D-Matrix is a tool for the construction of the conserved motif/pattern alignment, consensus sequence generation, alignment, frequency and weight matrix construction along with their possible regular expression signature or degenerate sequence of the motif with help of conserved sites/motif. D-Matrix program is based on heuristic algorithm to construct the position specific scoring matrix (PSSM) for DNA pattern set (Khan et al., 2008).
These matrices can be useful in the identification of genome wide unexplored conserved motifs through established weight matrix based motif discovery tools such as RSAT (Patser), PossuMsearch etc.