Computational Methods for Ab Initio and Comparative Gene Finding
Computational Methods for Ab Initio and Comparative Gene Finding
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DOI：
10.1007/978-1-60327-241-4_16
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发表时间：
2010-01-01
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影响因子：
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通讯作者：
Pesole, Graziano
中科院分区：
文献类型：
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作者：
Picardi, Ernesto;Pesole, Graziano
高通量DNA测序正在增加公开的完整基因组的数量，尽管还没有每个生物体的精确基因目录。在这种情况下，计算基因查找器在产生第一个和具有成本效益的注释方面发挥着关键作用。如今，基因预测工具的汇编已提供给科学界，尽管数量很大，但它们可以分为两大类：（1）从头开始和（2）基于证据。在下文中，我们将提供一个概述，主要的方法来预测正确的外显子-内含子结构的真核基因落在这些类别。我们还将考虑新的策略，通常采用比较基因组学或其他证据，如表达数据，完善从头预测。最后，我们将简要地介绍指标，以在核苷酸，外显子和基因水平的灵敏度和特异性方面的基因预测的病室评估是很好的。
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: (I) 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 ill 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 ill house evaluation of gene predictions in terms of sensitivity and specificity at nucleotide, exon, and gene levels is well.