As part of our research effort we design software tools.
The scripts were developed to aid the design of the single-stranded RNA origami structures we published in Science in 2014. We have also published a protocol describing the details of the RNA origami design process. Ligate is a Perl script that can merge several individual 3D RNA motifs within a PDB file into a single RNA structure. You can access the script and example files here: https://github.com/esa-lab/ligate. Trace is a Perl script that can trace a 2D blueprint of a single-stranded RNA origami structure, and output a code that can be used to design sequences in NUPACK that fold the desired RNA origami. You can access the script and example files here: https://github.com/esa-lab/trace. For usage please cite: A single-stranded architecture for cotranscriptional folding of RNA nanostructures. Geary, Rothemund, Andersen, Science 15 Aug 2014: Vol. 345, Issue 6198, pp. 799-804
In order to analyse the FRET output of single cells using confocal microscopy as was done in our apta-FRET paper, a MatLab program was developed: https://github.com/esa-lab/fretanalysis.
In 2008 we developed the SARSE - DNA origami design package. It is made available here as a historical reference. We also published a protocol for DNA origami design of 3D nanostructures using the SARSE software. The cadnano software has become the standard for DNA origami design, and we have published a tutorial for DNA origami design using the cadnano software. For usage please cite: DNA Origami Design of Dolphin-Shaped Structures with Flexible Tails. Andersen et al. ACS Nano, 2008, 2 (6), pp 1213–1218
A graphical sequence editor for working with structural alignments of RNA. The software is now available: Version 1.37 (2007-10-25) Complete package: sarse-1.37.tar.gz. Citation: For usage of the editor please cite: "Semiautomated improvement of RNA alignments" E. S. Andersen et al. RNA 13:1850-1859, 2007. Features: Basic alignment editing, Split view, Unlimited undo/redo across sessions, Embedded alignment analysis tools e.g. RNAdbtools, pfold, pcluster, Extendable with your own commandline tools, Interactive overview function, Support for fasta, wide-text and column formats. http://sarse.ku.dk
AU Labbook is a web-based system for research documentation and collaboration (found at labbook.au.dk) based on the Confluence system. We established the system in 2007 and have been developing it over the years into a University-wide solution for documenting research supported and run by the Faculty of Science and Technology. As of November 2018 there are approximately 1500 users with 2000 views and 400 edits per working day. 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 is the official description of AU Labbook.
