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Multiple biological sequence alignment : scoring functions, algorithms and applications / / Ken Nguyen, Xuan Guo, Yi Pan
| Multiple biological sequence alignment : scoring functions, algorithms and applications / / Ken Nguyen, Xuan Guo, Yi Pan |
| Autore | Nguyen Ken <1975-> |
| Pubbl/distr/stampa | Hoboken, New Jersey : , : John Wiley & Sons, Inc., , 2016 |
| Descrizione fisica | 1 online resource (286 p.) |
| Disciplina | 572.8 |
| Collana | Wiley series on bioinformatics: computational techniques and engineering |
| Soggetto topico | Sequence alignment (Bioinformatics) |
| ISBN |
1-119-27245-9
1-119-27375-7 1-119-27376-5 |
| Formato | Materiale a stampa  |
| Livello bibliografico | Monografia |
| Lingua di pubblicazione | eng |
| Nota di contenuto |
Title Page; Copyright; Table of Contents; Preface; Chapter 1: Introduction; 1.1 Motivation; 1.2 The Organization of this Book; 1.3 Sequence Fundamentals; Chapter 2: Protein/DNA/RNA Pairwise Sequence Alignment; 2.1 Sequence Alignment Fundamentals; 2.2 Dot-Plot Matrix; 2.3 Dynamic Programming; 2.4 Word Method; 2.5 Searching Sequence Databases; References; Chapter 3: Quantifying Sequence Alignments; 3.1 Evolution and Measuring Evolution; 3.2 Substitution Matrices and Scoring Matrices; 3.3 GAPS; 3.4 Scoring Multiple Sequence Alignments; 3.5 Circular Sum Score; 3.6 Conservation Score Schemes
3.7 Diversity Scoring Schemes3.8 Stereochemical Property Methods; 3.9 Hierarchical Expected Matching Probability Scoring Metric (HEP); Chapter 4: Sequence Clustering; 4.1 Unweighted Pair Group Method with Arithmetic Mean - UPGMA; 4.2 Neighborhood-Joining Method - NJ; 4.3 Overlapping Sequence Clustering; Chapter 5: Multiple Sequences Alignment Algorithms; 5.1 Dynamic Programming; 5.2 Progressive Alignment; 5.3 Consistency and Probabilistic MSA; 5.4 Genetic Algorithms; 5.5 New Development in Multiple Sequence Alignment Algorithms; 5.6 Test Data and Alignment Methods; 5.7 Results Chapter 6: Phylogeny in Multiple Sequence Alignments6.1 The Tree of Life; 6.2 Phylogeny Construction; 6.3 Inferring Phylogeny from Multiple Sequence Alignments; Chapter 7: Multiple Sequence Alignment on High-Performance Computing Models; 7.1 Parallel Systems; 7.2 Exiting Parallel Multiple Sequence Alignment; 7.3 Reconfigurable-Mesh Computing Models - (R-Mesh); 7.4 Pairwise Dynamic Programming Algorithms; 7.5 Progressive Multiple Sequence Alignment ON R-Mesh; Chapter 8: Sequence Analysis Services; 8.1 EMBL-EBI: European Bioinformatics Institute 8.2 NCBI: National Center for Biotechnology Information8.3 GenomeNet and Data Bank of Japan; 8.4 Other Sequence Analysis and Alignment Web Servers; 8.5 SeqAna: Multiple Sequence Alignment with Quality Ranking; 8.6 Pairwise Sequence Alignment and Other Analysis Tools; 8.7 Tool Evaluation; Chapter 9: Multiple Sequence for Next-Generation Sequences; 9.1 Introduction; 9.2 Overview of Next Generation Sequence Alignment Algorithms; Chapter 10: Multiple Sequence Alignment for Variations Detection; 10.1 Introduction; 10.2 Genetic Variants; 10.3 Variation Detection Methods Based on MSA 10.4 Evaluation Methodology10.5 Conclusion and Future Work; Chapter 11: Multiple Sequence Alignment for Structure Detection; 11.1 Introduction; 11.2 RNA Secondary Structure Prediction Based on MSA; 11.3 Protein Secondary Structure Prediction Based on MSA; 11.4 Conclusion and Future Work; References; Index; End User License Agreement |
| Record Nr. | UNINA-9910135021203321 |
Nguyen Ken <1975->
|
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| Hoboken, New Jersey : , : John Wiley & Sons, Inc., , 2016 | ||
| Materiale a stampa | ||
| Lo trovi qui: Univ. Federico II | ||
| ||
Multiple biological sequence alignment : scoring functions, algorithms and applications / / Ken Nguyen, Xuan Guo, Yi Pan
