Bioinformatics Algorithms: Design and Implementation in Python

ISBN-13: 9780128125205 / Angielski / Miękka / 2018 / 400 str.

Miguel Rocha; Pedro G. Ferreira

Opis

Bioinformatics Algorithms: Design and Implementation in Python provides a comprehensive book on many of the most important bioinformatics problems, putting forward the best algorithms and showing how to implement them. The book focuses on the use of the Python programming language and its algorithms, which is quickly becoming the most popular language in the bioinformatics field. Readers will find the tools they need to improve their knowledge and skills regarding algorithm development and implementation, and will also uncover prototypes of bioinformatics applications that demonstrate the main principles underlying real world applications.

• Presents an ideal text for bioinformatics students with little to no knowledge of computer programming
• Based on over 12 years of pedagogical materials used by the authors in their own classrooms
• Features a companion website with downloadable codes and runnable examples (such as using Jupyter Notebooks) and exercises relating to the book

Spis treści

Part I: Bioinformatics Basics1. Introduction2. Relevant Biological Concepts3. Algorithms and Python: Introduction4. Optimization: Basic Concepts and Algorithms

Part II: Sequence Analysis Algorithms5. Basic Processing of DNA Sequences: Transcription and Translation6. Finding Patterns in Sequences7. Pairwise Sequence Alignment8. Searching Similar Sequences in Databases9. Multiple Sequence Alignment10. Phylogenetic Analysis11. Motif Discovery12. Hidden Markov Models13. Stochastic Algorithms

Part III: Graph and Large-Scale Sequencing Data Processing14. Graphs15. Biological Networks16. Assembling Reads into Genomes17. Matching Reads to Reference Sequences

Part IV: Conclusions18. Further Reading and Resources19. Final Words

Appendix: Python Reference Functions