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Figure 2 | Genome Biology

Figure 2

From: A steganalysis-based approach to comprehensive identification and characterization of functional regulatory elements

Figure 2

Components and flow diagram of WordSpy. Starting with k = 1 and a grammar G0 with a single word node W b in background, the algorithm goes through the following steps, represented by the red numbers on the figure. 1. Model Gk-1 is optimized to which contains over-represented motifs shorter than k. 2. Use as a base model to detect over-represented exact words of length k. 3. Choose over-represented words for word clustering. 4. Evaluate all the words. Select and add background words to the background model. On the basis of similarity, cluster the rest of the words to form degenerate preliminary motifs. 5. Add the preliminary motifs to the motif sub-dictionary and create a new grammar G k . 6. Optimize G k . 7. Apply optimized to decipher the script and locate motifs.

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