Picardi Ernesto, Pesole Graziano
Dipartimento di Biochimica e Biologia Molecolare E Quagliariello, University of Bari, Bari, Italy.
Methods Mol Biol. 2010;609:269-84. doi: 10.1007/978-1-60327-241-4_16.
High-throughput DNA sequencing is increasing the amount of public complete genomes even though a precise gene catalogue for each organism is not yet available. In this context, computational gene finders play a key role in producing a first and cost-effective annotation. Nowadays a compilation of gene prediction tools has been made available to the scientific community and, despite the high number, they can be divided into two main categories: (1) ab initio and (2) evidence based. In the following, we will provide an overview of main methodologies to predict correct exon-intron structures of eukaryotic genes falling in such categories. We will take into account also new strategies that commonly refine ab initio predictions employing comparative genomics or other evidence such as expression data. Finally, we will briefly introduce metrics to in house evaluation of gene predictions in terms of sensitivity and specificity at nucleotide, exon, and gene levels as well.
高通量DNA测序正在增加公开的完整基因组数量，尽管尚未获得每个生物体的精确基因目录。在这种情况下，计算基因发现工具在生成首个且具有成本效益的注释方面发挥着关键作用。如今，一系列基因预测工具已提供给科学界，尽管数量众多，但它们可分为两大类：（1）从头预测和（2）基于证据的预测。在下文中，我们将概述预测属于此类别的真核基因正确外显子-内含子结构的主要方法。我们还将考虑通常利用比较基因组学或其他证据（如表达数据）来完善从头预测的新策略。最后，我们还将简要介绍在核苷酸、外显子和基因水平上对基因预测进行内部评估的敏感性和特异性指标。
