SynDCode
SynDCode provides the means to create collections of synthetic DNA strands with controlled properties such as resistance to crosshybridization. The user has the ability to verify the properties of an existing DNA code, expand a given DNA code or create an entirely new DNA code. The models built into SynDCode allow for the specification of thermodynamic properties of the generated DNA code and for collections of concatenated combinations of strands taken from the generated code. SynDCode can be used to construct DNA codes that do not adversely interact with functional oligonucleotides external to the code, e.g., priming sites, and it can construct codes that contain important motifs, e.g., restriction sites. Such codes can be used in the development of hybrid, self-assembling, nanoscale information systems. See link for a more detailed description of SynDCode.
SynDMatrix
Using dynamic programming, SynDCode captures the key of the nearest neighbor thermodynamic model for hybridized DNA duplexes in a computationally efficient way. All pairwise strand computations have complexity O(n^2) where n is the length of the strand. This is significant improvement, as other DNA code software tools based in nearest neighbor thermodynamics have complexity O(n^3). The dynamic weighted suffix and weighted computational matrices are given here. See link for a more detailed description of the metrics employed by SynDCode.
SynDAlign
SynDAlign constructs an example of the optimal alignment between any two DNA base sequences by integrating a backtracking algorithm into SynDCode's underlying thermodynamic mathematical methods. SynDAlign can also predict the optimal pseudoknotted structure contained within a single DNA strand.