Evolutionary modeling and prediction of non-coding RNAs in Drosophila.

ABSTRACT: We performed benchmarks of phylogenetic grammar-based ncRNA gene prediction, experimenting with eight different models of structural evolution and two different programs for genome alignment. We evaluated our models using alignments of twelve Drosophila genomes. We find that ncRNA prediction performance can vary greatly between different gene predictors and subfamilies of ncRNA gene. Our estimates for false positive rates are based on simulations which preserve local islands of conservation; using these simulations, we predict a higher rate of false positives than previous computational ncRNA screens have reported. Using one of the tested prediction grammars, we provide an updated set of ncRNA predictions for D. melanogaster and compare them to previously-published predictions and experime

SUBMITTER: Bradley RK 

PROVIDER: S-EPMC2721679 | biostudies-literature | 2009 Aug

REPOSITORIES: biostudies-literature