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In this paper, we describe the context sensitivity problem encountered inpartitioning a heterogeneous biological sequence into statistically homogeneoussegments. After showing signatures of the problem in the bacterial genomes ofEscherichia coli K-12 MG1655 and Pseudomonas syringae DC3000, when these aresegmented using two entropic segmentation schemes, we clarify the contextualorigins of these signatures through mean-field analyses of the segmentationschemes. Finally, we explain why we believe all sequence segmentation schemsare plagued by the context sensitivity problem.

The Context Sensitivity Problem in Biological Sequence Segmentation