| Multiple biological sequence alignment : scoring functions, algorithms and applications / / Ken Nguyen, Xuan Guo, Yi Pan |
| Autore | Nguyen Ken <1975-> |
| Pubbl/distr/stampa | Hoboken, New Jersey : , : John Wiley & Sons, Inc., , 2016 |
| Descrizione fisica | 1 online resource (286 p.) |
| Disciplina | 572.8 |
| Collana | Wiley series on bioinformatics: computational techniques and engineering |
| Soggetto topico | Sequence alignment (Bioinformatics) |
| ISBN |
1-119-27245-9
1-119-27375-7 1-119-27376-5 |
| Formato | Materiale a stampa |
| Livello bibliografico | Monografia |
| Lingua di pubblicazione | eng |
| Nota di contenuto |
Title Page; Copyright; Table of Contents; Preface; Chapter 1: Introduction; 1.1 Motivation; 1.2 The Organization of this Book; 1.3 Sequence Fundamentals; Chapter 2: Protein/DNA/RNA Pairwise Sequence Alignment; 2.1 Sequence Alignment Fundamentals; 2.2 Dot-Plot Matrix; 2.3 Dynamic Programming; 2.4 Word Method; 2.5 Searching Sequence Databases; References; Chapter 3: Quantifying Sequence Alignments; 3.1 Evolution and Measuring Evolution; 3.2 Substitution Matrices and Scoring Matrices; 3.3 GAPS; 3.4 Scoring Multiple Sequence Alignments; 3.5 Circular Sum Score; 3.6 Conservation Score Schemes
3.7 Diversity Scoring Schemes3.8 Stereochemical Property Methods; 3.9 Hierarchical Expected Matching Probability Scoring Metric (HEP); Chapter 4: Sequence Clustering; 4.1 Unweighted Pair Group Method with Arithmetic Mean - UPGMA; 4.2 Neighborhood-Joining Method - NJ; 4.3 Overlapping Sequence Clustering; Chapter 5: Multiple Sequences Alignment Algorithms; 5.1 Dynamic Programming; 5.2 Progressive Alignment; 5.3 Consistency and Probabilistic MSA; 5.4 Genetic Algorithms; 5.5 New Development in Multiple Sequence Alignment Algorithms; 5.6 Test Data and Alignment Methods; 5.7 Results Chapter 6: Phylogeny in Multiple Sequence Alignments6.1 The Tree of Life; 6.2 Phylogeny Construction; 6.3 Inferring Phylogeny from Multiple Sequence Alignments; Chapter 7: Multiple Sequence Alignment on High-Performance Computing Models; 7.1 Parallel Systems; 7.2 Exiting Parallel Multiple Sequence Alignment; 7.3 Reconfigurable-Mesh Computing Models - (R-Mesh); 7.4 Pairwise Dynamic Programming Algorithms; 7.5 Progressive Multiple Sequence Alignment ON R-Mesh; Chapter 8: Sequence Analysis Services; 8.1 EMBL-EBI: European Bioinformatics Institute 8.2 NCBI: National Center for Biotechnology Information8.3 GenomeNet and Data Bank of Japan; 8.4 Other Sequence Analysis and Alignment Web Servers; 8.5 SeqAna: Multiple Sequence Alignment with Quality Ranking; 8.6 Pairwise Sequence Alignment and Other Analysis Tools; 8.7 Tool Evaluation; Chapter 9: Multiple Sequence for Next-Generation Sequences; 9.1 Introduction; 9.2 Overview of Next Generation Sequence Alignment Algorithms; Chapter 10: Multiple Sequence Alignment for Variations Detection; 10.1 Introduction; 10.2 Genetic Variants; 10.3 Variation Detection Methods Based on MSA 10.4 Evaluation Methodology10.5 Conclusion and Future Work; Chapter 11: Multiple Sequence Alignment for Structure Detection; 11.1 Introduction; 11.2 RNA Secondary Structure Prediction Based on MSA; 11.3 Protein Secondary Structure Prediction Based on MSA; 11.4 Conclusion and Future Work; References; Index; End User License Agreement |
| Record Nr. | UNINA-9910817720203321 |
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Nguyen Ken <1975->
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| Hoboken, New Jersey : , : John Wiley & Sons, Inc., , 2016 | ||
| Materiale a stampa | ||
| Lo trovi qui: Univ. Federico II | ||
| ||
Multiple Sequenzalignments : which program fits my data? / / Theodor Sperlea
| Multiple Sequenzalignments : which program fits my data? / / Theodor Sperlea |
| Autore | Sperlea Theodor |
| Pubbl/distr/stampa | Berlin, Germany ; ; New York, New York : , : Springer-Verlag, , [2022] |
