing to the diagnosis of genetic disorders a brief overview -- Next-generation sequencing-based noninvasive prenatal diagnosis -- Diagnosis of inherited neuromuscular disorders by next-generation sequencing -- Application of next-generation sequencing in hearing loss diagnosis -- Exome sequencing as a discovery and a diagnostic tool -- Challenges of next-generation sequencing-based molecular diagnostics. |
| Record Nr. | UNINA-9910437836903321 |
Valencia C. Alexander
|
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| New York : , : Springer, , 2013 | ||
| Materiale a stampa | ||
| Lo trovi qui: Univ. Federico II | ||
| ||
Pattern discovery in biomolecular data [[electronic resource] ] : tools, techniques, and applications / / edited by Jason T.L. Wang, Bruce A. Shapiro, Dennis Shasha
| Pattern discovery in biomolecular data [[electronic resource] ] : tools, techniques, and applications / / edited by Jason T.L. Wang, Bruce A. Shapiro, Dennis Shasha |
| Pubbl/distr/stampa | New York, : Oxford University, 1999 |
| Descrizione fisica | 1 online resource (272 p.) |
| Disciplina | 572.8/5/0285 |
| Altri autori (Persone) |
WangJason T. L
ShapiroBruce A ShashaDennis Elliott |
| Collana | Oxford scholarship online |
| Soggetto topico |
Nucleotide sequence - Data processing
Amino acid sequence - Data processing Pattern recognition systems Information storage and retrieval systems - Nucleotide sequence |
| Soggetto genere / forma | Electronic books. |
| ISBN |
0-19-756125-X
1-280-76167-9 9786610761678 0-19-802806-7 |
| Formato | Materiale a stampa |
| Livello bibliografico | Monografia |
| Lingua di pubblicazione | eng |
| Nota di contenuto | pt. 1. Finding patterns in sequences -- pt. 2. Finding patterns in 3D structures -- pt. 3. System components for discovery. |
| Record Nr. | UNINA-9910453368003321 |
| New York, : Oxford University, 1999 | ||
| Materiale a stampa | ||
| Lo trovi qui: Univ. Federico II | ||
| ||
Pattern discovery in biomolecular data [[electronic resource] ] : tools, techniques, and applications / / edited by Jason T.L. Wang, Bruce A. Shapiro, Dennis Shasha
| Pattern discovery in biomolecular data [[electronic resource] ] : tools, techniques, and applications / / edited by Jason T.L. Wang, Bruce A. Shapiro, Dennis Shasha |
| Pubbl/distr/stampa | New York, : Oxford University, 1999 |
| Descrizione fisica | 1 online resource (272 p.) |
| Disciplina | 572.8/5/0285 |
| Altri autori (Persone) |
WangJason T. L
ShapiroBruce A ShashaDennis Elliott |
| Collana | Oxford scholarship online |
| Soggetto topico |
Nucleotide sequence - Data processing
Amino acid sequence - Data processing Pattern recognition systems Information storage and retrieval systems - Nucleotide sequence |
| ISBN |
0-19-756125-X
1-280-76167-9 9786610761678 0-19-802806-7 |
| Formato | Materiale a stampa |
| Livello bibliografico | Monografia |
| Lingua di pubblicazione | eng |
| Nota di contenuto | pt. 1. Finding patterns in sequences -- pt. 2. Finding patterns in 3D structures -- pt. 3. System components for discovery. |
| Record Nr. | UNINA-9910782600803321 |
| New York, : Oxford University, 1999 | ||
| Materiale a stampa | ||
| Lo trovi qui: Univ. Federico II | ||
| ||
Pattern discovery in biomolecular data : tools, techniques, and applications / / edited by Jason T.L. Wang, Bruce A. Shapiro, Dennis Shasha
| Pattern discovery in biomolecular data : tools, techniques, and applications / / edited by Jason T.L. Wang, Bruce A. Shapiro, Dennis Shasha |
| Edizione | [1st ed.] |
| Pubbl/distr/stampa | New York, : Oxford University, 1999 |
| Descrizione fisica | 1 online resource (272 p.) |
| Disciplina | 572.8/5/0285 |
| Altri autori (Persone) |
WangJason T. L
ShapiroBruce A ShashaDennis Elliott |
| Collana | Oxford scholarship online |
| Soggetto topico |
Nucleotide sequence - Data processing
Amino acid sequence - Data processing Pattern recognition systems Information storage and retrieval systems - Nucleotide sequence |
| ISBN |
0-19-028372-6
0-19-756125-X 1-280-76167-9 9786610761678 0-19-802806-7 |
| Formato | Materiale a stampa |
| Livello bibliografico | Monografia |
| Lingua di pubblicazione | eng |
| Nota di contenuto | pt. 1. Finding patterns in sequences -- pt. 2. Finding patterns in 3D structures -- pt. 3. System components for discovery. |
| Record Nr. | UNINA-9910824435403321 |
| New York, : Oxford University, 1999 | ||
| Materiale a stampa | ||
| Lo trovi qui: Univ. Federico II | ||
| ||
