It is a tool for sequence motif identification on the short nucleotide sequences. MDS2 integrates the graph algorithms and large-scale sampling techniques to detect the sequence motif on the short sequences. It balances the specificity and sensitivity of motif and utilizes the statistical evaluation to minimize the risk of false identification. It has been proven that MDS2 is capable of predicting the motifs as short as 4bp-long, which are usually overlooked by other motif finding tools, such as MEME and DREME. Tool is available at http://sbbi.unl.edu/MDS2/.