INF5340 – Algorithms in bioinformatics
Course content
The course covers many of the algorithms that form the basis for a wide range of practical computer tools used particularly for sequence analysis, but also for other types of analysis in bioinformatics. Both classical and modern methods will be studied in great detail, including the algorithms for pairwise and multiple sequence alignments (e.g. BLAST, SSAHA), creation of and searching with sequence profiles and Hidden Markov models (e.g. PSI-BLAST, HMMer). Selected other subjects may also be included (e.g. protein or RNA structure predictions, literature analysis, gene finding).
Learning outcome
The course is suitable for master and PhD students and should give a solid basis for understanding how some of the important algorithms in bioinformatics work and why they are able to solve the problems they are designed for. It should be an excellent background for those who want to fully exploit existing tools and for those who want to develop their own bioinformatics tools. The assignments will include reimplementation of core parts of some of the algorithms.
Admission
Students who are admitted to study programmes at UiO must each semester register which courses and exams they wish to sign up for in Studentweb.
If you are not already enrolled as a student at UiO, please see our information about admission requirements and procedures.
Prerequisites
Recommended previous knowledge
INF1020 – Algorithms and data structures (discontinued), INF2300 – Grunnkurs i bioinformatikk (discontinued)/INF3350 – Grunnkurs i bioinformatikk (discontinued)/INF4350 – Introductory Course in Bioinformatics (continued)/INF5330 – Bioinformatikk (discontinued)/INF325 and INF3330 – Problem solving with high level languages (discontinued)/ INF4330 – Problem solving with high level languages (discontinued).
Teaching
2 hours lectures and 2 hours tuition every week. Two mandatory
assignments must be completed and accepted during the course in order to be allowed to take the final exam.
Examination
Oral exam.
Grading scale
Grades are awarded on a scale from A to F, where A is the best grade and F is a fail. Read more about the grading system.
Resit an examination
This subject does not offer new examination in the beginning of the subsequent term for candidates who withdraw during an ordinary examination or fail an ordinary examination. For general information about new examination, see /studier/admin/eksamen/sykdom-utsatt/mn/index.html and www.matnat.uio.no/english/studies/examination/repeat.html