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. 2006 Nov 21;1:22. doi: 10.1186/1748-7188-1-22

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Copyright © 2006 Zhang and Zaki; licensee BioMed Central Ltd.

This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

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SMOTIF and SMARTFINDER Comparison: Random Motifs. The figure compares SMOTIF-1, SMOTIF-2 and SMARTFINDER, when searching for 100 randomly generated structured motifs in chromosome 20 of Homo sapiens. (a) shows how the running time varies with the sum of the number of occurrences of the simple motifs in each of the 100 random motifs. (b) shows the time with respect to the number of occurrences of the whole structured motif. (c) shows the effect of the number of simple motif components in the structured motif. (d) shows the impact of the number of IUPAC symbols in the structured motifs.