Computational Molecular Biology

Vakbeschrijving Computational Molecular Biology
Collegejaar: 2018-2019
Studiegidsnummer: 4343COMOB
Docent(en):
  • dr E.M. Bakker
  • Dr. A.P. Goultiaev
Voertaal: Engels
Blackboard: Nee
EC: 6.0
Niveau: 500
Periode: Semester 1 / 2
  • Wel Keuzevak
  • Geen Contractonderwijs
  • Wel Exchange
  • Wel Study Abroad
  • Geen Avondonderwijs
  • Geen A-la-Carte en Aanschuifonderwijs
  • Geen Honours Class

Admission requirements

C++, Bachelor's course Complexity.

Description

The course will cover both algorithms as well as practical aspects within the field of computation molecular biology. Important basic algorithms for pair wise alignment, computations of phylogenic trees, physical mapping of sequences, gene finding, multiple sequence alignment, heuristic sequence alignment and exact string matching will be discussed. Furthermore, the important field of protein structure prediction will be covered with the study of homology modeling, fold recognition, knowledge based potentials and ab initio methods for structure prediction. Finally RNA structure prediction will be discussed whereby methods based on energy minimization, comparative analysis as well as folding simulations are covered.

Course objectives

At the end of the course, students:

  • Will have acquired a thorough understanding of the basic algorithms for:


    • Sequence alignment
    • Models and Machine learning algorithms for bio-sequences.
    • Gene-finding
    • Profile and multiple alignment
    • Protein secondary and tertiary structure prediction
    • Next generation sequencing data processing
  • Will have acquired hands-on experience with several molecular biology applications of the important methods using the above listed algorithms.

Timetable

The most recent timetable can be found at the students' website.

Mode of instruction

  • Lectures
  • Workshops
  • Assignments
  • Reports



Course load



Hours of study: 168 (= 6 EC)
Lectures: 6 hrs
Practical work: 40 hrs
Exam: 22 hrs
Other (self-study): 80 hrs



Assessment method



“There will be several assignments and a final exam. The grade will be based on the assignments (40%) and the
exam (60%). The final grade will be determined using the formula: final grade = 0.6 * grade for the exam + 0.25 *
grade for the lab assignments + 0.15* the final assignment, where the grade for the exam should be >5.



Furthermore, after 4 lectures a set of lecture-assignments related to the contents of the slides will be handed out.
These will be graded either sufficient or insufficient. At least 3 of the 4 sets should be graded sufficient in order to
obtain a final grade.”



Reading list



Slides and other materials available on the website



Registration




  • You have to sign up for courses and exams (including retakes) in uSis. Check this link for information about how to register for courses.

Contact information

Lecturer: dr. Erwin bakker, dr. Alexandre Goultiaev
Website*: Computational Molecular Biology
* to be released soon.

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