Techniques and Tools for Bioinformatics

• Weekly hours
• Competences
• Objectives
• Contents
• Activities
• Teaching methodology
• Evaluation methodology
• Bibliography

Teachers

Person in charge

• Gabriel Valiente Feruglio ( )
• Xavier Messeguer Peypoch ( )

Weekly hours

Competences

Technical Competences of each Specialization

Direcció i gestió

• CDG1 - Capability to integrate technologies, applications, services and systems of Informatics Engineering, in general and in broader and multicisciplinary contexts.

Especifics

• CTE7 - Capability to understand and to apply advanced knowledge of high performance computing and numerical or computational methods to engineering problems.
• CTE9 - Capability to apply mathematical, statistical and artificial intelligence methods to model, design and develop applications, services, intelligent systems and knowledge-based systems.

Generic Technical Competences

Generic

• CG4 - Capacity for mathematical modeling, calculation and simulation in technology and engineering companies centers, particularly in research, development and innovation tasks in all areas related to Informatics Engineering.

Transversal Competences

Information literacy

• CTR4 - Capability to manage the acquisition, structuring, analysis and visualization of data and information in the area of informatics engineering, and critically assess the results of this effort.

Basic

• CB6 - Ability to apply the acquired knowledge and capacity for solving problems in new or unknown environments within broader (or multidisciplinary) contexts related to their area of study.

Objectives

1. Understand pattern matching algorithms and data structures and their implementation in a modern programming language, and apply them to solve practical problems in bioinformatics.
   Related competences: CB6, CTR4, CDG1, CTE7, CTE9, CG4,

Contents

1. Efficient search algorithms and data structures
   The most efficient algorithms for searching for patterns in texts based on the alphabet and the length and number of patterns will be shown. Data structures that are very useful for comparing genomes such as suffix trees, suffix arrays and the Burrows-Wheeler transform, will also be explained.
2. Sequence alignment
   Dynamic programming will be explained and we will discuss its application to compute the edit distance between two words, to the approximate search of a word in a text and to find the best alignment between two sequences. We will also study how to generalize the alignment to multiple sequences.
3. Data base searching: BLAST
   The computational and statistical foundations of the BLAST algorithm and its use for approximate searches in databases will be introduced.
4. Alignment of degenerate strings
   The generalization to pangenomes of pattern search problems will be explained and the extensions of the Boyes-Moore algorithm and the Burrows-Wheeler transform for the alignment of degenerate sequences will be introduced.

Activities

Activity Evaluation act

Teaching methodology

Evaluation methodology

Bibliography

Basic:

• Genome-scale algorithm design : bioinformatics in the era of high-throughput sequencing - Mäkinen, Veli; Belazzougui, Djamal; Cunial, Fabio; Tomescu, Alexandru I, Cambridge University Press, 2023. ISBN: 9781009341233
  https://discovery.upc.edu/permalink/34CSUC_UPC/8e3cvp/alma991005219277706711

Complementary:

• Bioinformatics : sequence and genome analysis - Mount, David W, Cold Spring Harbor Laboratory Press , cop. 2004. ISBN: 0879696877
  https://discovery.upc.edu/permalink/34CSUC_UPC/8e3cvp/alma991002934579706711