Prediction of genomic functional elements

As the number of sequenced genomes increases, the ability to deduce genome function becomes increasingly salient. For many genome sequences, the only annotation that will be available for the foreseeable future will be based on computational predictions and comparisons with functional elements in related species. Here we discuss computational approaches for automated genome-wide annotation of functional elements in mammalian genomes. These include methods for ab initio and comparative gene-structure predictions. Gene features such as intron splice sites, 3' untranslated regions, promoters, and cis-regulatory elements are discussed, as is a novel method for predicting DNaseI hypersensitive sites. Recent methodologies for predicting noncoding RNA genes, including microRNA genes and their targets, are also reviewed.