Lecture Notes for INF281 Basics of Bioinformatics Sequence Analysis

This repository contains the sources files of the lecture notes for INF281 Basics of bioinformatics sequence analysis. The generated PDFs are available on the Release page.

INF281 Exercises and Solutions are availabe here.

Course description

Prerequisites

Only basic mathematical background is required. We cover several mathematical concepts where needed. We assume that you know how to read and write basic computer programs, preferably in Java.

Learning Outcomes

After completing the course you should be able to: explain the basis of molecular biology pertaining to the course,

make local or global pairwise alignments by dynamic programming,
compare pairwise and multiple sequence alignment algorithms in terms of challenges and applications,
perform sequence based searches in biological databases and subsequent statistical analyses on the search results,
review classification performance measures in the fields of biological sequence analysis, and
create working implementations of basic bioinformatics algorithms.

Course structure

PART I Introduction

Introduction

PART II Pairwise alignment

Global pairwise alignment
Expansion of scoring scheme
Local pairwise alignment

PART III Database search and statistical evaluation

Database search and BLAST
Evaluation of alignment scores
Model evaluation

PART IV Multiple alignment and phylogenetic tree

Multiple alignment
Phylogenetic tree
Progressive alignment and CLUSTAL

PART V Scoring scheme and sequence patterns

Score matrix
Sequence profiles
Hidden Markov model
Sequence patterns

PART VI RNA structure prediction

RNA structure prediction

Readings

PROTEIN BIOINFORMATICS

An Algorithmic Approach to Sequence and Structure Analysis

I. Eidhammer, I. Jonassen, and W.R.Taylor

Chapters 1-7, Appendix A, B
Print ISBN: 9780470848395
Online ISBN: 9780470092620
DOI: 10.1002/9780470092620

takayasaito/INF281-Lecture-Notes