Download Matlab code of the
DeltaProt Toolbox here!
Abstract. In bioinformatics
there is an increasing desire for more statistical methods in the data
analysis. DeltaProt is a software toolbox that facilitates
importing, analyzing and visualizing data from multiple alignments of
proteins. We present statistical methods and trend-tests that are useful
when the aligned sequences can be divided into two or
more subgroups based on known phenotypic traits such as preference of
temperature, pH, salt concentration or pressure. The algorithms are
considered valuable for discovering differences between phenotypic
groups at a
molecular level, and the approach has been successfully applied in the
research on extremophile organisms. It has special relevance for
membrane proteins, since it is very difficult to obtain structural
models of this important group, and may be used for high-throughput
sequence analysis. The toolbox also
contains procedures for comparative plots of alignments and substitution matrices.
Edited by: Steinar Thorvaldsen
Latest update: October 25, 2010.
* Implemented statistical test in DeltaProt.
S. Thorvaldsen and E. Ytterstad: Environmental adaptation of proteins: Regression models with simple physicochemical properties. Computational Biology and Chemistry. Vol. 33 (5) 2009, pp. 351-356.
S. Thorvaldsen, E. Ytterstad and T. Flå: Property-dependent analysis of aligned proteins from two or more populations. Proceedings of the 4th Asia-Pacific Bioinformatics Conference (Eds.: T. Jiang et al.). Imperial College Press 2006, pp. 169-178.
S. Thorvaldsen, T. Flå and N. P. Willassen: Extracting molecular diversity between populations through sequence alignments. Lecture Notes in Bioinformatics, Vol. 3745, Springer-Verlag 2005, pp. 317-328.