| Descrizione fisica | 1 online resource (106 pages) |
| Disciplina | 572.8 |
| Soggetto topico |
Biology - Data processing
Sequence alignment (Bioinformatics) |
| ISBN |
9783662644737
9783662644720 |
| Formato | Materiale a stampa |
| Livello bibliografico | Monografia |
| Lingua di pubblicazione | eng |
| Record Nr. | UNISA-996464541803316 |
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Sperlea Theodor
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| Berlin, Germany ; ; New York, New York : , : Springer-Verlag, , [2022] | ||
| Materiale a stampa | ||
| Lo trovi qui: Univ. di Salerno | ||
| ||
Multiple Sequenzalignments : which program fits my data? / / Theodor Sperlea
| Multiple Sequenzalignments : which program fits my data? / / Theodor Sperlea |
| Autore | Sperlea Theodor |
| Pubbl/distr/stampa | Berlin, Germany ; ; New York, New York : , : Springer-Verlag, , [2022] |
| Descrizione fisica | 1 online resource (106 pages) |
| Disciplina | 572.8 |
| Soggetto topico |
Biology - Data processing
Sequence alignment (Bioinformatics) |
| ISBN |
9783662644737
9783662644720 |
| Formato | Materiale a stampa |
| Livello bibliografico | Monografia |
| Lingua di pubblicazione | eng |
| Record Nr. | UNINA-9910547299003321 |
|
Sperlea Theodor
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| Berlin, Germany ; ; New York, New York : , : Springer-Verlag, , [2022] | ||
| Materiale a stampa | ||
| Lo trovi qui: Univ. Federico II | ||
| ||
Next generation sequencing and data analysis / / Melanie Kappelmann-Fenzl, editor
| Next generation sequencing and data analysis / / Melanie Kappelmann-Fenzl, editor |
| Edizione | [1st ed. 2021.] |
| Pubbl/distr/stampa | Cham, Switzerland : , : Springer, , [2021] |
| Descrizione fisica | 1 online resource (XII, 218 p. 54 illus., 51 illus. in color.) |
| Disciplina | 572.8 |
| Collana | Learning materials in biosciences |
| Soggetto topico |
Sequence alignment (Bioinformatics)
Biologia computacional |
| Soggetto genere / forma | Llibres electrònics |
| ISBN | 3-030-62490-0 |
| Formato | Materiale a stampa |
| Livello bibliografico | Monografia |
| Lingua di pubblicazione | eng |
| Nota di contenuto | Chapter 1. Next Generation Sequencing (NGS)- What can be sequenced? -- Opportunities and Perspectives of NGS Applications in Cancer Research -- Chapter 3. Library Construction for NGS -- Chapter 4. NGS Technologies -- Chapter 5. Computer Setup -- Chapter 6. Introduction to Command Line -- Chapter 7. NGS Data -- Chapter 8. Reference Genome -- Chapter 9. Alignment -- Chapter 10. Identification of Genetic Variants and de novo Mutations Based on NGS -- Chapter 11. Design and Analysis of RNA Sequencing Data -- Chapter 12. Design and Analysis of Epigenetics and ChIP-Sequencing Data -- APPENDIX. |
| Record Nr. | UNINA-9910483440003321 |
| Cham, Switzerland : , : Springer, , [2021] | ||
| Materiale a stampa | ||
| Lo trovi qui: Univ. Federico II | ||
| ||
Next-generation sequencing : current technologies and applicaitons / / edited by Jianping Xu
| Next-generation sequencing : current technologies and applicaitons / / edited by Jianping Xu |
| Pubbl/distr/stampa | Norfolk, England : , : Caister Academic Press, , [2014] |
| Descrizione fisica | 1 online resource (173 p.) |
| Disciplina | 570.285 |
| Soggetto topico |
Bioinformatics
Nucleotide sequence Sequence alignment (Bioinformatics) Sequential analysis |
| Soggetto genere / forma | Electronic books. |
| ISBN | 1-908230-95-9 |
| Formato | Materiale a stampa |
| Livello bibliografico | Monografia |
| Lingua di pubblicazione | eng |
| Nota di contenuto |
