The Context Sensitivity Problem in Biological Sequence Segmentation

Cheong, Siew-Ann; Stodghill, Paul; Schneider, David J.; Cartinhour, Samuel W.; Myers, Christopher R.

The Context Sensitivity Problem in Biological Sequence Segmentation

Authors

Cheong, Siew-Ann

Stodghill, Paul

Schneider, David J.

Cartinhour, Samuel W.

Myers, Christopher R.

Description

In this paper, we describe the context sensitivity problem encountered in partitioning a heterogeneous biological sequence into statistically homogeneous segments. After showing signatures of the problem in the bacterial genomes of Escherichia coli K-12 MG1655 and Pseudomonas syringae DC3000, when these are segmented using two entropic segmentation schemes, we clarify the contextual origins of these signatures through mean-field analyses of the segmentation schemes. Finally, we explain why we believe all sequence segmentation schems are plagued by the context sensitivity problem.
IEEEtran class, 39 pages, 20 figures