Publication Date:
2012-02-17
Description:
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 – plot. GeoPCA can be accessed via http://pca.limlab.ibms.sinica.edu.tw .
Keywords:
Nucleic acid structure, Computational Methods
Print ISSN:
0305-1048
Electronic ISSN:
1362-4962
Topics:
Biology
