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Protein families : relating protein sequence, structure, and function / / edited by Christine A. Orengo, Alex Bateman
| Protein families : relating protein sequence, structure, and function / / edited by Christine A. Orengo, Alex Bateman |
| Pubbl/distr/stampa | Hoboken, New Jersey : , : Wiley, , [2014] |
| Descrizione fisica | 1 online resource (567 p.) |
| Disciplina | 572/.6 |
| Altri autori (Persone) |
OrengoChristine A. <1955->
BatemanAlex <1972-> |
| Collana | Wiley series in protein and peptide science |
| Soggetto topico |
Proteins
Proteomics Molecular biology - Data processing Bioinformatics |
| ISBN |
1-118-74281-8
1-118-74308-3 1-118-74285-0 |
| Classificazione | COM082000 |
| Formato | Materiale a stampa  |
| Livello bibliografico | Monografia |
| Lingua di pubblicazione | eng |
| Nota di contenuto |
Cover; Title Page; Contents; Introduction; Contributors; Part I Concepts Underlying Protein Family Classification; Chapter 1 Automated Sequence-Based Approaches for Identifying Domain Families; 1.1 Introduction; 1.2 Motivation Behind Automated Classification; 1.3 Clustering the Sequence Space Graph; 1.4 Historical Overview of Sequence Clustering Algorithms; 1.5 Related Methods; 1.6 Quality Assessment; 1.7 ADDA-The Automatic Domain Delineation Algorithm; 1.8 Results; 1.9 Conclusions; References; Chapter 2 Sequence Classification of Protein Families: Pfam and other Resources; 2.1 Introduction
2.2 Pfam2.3 Smart, Prosite Profiles, CDD and Tigrfams; 2.4 Philosophy of Pfam; 2.5 HMMER3 and Jackhmmer; 2.6 Sources of New Families; 2.7 Annotation of Families; 2.8 The InterPro Collection; 2.9 The Future of Sequence Classification; References; Chapter 3 Classifying Proteins into Domain Structure Families; 3.1 Introduction; 3.2 The Classification Hierarchies Adopted by Scop and Cath; 3.3 Challenges in Identifying Domains in Proteins; 3.4 Structure-Based Approaches for Identifying Related Folds and Homologs; 3.5 Approaches to Structure Comparison; 3.6 The DALI Algorithm 3.7 The SSAP Algorithm Used for Fold Recognition in CATH3.8 Fast Approximate Methods Used to Recognize Folds in CATH; 3.9 Measuring Structural Similarity; 3.10 Multiple Structure Alignment; 3.11 Classification Protocols; 3.12 Population of the Hierarchy; 3.13 Comparisons Between Scop and CATH; 3.14 Hierarchical Classifications Versus Structural Continuum; 3.15 Websites; References; Chapter 4 Structural Annotations of Genomes with Superfamily and Gene3D; 4.1 Introduction; 4.2 The Importance of Being High Throughput; 4.3 The Use of Structural Information; 4.4 Applications; 4.5 History 4.6 Technology4.7 Hidden Markov Models; 4.8 Building Models; 4.9 Domain Annotations; 4.10 High Throughput Computation; 4.11 Development of New Bioinformatics Algorithms; 4.12 Genomes; 4.13 e-Value Scores; 4.14 Other Sequence Sets; 4.15 Data Access; 4.16 Analysis Tools; 4.17 Conclusion; References; Chapter 5 Phylogenomic Databases and Orthology Prediction; 5.1 The Evolution of Novel Functions and Structures in Gene Families; 5.2 Homologs, Orthologs, Paralogs, and Other Evolutionary Terms; 5.3 The Standard Functional Annotation Protocol; 5.4 Orthology Identification Methods and Databases 5.5 Challenges in Phylogenetic Methods of Ortholog Identification5.6 Evaluating Ortholog Identification Methods; 5.7 Orthology Databases; 5.8 Phylogenomic Databases; 5.9 PhyloFacts; 5.10 Subfamily Classification in Phylofacts; 5.11 PhyloFacts 3.0; 5.12 PhylomeDB; 5.13 Panther; 5.14 Structural Phylogenomics: Improved Functional Annotation Through Integration of Information from Structure and Evolution; 5.15 Specific Issues in Phylogenomic Pipelines; 5.16 Improving Functional Inference using Information from Protein Structure; 5.17 Example Case Studies; 5.18 Review of Key Points; References Part II In-Depth Reviews of Protein Families |
| Record Nr. | UNINA-9910139014903321 |
| Hoboken, New Jersey : , : Wiley, , [2014] | ||
| Materiale a stampa | ||
