Understanding BioinformaticsSuitable for advanced undergraduates and postgraduates, Understanding Bioinformatics provides a definitive guide to this vibrant and evolving discipline. The book takes a conceptual approach. It guides the reader from first principles through to an understanding of the computational techniques and the key algorithms. Understanding Bioinformatics is an invaluable companion for students from their first encounter with the subject through to more advanced studies. The book is divided into seven parts, with the opening part introducing the basics of nucleic acids, proteins and databases. Subsequent parts are divided into 'Applications' and 'Theory' Chapters, allowing readers to focus their attention effectively. In each section, the Applications Chapter provides a fast and straightforward route to understanding the main concepts and 'getting started'. Each of these is then followed by Theory Chapters which give greater detail and present the underlying mathematics. In Part 2, Sequence Alignments, the Applications Chapter shows the reader how to get started on producing and analyzing sequence alignments, and using sequences for database searching, while the next two chapters look closely at the more advanced techniques and the mathematical algorithms involved. Part 3 covers evolutionary processes and shows how bioinformatics can be used to help build phylogenetic trees. Part 4 looks at the characteristics of whole genomes. In Parts 5 and 6 the focus turns to secondary and tertiary structure - predicting structural conformation and analysing structure-function relationships. The last part surveys methods of analyzing data from a set of genes or proteins of an organism and is rounded off with an overview of systems biology. The writing style of Understanding Bioinformatics is notable for its clarity, while the extensive, full-color artwork has been designed to present the key concepts with simplicity and consistency. Each chapter uses mind-maps and flow diagrams to give an overview of the conceptual links within each topic. |
Contents
Background Basics | 1 |
Evolutionary Processes | 7 |
Translation involves transfer RNAs | 13 |
Gene Detection and Genome Annotation | 45 |
Dealing with Databases | 46 |
22 | 52 |
Automated methods can be used to check for data | 63 |
amino acids are due to their side chains | 67 |
NetPlantGene uses neural networks with | 395 |
Comparison of related genomes can help resolve | 403 |
Secondary Structures | 409 |
Secondary Structures | 435 |
What to choose | 447 |
of the COILS algorithm | 453 |
Theory Chapter | 461 |
APPLICATIONS CHAPTER | 469 |
Sequence Alignments | 69 |
Applications Chapter | 71 |
The PAM substitution matrices use substitution | 104 |
Theory Chapter | 115 |
109 | 153 |
Summary | 159 |
Alignments | 165 |
The BLOSUM matrices were designed to find | 171 |
126 | 179 |
Optimal global alignments are produced using | 187 |
Time can be saved with a loss of rigor by | 193 |
Theory Chapter | 267 |
Evolutionary Processes | 271 |
232 | 278 |
Different codon positions have different | 285 |
249 | 291 |
All phylogenetic analyses must start with | 297 |
Applications Chapter | 315 |
Bayesian methods can also be used to reconstruct | 341 |
APPLICATIONS CHAPTER | 354 |
Theory Chapter | 357 |
Homology can be used to identify genes in both | 361 |
A set of models has been designed to locate | 383 |
Predicting eukaryotic transcription | 389 |
The simplest prediction methods are based on | 476 |
Predictions can be significantly improved | 484 |
Tertiary Structures | 519 |
Molecular dynamics and simulated annealing | 528 |
Closely related target and template sequences give | 539 |
The modeled core is checked for misfits before | 545 |
How far can homology models be trusted? | 551 |
SwissPdb Viewer can be used for manual | 557 |
Fragment docking identifies potential substrates | 591 |
Cells and Organisms | 597 |
The water molecules in binding sites should also | 622 |
Serial analysis of gene expression SAGE is also | 628 |
Selforganizing tree algorithms SOTAs cluster | 635 |
614 | 641 |
The validity of clusters is determined | 650 |
APPENDICES Background Theory | 695 |
660 | 698 |
Systems Biology | 704 |
Function Optimization | 709 |
678 | 711 |
Living systems can switch from one state | 721 |
The choice of substitution matrix depends on | 737 |
| 751 | |