Analysis of Amino Acid Sequences
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Table of contents
- CONTENTSv
- PREFACExi
- Chapter 1. Mass Spectrometric Analysis of Proteins1
- I. Introduction1
- II. Ionization Techniques and Mass Spectrometers2
- III. Protein Identification and Sequencing with Mass Spectrometry7
- IV. Characterization of Posttranslational Modifications with Mass Spectrometry17
- V. Applications of Protein Characterization with Mass Spectrometry: Proteomics24
- References28
- Chapter 2. Protein Sequence Databases31
- I. Introduction31
- II. Protein Information Resource32
- III. SWISS-PROT32
- IV. TrEMBL47
- V. Swiss-prot + TrEMBL: A Complete and Nonredundant View on Protein World65
- VI. Specialized Protein Sequence Databases68
- References70
- Chapter 3. Amino Acid Substitution Matrices73
- I. Introduction73
- II. Scoring Basics74
- III. Theory77
- IV. Models for Substitution Scores78
- V. Special Substitution Scores82
- VI. Gap Scores83
- VII. Evaluating Scoring Functions87
- VIII. Position-Specific Scores91
- IX. Using Multiple Substitution Matrices94
- X. Conclusions95
- References96
- Chapter 4. Amino Acid-Based Phylogeny and Alignment99
- I. Introduction99
- II. Trees102
- III. Sequences109
- IV. Multiple Alignment.115
- V. Phylogenetic Reconstruction120
- References133
- Chapter 5. Searching Databases to Find Protein Domain Organization137
- I. Introduction137
- II. Protein Domains138
- III. Domain Databases143
- IV. Finding New Domains148
- V. Profile Methods149
- References155
- Chapter 6. Identifying Nature’s Protein Lego Set159
- I. Introduction159
- II. Background160
- III. Methods.167
- IV. Validation and Comparison175
- V. Sensitivity and Specificity177
- VI. Domain Recognition180
- VII. Conclusions180
- References182
- Chapter 7. Evolution of Domain Families185
- I. Introduction185
- II. Domain Families in Archaea, Bacteria, and Eukarya213
- III. Domain Orginating Early in Eukaryotic Lineage222
- IV. Domain Families in Multicellular Organisms232
- V. Domains in Diverse Molecular Contexts234
- VI. Conclusions237
- References237
- Chapter 8. Protein Fold Recognition Using Sequence Profiles and Its Application in Structural Genomi245
- I. Introduction246
- II. Detecting Nontrivial Structural and Evolutionary Relationships between Proteins Using Position-S248
- III. Application of PSSMs in Structural-Genomic Analysis257
- IV. Conclusions and Perspective269
- References270
- Chapter 9. Protein Sorting Signals and Prediction of Subcellular Localization277
- I. Introduction277
- II. Sorting of Bacterial Proteins278
- III. Sorting of Eukaryotic Proteins.302
- IV. Concluding Remarks330
- References331
- Chapter 10. Gene and Context: Integrative Approaches to Genome Analysis345
- I. Introduction345
- II. Measuring Genome Evolution347
- III. Gene and Function Prediction by Conservation of Genomic Context357
- IV. Variation of Genomic Context369
- V. Discussion375
- References376
- Chapter 11. Pathway Databases and Higher Order Function381
- I. Introduction381
- II. KEGG Pathways and Ortholog Groups383
- III. Prediction of Higher Order Function396
- IV. Concluding Remarks406
- References407
- Chapter 12. Individual Variation in Protein-Coding Sequences of Human Genome409
- I. Introduction409
- II. Polymorphism versus Mutation„Neutral Drift versus Selection412
- III. Population Dynamics of Sequence Variation412
- IV. Species Difference versus Intraspecies Variation415
- V. Studies on Single-Nucleotide Polymorphism415
- VI. ESTs as Data Source418
- VII. Conclusions432
- VIII. References433
- AUTHOR INDEX439
- SUBJECT INDEX467
Amino acid sequence analysis is useful for the study of problems ranging from modifications of single molecules to complex networks and interactions of species. Many available amino acid sequences are providing the basis for various studies at the proteome level.
The dynamics of protein expression and the simulation of complex biological systems in which proteins interact with certain kinetics and in their respective compartments are just about to be tackled. Amino acid sequences will be crucial reference points for such studies.
Key Features
* Mass spectrometric analysis of proteins
* Protein sequence databases
* Amino acid substitution matrices
* Amino acid-based phylogeny and alignment
* Individual variation in protein-coding sequences of the human genome
* Identifying nature's protein Lego(r) set
The dynamics of protein expression and the simulation of complex biological systems in which proteins interact with certain kinetics and in their respective compartments are just about to be tackled. Amino acid sequences will be crucial reference points for such studies.
Key Features
* Mass spectrometric analysis of proteins
* Protein sequence databases
* Amino acid substitution matrices
* Amino acid-based phylogeny and alignment
* Individual variation in protein-coding sequences of the human genome
* Identifying nature's protein Lego(r) set