Contents; Current books of interest; Contributors; Preface; 1; An Overview of Next-generation Genome Sequencing Platforms; Introduction; Second generation sequencing platforms; Third-generation sequencing platforms; Concluding remarks; 2: Attomole-level Genomics with Single-molecule Direct DNA, cDNA and RNA Sequencing Technologies; Introduction; Materials; Methods; 3: SNP Assessment on Draft Genomes from Next-generation Sequencing Data; Background; Single nucleotide polymorphisms (SNPs); SNP calling with one sample on draft genomes with ACCUSA
Head-to-head comparisons of sequenced samples with ACCUSA 2Conclusions; 4: Processing Large-scale Small RNA Datasets in Silico; Introduction; Library preparation and sequencing; Helper tools; Analysis tools; Visualization tools; Discussion; 5: Utility of High-throughput Sequence Data in Rare Variant Detection; What is a rare variant?; Why is variant detection needed?; Utility of non-HTS methods for minority and rare variant detection; Status of rare variant detection by analysis of HTS data; How much HTS data is needed to accurately detect rare variants? Testing the feasibility of analysing HTS for rare SNP detectionSources of errors; Experimental validation of correction approaches; Conclusions; 6: Detecting Breakpoints of Insertions and Deletions from Paired-end Short Reads; Introduction; Pindel: a pattern growth method to identify precise breakpoints of indels and SVs; Performance on real data (NA18507); Recent developments; Further advances of split-read approaches; Conclusion and future perspectives; 7: Novel Insights from Re-sequencing of Human Exomes Through NGS; Introduction; The protocol; Exome capture platforms and kits Quality control and performance evaluationBioinformatics analysis; Applications in human disease research; Perspective; 8: Insights on Plant Development Using NGS Technologies; Introduction; Use RNA-seq to dissect transcription at the cellular resolution; Use ChIP-seq to dissect transcriptional networks; Use ChIP-seq to analyse the epigenome; Conclusions and perspectives; 9: Next-generation Sequencing and the Future of Microbial Metagenomics; Introduction; Tracking microbial diversity; Applying omics technologies; Designing experiments; Modelling microbial diversity; Concluding remarks 10: Next-generation Sequencing, Metagenomes and the Human MicrobiomeIntroduction; Marker-specific microbial community surveys; Metagenomics - high-throughput shotgun (HTS sequencing) of microbial communities; Applications of metagenomics to the study of human health and disease; Beyond the omes - systems biology views onto the host-microbiome interactions; The new generation of cloud-based informatics solutions for next-generation sequencing; Conclusion; Index |
| Record Nr. | UNINA-9910465038903321 |
| Norfolk, England : , : Caister Academic Press, , [2014] | ||
| Materiale a stampa | ||
| Lo trovi qui: Univ. Federico II | ||
| ||
Next-generation sequencing : current technologies and applications / / edited by Jianping Xu
| Next-generation sequencing : current technologies and applications / / edited by Jianping Xu |
| Pubbl/distr/stampa | Norfolk, England : , : Caister Academic Press, , [2014] |
| Descrizione fisica | 1 online resource (173 p.) |
| Disciplina | 570.285 |
| Soggetto topico |
Bioinformatics
Nucleotide sequence Sequence alignment (Bioinformatics) Sequential analysis |
| ISBN | 1-908230-95-9 |
| Formato | Materiale a stampa |
| Livello bibliografico | Monografia |
| Lingua di pubblicazione | eng |
| Nota di contenuto |
Contents; Current books of interest; Contributors; Preface; 1; An Overview of Next-generation Genome Sequencing Platforms; Introduction; Second generation sequencing platforms; Third-generation sequencing platforms; Concluding remarks; 2: Attomole-level Genomics with Single-molecule Direct DNA, cDNA and RNA Sequencing Technologies; Introduction; Materials; Methods; 3: SNP Assessment on Draft Genomes from Next-generation Sequencing Data; Background; Single nucleotide polymorphisms (SNPs); SNP calling with one sample on draft genomes with ACCUSA
