Multisubjective

Multisubjective is a nucleic acid design tool that identifies and removes strong spurious base pairing in arbitrary user-defined systems, with special features targeted towards dynamic strand-displacement systems used in developmental self-assembly. Multisubjective identifies the small subset of bases responsible for the spurious base pairing, and uses a client designer to select new identities for those bases.

Multisubjective’s algorithm is based on multiple iterations of an analysis–redesign cycle with the goal of finding a design that has very few strong undesired base pairs. Multisubjective uses a thermodynamic analysis to identify a minimal set of bases that need to be changed because they are responsible for undesired secondary structure, or because they are part of a user-defined prevented sequence. This analysis is passed to the client designer to redesign only those bases identified as problematic by Multisubjective, holding the others constant. Multisubjective interacts automatically with an implementation of the combinatorial heuristics-based Domain Design (DD) software, and is also capable of automatically submitting a design to the NUPACK multi-objective designer on their web server and automatically retrieving the results.

Documentation:

• Quick start guide
• Full user documentation
• Sample specification file

How to use:

• Option 1: GUI through DyNAMiC Workbench. Multisubjective is one of many tools available on DyNAMiC Workbench, an integrated development environment for nucleic acid design, which includes a convenient front-end graphical user interface for Multisubjective. As Workbench is currently in limited alpha release, users must request access in order to create an account. See the quick start quide for detailed instructions.
• Option 2: Source code for console version. Source code is available for the standalone console version, which can take input either interactively from the user or as part of a command line call. Multisubjective is written in C++ and can be compiled with gcc-derived compilers including XCode. In order to use Multisubjective, you will also need to download and install NUPACK locally, and depending on what features you're planning to use, you may need Node.js and/or cURL. See the user documentation for detailed installation instructions.