RNA search with decision trees and partial covariance models.

ABSTRACT: The use of partial covariance models to search for RNA family members in genomic sequence databases is explored. The partial models are formed from contiguous subranges of the overall RNA family multiple alignment columns. A binary decision-tree framework is presented for choosing the order to apply the partial models and the score thresholds on which to make the decisions. The decision trees are chosen to minimize computation time subject to the constraint that all of the training sequences are passed to the full covariance model for final evaluation. Computational intelligence methods are suggested to select the decision tree since the tree can be quite complex and there is no obvious method to build the tree in these cases. Experimental results from seven RNA families shows execution ti

SUBMITTER: Smith JA 

PROVIDER: S-EPMC3646588 | biostudies-literature | 2009 Jul-Sep

REPOSITORIES: biostudies-literature