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Software

As part of our research effort we design software tools.

DNA origami design software

In 2008 we developed the SARSE RNA design package. It will be made available here as a historical reference. The Cadnano software has become the standard for DNA origami design (link). We have published a tutorial for DNA origami design (link to book chapter).

RNA design software

RNA sequence design algorithms

H-bonds geometry server

Research documentation and collaboration

AU Labbook is a web-based system for research documentation and collaboration (found at labbook.au.dk). Labbook was established by iNANO researchers and is based on Confluence. The system is now supported and run by the Faculty of Science and Technology and is offered (and recommended) as a platform for documenting your research. The decision to use the system for research documentation lies with the VIP of a research group. By choosing a common platform for research documentation it becomes easier for the individual researcher to follow the rules for responsible conduct of research.

 

 

Here you find a list of programs and scripts that are useful tools for RNA design.

Ligate.pl (perl script)

Trace.pl (perl script)

Swiss PDB Viewer

Swiss-PdbViewer (aka. DeepVeiw) is a 3D modeling software that can be used to display and manipulate multiple pdb structures at the same time. Furthermore, the program has an interface that provides a good overview of the structure and its corresponding sequence. Although developed for proteins the program functions well for RNA structure modeling as well. The program can be used to align multiple RNA modules by hand.

The program can be downloaded from http://spdbv.vital-it.ch