Head-to-head comparisons of sequenced samples with ACCUSA 2Conclusions; 4: Processing Large-scale Small RNA Datasets in Silico; Introduction; Library preparation and sequencing; Helper tools; Analysis tools; Visualization tools; Discussion; 5: Utility of High-throughput Sequence Data in Rare Variant Detection; What is a rare variant?; Why is variant detection needed?; Utility of non-HTS methods for minority and rare variant detection; Status of rare variant detection by analysis of HTS data; How much HTS data is needed to accurately detect rare variants? Testing the feasibility of analysing HTS for rare SNP detectionSources of errors; Experimental validation of correction approaches; Conclusions; 6: Detecting Breakpoints of Insertions and Deletions from Paired-end Short Reads; Introduction; Pindel: a pattern growth method to identify precise breakpoints of indels and SVs; Performance on real data (NA18507); Recent developments; Further advances of split-read approaches; Conclusion and future perspectives; 7: Novel Insights from Re-sequencing of Human Exomes Through NGS; Introduction; The protocol; Exome capture platforms and kits Quality control and performance evaluationBioinformatics analysis; Applications in human disease research; Perspective; 8: Insights on Plant Development Using NGS Technologies; Introduction; Use RNA-seq to dissect transcription at the cellular resolution; Use ChIP-seq to dissect transcriptional networks; Use ChIP-seq to analyse the epigenome; Conclusions and perspectives; 9: Next-generation Sequencing and the Future of Microbial Metagenomics; Introduction; Tracking microbial diversity; Applying omics technologies; Designing experiments; Modelling microbial diversity; Concluding remarks 10: Next-generation Sequencing, Metagenomes and the Human MicrobiomeIntroduction; Marker-specific microbial community surveys; Metagenomics - high-throughput shotgun (HTS sequencing) of microbial communities; Applications of metagenomics to the study of human health and disease; Beyond the omes - systems biology views onto the host-microbiome interactions; The new generation of cloud-based informatics solutions for next-generation sequencing; Conclusion; Index |
| Record Nr. | UNINA-9910789161903321 |
| Norfolk, England : , : Caister Academic Press, , [2014] | ||
| Materiale a stampa | ||
| Lo trovi qui: Univ. Federico II | ||
| ||
Next-generation sequencing : current technologies and applications / / edited by Jianping Xu
| Next-generation sequencing : current technologies and applications / / edited by Jianping Xu |
| Pubbl/distr/stampa | Norfolk, England : , : Caister Academic Press, , [2014] |
| Descrizione fisica | 1 online resource (173 p.) |
| Disciplina | 570.285 |
| Soggetto topico |
Bioinformatics
Nucleotide sequence Sequence alignment (Bioinformatics) Sequential analysis |
| ISBN | 1-908230-95-9 |
| Formato | Materiale a stampa |
| Livello bibliografico | Monografia |
| Lingua di pubblicazione | eng |
| Nota di contenuto |
Contents; Current books of interest; Contributors; Preface; 1; An Overview of Next-generation Genome Sequencing Platforms; Introduction; Second generation sequencing platforms; Third-generation sequencing platforms; Concluding remarks; 2: Attomole-level Genomics with Single-molecule Direct DNA, cDNA and RNA Sequencing Technologies; Introduction; Materials; Methods; 3: SNP Assessment on Draft Genomes from Next-generation Sequencing Data; Background; Single nucleotide polymorphisms (SNPs); SNP calling with one sample on draft genomes with ACCUSA
