Bioinformatics Algorithms

Miguel Rocha is an Associate Professor at the University of Minho (Portugal), where heteaches in the Informatics Department and has a senior researcher position in the Centreof Biological Engineering. He is the Director and founder of the Master in Bioinformaticssince 2007, teaching and coordinating curricular units related to Bioinformatics algorithmsand tools, data analysis and machine learning. His research is mainly devoted toBioinformatics subjects, including the development of tools and algorithms for metabolicmodelling andomics data analysis. 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.

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