GeoPCA: a new tool for multivariate analysis of dihedral angles based on principal component geodesics.

Karen Sargsyan, Jon Wright, Carmay Lim

Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan. karsar@ibms.sinica.edu.tw

Nucleic acids research 2012 Feb

filter terms:

The GeoPCA package is the first tool developed for multivariate analysis of dihedral angles based on principal component geodesics. Principal component geodesic analysis provides a natural generalization of principal component analysis for data distributed in non-Euclidean space, as in the case of angular data. GeoPCA presents projection of angular data on a sphere composed of the first two principal component geodesics, allowing clustering based on dihedral angles as opposed to Cartesian coordinates. It also provides a measure of the similarity between input structures based on only dihedral angles, in analogy to the root-mean-square deviation of atoms based on Cartesian coordinates. The principal component geodesic approach is shown herein to reproduce clusters of nucleotides observed in an η-θ plot. GeoPCA can be accessed via http://pca.limlab.ibms.sinica.edu.tw.

Citation

Karen Sargsyan, Jon Wright, Carmay Lim. GeoPCA: a new tool for multivariate analysis of dihedral angles based on principal component geodesics. Nucleic acids research. 2012 Feb;40(3):e25