A vast amount relevant of software and browser based tools is available on the internet. This page mentions a few important ones.


You can use NaviGene as a guide to the following applications.

3D protein visualisation

Studying proteins is an important subject in bioinformatics. Several programs that enable you to look at protein structures in 3D exist. This kind of software also enables you to introduce mutations and combine different structures (enzyme-substrate complexes). Using these methods, bioinformaticians can predict protein functions, active sites and even unknown protein structures.

The bioinformatics department at the Radboud University uses Yasara. For education purposes it is best to use our adapted version of Yasara which can be downloaded here. A free version of the software is available at A brief introduction can be downloaded here. Yasara itself also features some tutorials, which you can find at ‘help movies’ in the navigation bar.

Another example of a visualisation program is Jmol. Protein files can be downloaded from the PDBdatabase. Protopedia might help you with finding the right protein.


Bioinformaticians compare genes and proteins by looking at the basepair and amino acid sequences. In an alignment, the basepairs or amino acids of two or more sequences are compared one by one. The higher the similarity, the higher the alignment score.

ClustalOmega is an online tool with exactly this function. You can find instructions for it in NaviGene on page 9. When comparing multiple sequences, the software comes up with a fylogenetic tree based on the individual alignment scores.