Software Package aSHAPE as a Tool to Study the Spatial Conformation of the Bacterial Genome Sites
Panyukov V.V., Nazipova N.N., Ozoline O.N.
Institute of Mathematical Problems of Biology, Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russian Federation
Institute of Cell Biophysics, Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russian Federation
panyukov@itaec.ru
Abstract. The paper describes an interactive package aSHAPE capable to reveal common features and conformational peculiarities in the families of three-dimensional models of the DNA double helices. An applicability of aSHAPE to characterize promoter regions in the genome of Escherichia coli has been demonstrated.
Key words: conformational chain, deformation, discriminant analysis, partitioning function, DNA double helix, promoter.