Course: Comparative Genomics: from evolution to function (2nd edition)


June 2 – June 6, 2014, Amsterdam


  • dr. Berend Snel (UU)
  • prof. dr. Martijn Huynen (Radboudumc)
  • prof. dr. Jaap Heringa (VU Amsterdam)
  • dr. Celia van Gelder (NBIC/BioSB)


VU University, Amsterdam, the Netherlands


This course is made possible by the generous support of Gencodys.

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Target audience

The course is intended for PhD students and master students in bioinformatics, especially those interested in evolution and/or those who want to compare various genomics data between species. Participants are expected to have some hands on experience with blast, constructing multiple sequence alignments and phylogenetic trees, and in addition to have some familiarity with concepts such as orthology, synteny and protein domains.


Comparative genomics between species and between types of data facilitates the understanding of what these data really reflect about the underlying processes. Comparative genomics therewith relies on a solid understanding of basic elements of Bioinformatics like homology and orthology. Moreover it is important to know the assumptions and heuristics of bioinformatic methods for comparative genomics and hence we aim to let participants develop an understanding of why they fail (or misdetect) as a consequence of a variety of biological /evolutionary causes.

The first two days of the course provide a basis for the course with the aim to move “beyond blast” in terms of more sensitive homology searches, domain level analysis of protein evolution as well as more fine grained definitions of relatedness as can be obtained from the proper interpretation of gene trees (i.e. various levels of orthology).This foundation is used to discuss in the three following days in more detail three topics: (1) the study of  functional and evolutionary consequence of (genome) duplications, (2) the evolution of interactions and complexes and (3) the prediction and evolution of genomic regulatory elements.


For the latest version of the programme, please click here.

Monday June 2: Distant homology and protein domains  (lecturer Jaap Heringa)
Topics & Tools: Divergent and convergent evolution, (multiple) sequence alignment,  psiblast, hhsearch, pfam, homology and function, undetected orthology from failure to detect homology, paralogs and function specificity prediction

Tuesday June 3: Comparative Interactomics  (lecturers Jaap Heringa, Martijn Huynen/John van Dam)
Topics & Tools: network alignment, phylogenetic profiles, biogrid, cytoscape, Bayesian data integration, neofunctionalization vs subfunctionalization

Wednesday June 4: Small scale orthology and large scale databases  (lecturers Martijn Huynen, Berend Snel)
Topics & Tools: tree reconciliation, relation between homology and orthology, ensembl compara, COGs, inparalogs vs outparalogs, fusion and fission

Thursday June 5: Genome duplications (lecturer Berend Snel)
Topics & Tools: yeast gene order browser, synteny, consequences of genome duplications, timing of duplications, ensembl biomart

Friday June 6: Finding functional elements in DNA and RNA sequences, Biased gene conversion (lecturer Martijn Huynen)
Topics & Tools: phylogenetic footprinting, (phylogeny aware) gibbs sampling, RNA secondary structure prediction based on sequences and on experimental data, biased gene conversion & positive selection.

Daily time schedule

09:00-10:30 lectures
10.30-11.00 coffee break
11.00-12.00 discussion preparation
12.00-12.30 discussion and evaluation
12:30-13:30 lunch
13:30-16:30 computer exercises and wrap-up


Papers will be sent to the participants before the course. You are strongly advised to read the papers before the start of the course. On each day the group of participants will be split in two subgroups. One subgroup will have to defend the paper and one subgroup will have to critique the paper. Each subgroup will have approximately an hour to discuss each article in order to prepare a defense or a critique. After a short break we will then have the discussion.

Travel and lodging

More information will be sent to the course participants before the course.

Registration and course fee

Registration closed.

More information

For more information about the course programme you can contact us at