Bioinformatic Algorithms - 1st Edition - ISBN: 9780128125205

Bioinformatic Algorithms

1st Edition

Design and Implementation in Python

Authors: Miguel Rocha Pedro G. Ferreira
Paperback ISBN: 9780128125205
Imprint: Academic Press
Published Date: 1st June 2018
Page Count: 420
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Description

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.

Key Features

  • 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

Readership

Bioinformatics and Computational Biology researchers, biomedical engineers, as well as undergrad and postgraduate students in Bioinformatics and Computational Biology

Table of Contents

Part I: Bioinformatics Basics
1. Introduction
2. Relevant Biological Concepts
3. Algorithms and Python: Introduction
4. Optimization: Basic Concepts and Algorithms

Part II: Sequence Analysis Algorithms
5. Basic Processing of DNA Sequences: Transcription and Translation
6. Finding Patterns in Sequences
7. Pairwise Sequence Alignment
8. Searching Similar Sequences in Databases
9. Multiple Sequence Alignment
10. Phylogenetic Analysis
11. Motif Discovery
12. Hidden Markov Models
13. Stochastic Algorithms

Part III: Graph and Large-Scale Sequencing Data Processing
14. Graphs
15. Biological Networks
16. Assembling Reads into Genomes
17. Matching Reads to Reference Sequences

Part IV: Conclusions
18. Further Reading and Resources
19. Final Words

Appendix: Python Reference Functions

Details

No. of pages:
420
Language:
English
Copyright:
© Academic Press 2018
Published:
Imprint:
Academic Press
Paperback ISBN:
9780128125205

About the Author

Miguel Rocha

Miguel Rocha is an Associate Professor at the University of Minho (Portugal), where he

teaches in the Informatics Department and has a senior researcher position in the Centre

of Biological Engineering. He is the Director and founder of the Master in Bioinformatics

since 2007, teaching and coordinating curricular units related to Bioinformatics algorithms

and tools, data analysis and machine learning. His research is mainly devoted to

Bioinformatics subjects, including the development of tools and algorithms for metabolic

modelling andomics data analysis.

Affiliations and Expertise

Associate Professor of Informatics and Senior Researcher, University of Minho, Portugal

Pedro G. Ferreira

Pedro G. Ferreira is an Assistant Researcher at Ipatimup/i3S (Portugal), where he has an FCT Investigator Starting grant. He develops research on computational biology in particular in the fields of cancer and population genomics. He has collaborated with several research groups and has been involved in different international consortia including ICGC-CLL, GEUVADIS or GTEx. He has intensive training in Bioinformatics and experience in genomics start-up environment where he has developed information systems for personal genomics data interpretation.

Affiliations and Expertise

Assistant Researcher, Ipatimup/i3S, Portugal