A horizontal alignment tool for numerical trend discovery in sequence data: application to protein hydropathy.

ABSTRACT: An algorithm is presented that returns the optimal pairwise gapped alignment of two sets of signed numerical sequence values. One distinguishing feature of this algorithm is a flexible comparison engine (based on both relative shape and absolute similarity measures) that does not rely on explicit gap penalties. Additionally, an empirical probability model is developed to estimate the significance of the returned alignment with respect to randomized data. The algorithm's utility for biological hypothesis formulation is demonstrated with test cases including database search and pairwise alignment of protein hydropathy. However, the algorithm and probability model could possibly be extended to accommodate other diverse types of protein or nucleic acid data, including positional thermodynamic

SUBMITTER: Hadzipasic O 

PROVIDER: S-EPMC3794901 | biostudies-literature | 2013

REPOSITORIES: biostudies-literature