Courses: INF281 Basics of bioinformatics sequence analysis - Spring 2017

Credits

10.0

Language of Instruction

English

Teaching semester

Spring.

Objectives and Content

The course covers the basics of bioinformatics sequence analysis, in particular the analysis of protein sequences, rounded off with RNA secondary structure prediction for comparison. Topics covered are global and local pairwise alignment, multiple alignment, phylogenetic trees, score matrices, protein database search, p- and Evalues, measures of classification performance, profiles, Hidden Markov Models, sequence patterns, and prediction of RNA secondary structure. The course also briefly reviews the necessary basics of Molecular Biology.

Learning Outcomes

At the end of the course a student should be able to:
- paraphrase the molecular biology and evolution basics pertaining to the course and connect them with the various algorithms
- compare technical aspects of pairwise local and global sequence alignment algorithms
- compare pairwise and multiple sequence alignment in terms of challenges and application
- review classification performance measures in the fields of biological sequence analysis
- create working implementations of basic bioinformatics algorithms

Required Previous Knowledge

Recommended Previous Knowledge

Students need to be able to implement basic algorithms in a programming language of their choice. A basic understanding of algorithms and efficiency is required.

Access to the Course

Access to the course requires admission to a programme of study at The Faculty of Mathematics and Natural Sciences.

Compulsory Assignments and Attendance

Compulsory exercises

Forms of Assessment

Written exam. If less than 20 students take the course, an oral exam might be arranged.
Compulsory exercises count towards the final grade.

Examination Support Material

Non-programmable calculator, according to the faculty regulations.

Grading Scale

The grading scale used is A to F. Grade A is the highest passing grade in the grading scale, grade F is a fail.

Subject Overlap

INF280: 5 ECTS, INF282: 5 ECTS

Assessment Semester

Examination both spring semester and autumn semester. In semesters without teaching the examination will be arranged at the beginning of the semester.

Programme Committee

The Programme Committee is responsible for the content, structure and quality of the study programme and courses.