Computational Molecular Biology

Spring 2019

( Last update: 17-6 2019 )
Reminder: Final Retake on Tuesday June 18th 14.00 - 17.00 in Room B02.


Organizer: Dr. Alexander P. Goultiaev and Dr Erwin M Bakker

Assistant: -


Period: February - May 2019

Place:   Room 401 (LIACS, Snelliusgebouw)

Time:   Tuesday 13.30 - 15.15




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. RNA structure prediction will be discussed whereby methods based on energy minimization, comparative analysis as well as folding simulations are covered. 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, bio polymer design, and protein protein docking and interaction will be studied.



There will be several assignments and a final exam. The grade will be based on the assignments (40%) and the exam (60%).

The grade for the exam should always be greater than 5.

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.

Furthermore, 4 sets 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.



Date: Wednesday May 29th 2019

Time: 14.00 - 17.00

Place:  Snellius Room B03


Date: Tuesday June 18th 2019

Time: 14.00 - 17.00

Place:  Snellius Room B02


Materials: All lecture slides, together with the materials

                  listed under the Materials Section on this web-page.

                  Please note, it is a closed book exam.

Sample Exams: 2014 , 2015, 2016, 2017, 2018

Schedule (tentative, will be regularly update, please check before each lecture!:



  Subject   Slides
5-2   Sequence Alignment
  slides & homework
12-2   Multiple Sequence Alignment
19-2   Multiple Sequence Alignment (k-mers)
  slides & homework & sequences
26-2   Introduction Bioinformatics and CMB
5-3   RNA Structure Prediction
  RNA Motifs
  slides & assignments
19-3   Next Generation Sequencing I (BWT)   slides
26-3   Next Generation Sequencing II   slides
2-4   Lab Review.
9-4   Novel Methods and Algorithms for CMB I
16-4   Protein 3D Structure Prediction   slides & assignment
23-4   Bio Polymer Design   slides
30-4   Protein Protein Docking and Interaction   slides & solutions
  Novel Methods and Algorithms for CMB II   slides & Final Assignment


Note: Slides or reading materials will be available the day before the lectures.


Lecture Notes


  1. Lab Assignment 1.

  2. Lab Assignment 2.

  3. Lab Assignment 3.

  4. Final Assignment.


Exam Materials (Please note: This list is tentative, it will be updated after each lecture!)


Lecture 1

  1. EMBL, Ensembl, UniProt

  2. NCBI, ENTREZ, GenBank

  3. DDBJ

  4. Introduction to molecular biology. (for reference only, not exam material)


End Exam Materials



Other Self-Study Materials (will not be examined):



Databases publicly available on the web:

Database Function Organization Address
GenBank Nucleotide National Center for Biotechnology Information BLAST!
  search ENTREZ for:

EMBL Nucleotide European Bioinformatics Institute
SWISSPROT Amino acid Swiss Institute of Bioinformatics
  ExPASy (Expert Protein Analysis System) proteomics server
PSIPRED Protein structure
  Protein Structure Prediction Server
MFOLD RNA structure Bioinformatics Center at Rensselaer and Wadsworth