| Lo trovi qui: Univ. Federico II | ||
| ||
Protein families : relating protein sequence, structure, and function / / edited by Christine A. Orengo, Alex Bateman
| Protein families : relating protein sequence, structure, and function / / edited by Christine A. Orengo, Alex Bateman |
| Pubbl/distr/stampa | Hoboken, New Jersey : , : Wiley, , [2014] |
| Descrizione fisica | 1 online resource (567 p.) |
| Disciplina | 572/.6 |
| Altri autori (Persone) |
OrengoChristine A. <1955->
BatemanAlex <1972-> |
| Collana | Wiley series in protein and peptide science |
| Soggetto topico |
Proteins
Proteomics Molecular biology - Data processing Bioinformatics |
| ISBN |
1-118-74281-8
1-118-74308-3 1-118-74285-0 |
| Classificazione | COM082000 |
| Formato | Materiale a stampa |
| Livello bibliografico | Monografia |
| Lingua di pubblicazione | eng |
| Nota di contenuto |
Cover; Title Page; Contents; Introduction; Contributors; Part I Concepts Underlying Protein Family Classification; Chapter 1 Automated Sequence-Based Approaches for Identifying Domain Families; 1.1 Introduction; 1.2 Motivation Behind Automated Classification; 1.3 Clustering the Sequence Space Graph; 1.4 Historical Overview of Sequence Clustering Algorithms; 1.5 Related Methods; 1.6 Quality Assessment; 1.7 ADDA-The Automatic Domain Delineation Algorithm; 1.8 Results; 1.9 Conclusions; References; Chapter 2 Sequence Classification of Protein Families: Pfam and other Resources; 2.1 Introduction
2.2 Pfam2.3 Smart, Prosite Profiles, CDD and Tigrfams; 2.4 Philosophy of Pfam; 2.5 HMMER3 and Jackhmmer; 2.6 Sources of New Families; 2.7 Annotation of Families; 2.8 The InterPro Collection; 2.9 The Future of Sequence Classification; References; Chapter 3 Classifying Proteins into Domain Structure Families; 3.1 Introduction; 3.2 The Classification Hierarchies Adopted by Scop and Cath; 3.3 Challenges in Identifying Domains in Proteins; 3.4 Structure-Based Approaches for Identifying Related Folds and Homologs; 3.5 Approaches to Structure Comparison; 3.6 The DALI Algorithm 3.7 The SSAP Algorithm Used for Fold Recognition in CATH3.8 Fast Approximate Methods Used to Recognize Folds in CATH; 3.9 Measuring Structural Similarity; 3.10 Multiple Structure Alignment; 3.11 Classification Protocols; 3.12 Population of the Hierarchy; 3.13 Comparisons Between Scop and CATH; 3.14 Hierarchical Classifications Versus Structural Continuum; 3.15 Websites; References; Chapter 4 Structural Annotations of Genomes with Superfamily and Gene3D; 4.1 Introduction; 4.2 The Importance of Being High Throughput; 4.3 The Use of Structural Information; 4.4 Applications; 4.5 History 4.6 Technology4.7 Hidden Markov Models; 4.8 Building Models; 4.9 Domain Annotations; 4.10 High Throughput Computation; 4.11 Development of New Bioinformatics Algorithms; 4.12 Genomes; 4.13 e-Value Scores; 4.14 Other Sequence Sets; 4.15 Data Access; 4.16 Analysis Tools; 4.17 Conclusion; References; Chapter 5 Phylogenomic Databases and Orthology Prediction; 5.1 The Evolution of Novel Functions and Structures in Gene Families; 5.2 Homologs, Orthologs, Paralogs, and Other Evolutionary Terms; 5.3 The Standard Functional Annotation Protocol; 5.4 Orthology Identification Methods and Databases 5.5 Challenges in Phylogenetic Methods of Ortholog Identification5.6 Evaluating Ortholog Identification Methods; 5.7 Orthology Databases; 5.8 Phylogenomic Databases; 5.9 PhyloFacts; 5.10 Subfamily Classification in Phylofacts; 5.11 PhyloFacts 3.0; 5.12 PhylomeDB; 5.13 Panther; 5.14 Structural Phylogenomics: Improved Functional Annotation Through Integration of Information from Structure and Evolution; 5.15 Specific Issues in Phylogenomic Pipelines; 5.16 Improving Functional Inference using Information from Protein Structure; 5.17 Example Case Studies; 5.18 Review of Key Points; References Part II In-Depth Reviews of Protein Families |
| Record Nr. | UNINA-9910823125703321 |
| Hoboken, New Jersey : , : Wiley, , [2014] | ||
| Materiale a stampa | ||
| Lo trovi qui: Univ. Federico II | ||
| ||