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Background  In transcription factor binding site discovery, the true width of the motif to be discovered is generally not known  a priori . The ability to compute the most likely width of a motif is therefore a highly desirable property for motif discovery algorithms. However, this is a challenging computational problem as a result of changing model dimensionality at changing motif widths. The complexity of the problem is increased as the discovered model at the  true  motif width need not be the most statistically significant in a set of candidate motif models. Further, the core motif discovery algorithm used cannot guarantee to return the best possible result at each candidate width.    Results  We present MCOIN, a novel heuristic for automatically determining transcription factor binding site motif width, based on motif containment and information content. Using realistic synthetic data and previously characterised prokaryotic data, we show that MCOIN outperforms the current most popular method (E-value of the resulting multiple alignment) as a predictor of motif width, based on mean absolute error. MCOIN is also shown to choose models which better match known sites at higher levels of motif conservation, based on ROC analysis.    Conclusions  We demonstrate the performance of MCOIN as part of a deterministic motif discovery algorithm and conclude that MCOIN outperforms current methods for determining motif width.

MCOIN: a novel heuristic for determining transcription factor binding site motif width