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.

中文翻译：

---

基因组功能元件的预测。

随着测序的基因组数量的增加，推断基因组功能的能力变得越来越重要。对于许多基因组序列，在可预见的将来唯一可用的注释将基于计算预测以及与相关物种中功能元件的比较。在这里，我们讨论了哺乳动物基因组中功能元件自动全基因组注释的计算方法。这些方法包括从头算和比较基因结构预测的方法。讨论了诸如内含子剪接位点，3'非翻译区，启动子和顺式调控元件等基因特征，这是一种预测DNaseI超敏位点的新方法。还综述了预测非编码RNA基因（包括microRNA基因及其靶标）的最新方法。