General information

Module title Bioinformatics – principles of biological sequences analysis by example
Language English
Module lecturer prof. dr hab. Wojciech Karłowski
Lecturer's email wmk@amu.edu.pl
Lecturer position profesor
Faculty Faculty of Biology
Semester 2021/2022 (winter)
Duration 50
ECTS 6
USOS code 01-BIOLSEQ-PIE

Timetable

Module aim (aims)

The aim of the course is to provide the students with the basic knowledge of the theoretical basics of biological sequence analysis and to develop skills necessary for 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 informationWeek 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 systemsWeek 6 Pairwise sequence alignments – methods, tools and applicationsWeek 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 FASTAWeek 9 Motifs in biological sequences – consensus sequences vs. sequence profilesWeek 10 Multiple sequence alignments – methods, tools and applicationsWeek 11 Molecular phylogeny – principles and tools for evolutionary analysis using sequence dataWeek 12 RNA secondary structure prediction and its applicationsWeek 13 Principles and data processing of modern high-throughput sequencing technologiesWeek 14 From sequence to function – major steps and methods in genomic DNA annotationWeek 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)