Kaisa_2012_3_photo by Veikko Somerpuro

Enrol
13.8.2019 at 09:00 - 2.9.2019 at 23:59

Timetable

Description

Optional course.

Master's Programme in Computer Science is responsible for the course.

The course belongs to the Discrete Algorithms CSM12100 and Discrete Algorithms (elective) CSM22100 modules.

The course is available to students from other degree programmes.

Some algorithms course and some bioinformatics course.

Biological Sequence Analysis

Other courses that support the further development of the competence provided by this
course: Research Seminar in Discrete Algorithms

Student

  • Can explain solutions / complexity of several core problems of fragment assembly, like read error correction, contig assembly, scaffolding, and gap filling.
  • Can describe reductions from several transcriptomics problems (genomes known/unknown, short/ long reads, sequence estimation / differential expression as the goal) to problems in graphs.
  • Can explain how splicing graphs and subpath constraints are derived using read alignments and co-linear chaining.
  • Can explain solutions / complexity of several evolution-related problems, like haplotype assembly, motif discovery, permutation patterns, perfect phylogeny, and genome rearrangements.

Recommended time/stage of studies for completion:

After an earlier course in algorithms and earlier course in bioinformatics.

Term/teaching period when the course will be offered:

Spring term, period III, each odd year

The course covers selected algorithm design areas that have grown around molecular biology problems, including perfect phylogenies, genome rearrangements, and motif discovery, and some selected molecular biology problems in transcriptomics and genomics, that exploit reductions to graph problems.

The course follows a textbook partly: Mäkinen, Belazzougui, Cunial, Tomescu. Genome-Scale Algorithm Design. Cambridge University Press, 2015.

The course follows a lecture->study group->exercise cycle. The lecture gives an overview. The study group aims at in-depth understanding of selected topics. Exercises work as individual reflection, and also as mini-exams, as the grading is solely based on them.

There will be continuous assessment, as grading is based on the exercises. Half the exercise points gives 1 and some 80-90% gives 5.

Separate exams last 3 hours and 30 minutes. Renewal exam (marked with "(U)") is the first separate exam after the course and also a renewal exam of course exam(s). In a renewal exam the points student has earned during the course are taken into account. Exams marked with "(HT)" are allowed only to students who have completed the obligatory projects or other exercises included in those courses. Exams marked with "(HT/U)" are renewals to students who have completed the obligatory projects during the course. Separate exams might cover different area than the lectured course. Check the course web page and contact the responsible teacher if in doubt.

Assessment will be by exercises. No course exam.

Alternatively one can take a separate exam.