Head-to-head comparisons of sequenced samples with ACCUSA 2Conclusions; 4: Processing Large-scale Small RNA Datasets in Silico; Introduction; Library preparation and sequencing; Helper tools; Analysis tools; Visualization tools; Discussion; 5: Utility of High-throughput Sequence Data in Rare Variant Detection; What is a rare variant?; Why is variant detection needed?; Utility of non-HTS methods for minority and rare variant detection; Status of rare variant detection by analysis of HTS data; How much HTS data is needed to accurately detect rare variants? Testing the feasibility of analysing HTS for rare SNP detectionSources of errors; Experimental validation of correction approaches; Conclusions; 6: Detecting Breakpoints of Insertions and Deletions from Paired-end Short Reads; Introduction; Pindel: a pattern growth method to identify precise breakpoints of indels and SVs; Performance on real data (NA18507); Recent developments; Further advances of split-read approaches; Conclusion and future perspectives; 7: Novel Insights from Re-sequencing of Human Exomes Through NGS; Introduction; The protocol; Exome capture platforms and kits Quality control and performance evaluationBioinformatics analysis; Applications in human disease research; Perspective; 8: Insights on Plant Development Using NGS Technologies; Introduction; Use RNA-seq to dissect transcription at the cellular resolution; Use ChIP-seq to dissect transcriptional networks; Use ChIP-seq to analyse the epigenome; Conclusions and perspectives; 9: Next-generation Sequencing and the Future of Microbial Metagenomics; Introduction; Tracking microbial diversity; Applying omics technologies; Designing experiments; Modelling microbial diversity; Concluding remarks 10: Next-generation Sequencing, Metagenomes and the Human MicrobiomeIntroduction; Marker-specific microbial community surveys; Metagenomics - high-throughput shotgun (HTS sequencing) of microbial communities; Applications of metagenomics to the study of human health and disease; Beyond the omes - systems biology views onto the host-microbiome interactions; The new generation of cloud-based informatics solutions for next-generation sequencing; Conclusion; Index |
| Record Nr. | UNINA-9910828718203321 |
| Norfolk, England : , : Caister Academic Press, , [2014] | ||
| Materiale a stampa | ||
| Lo trovi qui: Univ. Federico II | ||
| ||
Next-generation sequencing and agriculture / / edited by Philipp E. Bayer and David Edward
| Next-generation sequencing and agriculture / / edited by Philipp E. Bayer and David Edward |
| Pubbl/distr/stampa | Wallingford, Oxfordshire : , : CAB International, , [2022] |
| Descrizione fisica | 1 online resource (x, 203 pages) |
| Disciplina | 630.2085 |
| Altri autori (Persone) | EdwardsDavid |
| Collana | CABI biotechnology series |
| Soggetto topico |
Agricultural genome mapping
Agricultural informatics Sequence alignment (Bioinformatics) |
| ISBN |
1-78924-783-7
1-78924-784-5 |
| Formato | Materiale a stampa |
| Livello bibliografico | Monografia |
| Lingua di pubblicazione | eng |
| Record Nr. | UNINA-9910760496303321 |
| Wallingford, Oxfordshire : , : CAB International, , [2022] | ||
| Materiale a stampa | ||
| Lo trovi qui: Univ. Federico II | ||
| ||
Sequencing
| Sequencing |
| Pubbl/distr/stampa | Cairo : , : Hindawi Pub. Corp., , 2010- |
| Descrizione fisica | 1 online resource |
| Disciplina | 540 |
| Soggetto topico |
Gene mapping
Biotechnology Genetics - Technique Sequence alignment (Bioinformatics) Genetic Techniques Sequence Alignment Sequence Analysis Cartes chromosomiques Biotechnologie Génétique - Technique Homologie de séquence (Bio-informatique) |
| Soggetto genere / forma |
Serial publications.
Periodical periodicals. Periodicals Périodiques. |
| ISSN | 2090-0333 |
| Formato | Materiale a stampa |
| Livello bibliografico | Periodico |
| Lingua di pubblicazione | eng |
| Record Nr. | UNISA-996335518603316 |
| Cairo : , : Hindawi Pub. Corp., , 2010- | ||
| Materiale a stampa | ||
| Lo trovi qui: Univ. di Salerno | ||
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