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Undergraduate course

Basics of bioinformatics sequence analysis

ECTS Credits

10

Level of Study

Bachelor/master

Full-time/Part-time

Full-time

Teaching semester

Spring.

Objectives and Content

The course covers the basics of bioinformatics sequence analysis, in particular the analysis of protein sequences. Topics covered are global and local pairwise alignment, multiple alignment, phylogenetic trees, score matrices, protein database search, p- and e-values, measures of classification performance, profiles, hidden Markov models, and sequence patterns. The course also briefly reviews the necessary basics of molecular biology.

Learning Outcomes

On completion of the course the student should have the following learning outcomes defined in terms of knowledge, skills and general competence:

  • understand and be able to explain basics of molecular biology and evolution pertaining to sequence alignment and connect them with the various algorithms
  • be able to compare technical aspects of pairwise local and global sequence alignment algorithms
  • be able to compare pairwise and multiple sequence alignment algorithms and their computational complexity linked to their application
  • be able to use and understand different classification performance measures in the fields of biological sequence analysis
  • be able to create working implementations of basic bioinformatics algorithms and to use such algorithms for analysis of concrete data

Required Previous Knowledge

None

Recommended Previous Knowledge

Be able to implement basic algorithms in a programming language of your own choice. A basic understanding of algorithms and efficiency is required

Credit Reduction due to Course Overlap

INF280: 5 ECTS, INF282: 5 ECTS

Access to the Course

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

Teaching and learning methods

Lectures, 4 hours per week

Exercises, 2 hours per week

Compulsory Assignments and Attendance

Compulsory exercises are valid for one subsequent semester.

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.

Assessment Semester

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

Reading List

The reading list will be available within June 1st for the autumn semester and December 1st for the spring semester

Course Evaluation

The course will be evaluated by the students in accordance with the quality assurance system at UiB and the department

Programme Committee

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

Course Coordinator

Course coordinator and administrative contact person can be found on Mitt UiB, or contact mailto:studieveileder@ii.uib.no Student adviser

Course Administrator

The Faculty of Mathematics and Natural Sciences represented by the Department of Informatics is the course administrator for the course and study programme.

Contact

Contact Information

Student adviser:

mailto:studieveileder@ii.uib.no Student adviser

T: 55 58 42 00

Exam information

  • For written exams, please note that the start time may change from 09:00 to 15:00 or vice versa until 14 days prior to the exam. The exam location will be published 14 days prior to the exam.

  • Type of assessment: Written examination

    Date
    25.05.2018, 15:00
    Duration
    3 hours
    Withdrawal deadline
    11.05.2018
    Location