Bioinformatics – Principles Of Biological Sequences Analysis By Example

Timetable

Module aim (aims)

The aim of the course is to provide the students with the basic knowledge of the theoretical aspects of biological sequence analysis and to help to develop skills necessary for the utilization of bioinformatic tools and biological databases. The lectures are focused on the demonstration of the principles underlying commonly used bioinformatic techniques. Topics will cover molecular biology databases, sequence alignments, phylogenetic analysis, homologous sequence searches, RNA analysis and identification of sequence motifs.

Pre-requisites in terms of knowledge, skills and social competences (where relevant)

Basics of molecular biology

Syllabus

Week 1 What is bioinformatics and how can I benefit from it? Week 2 Biological databases – primary and secondary sources of information Week 3 Sequence data formats and annotations – how to read sequence database records? Week 4 Introduction to perl scripting language – how to make life of a biologist easier and do the work faster? Week 5 Searching molecular data resources – NCBI Entrez and EBI SRS – integrated biological database systems Week 6 Pairwise sequence alignments – methods, tools and applications Week 7 Substitution tables for sequence comparison – how to choose the correct parameters for the analysis? Week 8 Identification of similar sequences within biological databases – BLAST and FASTA Week 9 Motifs in biological sequences – consensus sequences vs. sequence profiles Week 10 Multiple sequence alignments – methods, tools and applications Week 11 Molecular phylogeny – principles and tools for evolutionary analysis using sequence data Week 12 RNA secondary structure prediction and its applications Week 13 Principles and data processing of modern high-throughput sequencing technologies Week 14 From sequence to function – major steps and methods in genomic DNA annotation Week 15 Current trends and challenges in bioinformatics.

Reading list

1. David S. Mount Bioinformatics: Sequence and Genome Analysis, Cold Spring Harbor Laboratory Press, 2004. (ISBN:0879697121)2. Arthur Lesk Introduction to Bioinformatics, Oxford University Press, 2008. (ISBN:0199208042)