Property-Dependent Analysis of Aligned Proteins from Two Or More Populations

Multiple sequence alignments can provide information for comparative analyses of proteins and protein populations. We present some statistical trend-tests that can be used when an aligned data set can be divided into two or more populations based on phenotypic traits such as preference of temperature, pH, salt concentration or pressure. The approach is based on estimation and analysis of the variation between the values of physicochemical parameters at positions of the sequence alignment. Monotonic trends are detected by applying a cumulative Mann-Kendall test. The method is found to be useful to identify significant physicochemical mechanisms behind adaptation to extreme environments and uncover molecular differences between mesophile and extremophile organisms. A filtering technique is also presented to visualize the underlying structure in the data. All the comparative statistical methods are available in the toolbox DeltaProt.