Team:Heidelberg/Software/MAWS
MAWS 2.0
Revised aptamer design software
As aptamer-based riboswitches are the most promising regulatory element to couple the PACE/PREDCEL selection system to the intracellular level of a small molecule, the availbability of suitable aptamers is the limiting factor for enzyme PACE/PREDCEL experiments. The state of the art method to generate aptamers and riboswitches is based on the in vitro selection of sequences from a random oligonucleotide library using the SELEX method. This requires the establishment of suitable protocols and can be labor and cost intensive. Therefore the 2015 iGEM Heidelberg team developed a aptamer design tool called MAWS (Making Aptamers Without SELEX) which tries to predict aptamers by progressive selection of appropriate bases using an entropic criterion. As the initial version was based on a purposely written collection of scripts, the flexibility and compatibility with different platforms was limited and extension or adaptation would require intricate knowledge of the source code. Here the initial developer of MAWS presents a new modular version aimed at improving the usability for developers to establish aptamer design workflows with MAWS routines.
Changelog
- Removed problematic dependencies.
- Modularized the software into classes for all necessary components.
- Possible use as an API for entropic criterion based drug design enabled
- Complete reimplementation of the algebraic backend
- Added flexibility to use DNA, RNA, Peptides or other monomers for aptamer design
- Improved logging of the entropy statistics
- MPI support
- Multiple bugs and stability issues fixed
