Swiss-PDB Viewer (Deep View).
Swiss-PDB Viewer (Deep View).
复制标题
DOI：
10.1093/bib/2.2.195
复制
发表时间：
2001-05-01
影响因子：
9.5
通讯作者：
Littlejohn, T G
中科院分区：
文献类型：
--
作者：
Kaplan, W;Littlejohn, T G
介绍了七种流行的真核生物基因预测程序，并根据可供内部和在线使用以及预测精度进行了评估。这份报告概述了计算基因预测的一般适用方法和该领域的已知限制。真核基因组编码区的计算确定是一个重要的问题1，2基因组测序的进展已经引起了人们的关注。3-5自从人类基因组发表以来，公众对基因发现的兴趣有所下降，但这种时尚的变化并没有使计算基因预测的问题变得更加有效或有用。虽然很明显，目前没有一种计算机算法能够以全自动的方式对新测序的基因组进行注释，但基因寻找程序有很大的实用价值，特别是当它们与大量实验数据结合在一起时。3本综述的目的是描述和比较普通用户可用于在真核生物中寻找基因的计算机程序，并描述在实践中出现的限制和考虑因素。讨论了以下7个程序：Fgene S、6个Genie、7个GenScan 8及其衍生的GenomeScan、9个HMM基因、10个GenID 11和GlimmerM。12这些并不是迄今为止开发的所有基因发现程序。相反，这些是最现代和最先进的方法，能够预测未经注释的DNA序列中的多个、完整的真核基因结构，在某些情况下，能够在理论预测中包括同源性信息。后五种方法也适用于
Seven popular programs for gene prediction in eukaryotic organisms are described and evaluated on the basis of availability for in-house and on-line use and prediction accuracy. This report outlines generally applicable approaches to computational gene prediction and known limitations in this field.Computational determination of coding regions in eukaryotic genomes is an important problem 1, 2 that has been brought into the spotlight by advances in genomic sequencing. 3–5 Since the publication of the human genome, public interest in gene finding has somewhat declined, but this change in fashion does not make the problem of computational gene prediction any less valid or useful. While it is clear that at present no computer algorithm would be able to annotate a newly sequenced genome in a fully automated fashion, gene-finding programs have substantial utility, in particular when they are combined with large volumes of experimental data. 3 The goal of this review is to describe and compare the computer programs for gene finding in eukaryotic organisms that are available to the average user, and to describe limitations and considerations that arise in practice. The following seven programs are discussed: FgeneS, 6 Genie, 7 GenScan 8 and derived from it GenomeScan, 9 HMMGene, 10 geneid 11 and GlimmerM. 12 These are not all the gene-finding programs developed to date. Rather these are the most modern and advanced methods, able to predict multiple, complete eukaryotic gene structures in an unannotated DNA sequence, and in some cases able to include homology information in the theoretical prediction. The last five methods are also suited for