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本文引用的文献

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A re-annotation of the Saccharomyces cerevisiae genome.酿酒酵母基因组的重新注释。
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2
Surveying Saccharomyces genomes to identify functional elements by comparative DNA sequence analysis.通过比较DNA序列分析来勘测酿酒酵母基因组以识别功能元件。
Genome Res. 2001 Jul;11(7):1175-86. doi: 10.1101/gr.182901.
3
Initial sequencing and analysis of the human genome.人类基因组的初步测序与分析。
Nature. 2001 Feb 15;409(6822):860-921. doi: 10.1038/35057062.
4
Genomic exploration of the hemiascomycetous yeasts: 4. The genome of Saccharomyces cerevisiae revisited.半子囊菌酵母的基因组探索：4. 重新审视酿酒酵母的基因组。
FEBS Lett. 2000 Dec 22;487(1):31-6. doi: 10.1016/s0014-5793(00)02275-4.
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An assessment of gene prediction accuracy in large DNA sequences.大型DNA序列中基因预测准确性的评估。
Genome Res. 2000 Oct;10(10):1631-42. doi: 10.1101/gr.122800.
6
Recognition of protein coding genes in the yeast genome at better than 95% accuracy based on the Z curve.基于Z曲线，在酵母基因组中识别蛋白质编码基因，准确率超过95%。
Nucleic Acids Res. 2000 Jul 15;28(14):2804-14. doi: 10.1093/nar/28.14.2804.
7
Gene-finding approaches for eukaryotes.真核生物的基因寻找方法。
Genome Res. 2000 Apr;10(4):394-7. doi: 10.1101/gr.10.4.394.
8
Origin and properties of non-coding ORFs in the yeast genome.酵母基因组中非编码开放阅读框的起源与特性
Nucleic Acids Res. 1999 Sep 1;27(17):3503-9. doi: 10.1093/nar/27.17.3503.
9
Comparative study of overlapping genes in the genomes of Mycoplasma genitalium and Mycoplasma pneumoniae.生殖支原体与肺炎支原体基因组中重叠基因的比较研究
Nucleic Acids Res. 1999 Apr 15;27(8):1847-53. doi: 10.1093/nar/27.8.1847.
10
Finding the genes in genomic DNA.在基因组DNA中寻找基因。
Curr Opin Struct Biol. 1998 Jun;8(3):346-54. doi: 10.1016/s0959-440x(98)80069-9.

酵母基因组中的开放阅读框（ORF）组织与基因识别

ORF organization and gene recognition in the yeast genome.

作者信息

Luo Liaofu, Li Hong, Zhang Lirong

机构信息

Laboratory of Theoretical Biophysics, Faculty of Science and Technology, Inner Mongolia University, Hohhot 010021, China.

出版信息

Comp Funct Genomics. 2003;4(3):318-28. doi: 10.1002/cfg.292.

DOI:10.1002/cfg.292
PMID:18629282
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC2448446/
Abstract

Some rules on gene recognition and ORF organization in the Saccharomyces cerevisiae genome are demonstrated by statistical analyses of sequence data. This study includes: (a) The random frame rule-that the six reading frames W1, W2, W3, C1, C2 and C3 in the double-stranded genome are randomly occupied by ORFs (related phenomena on ORF overlapping are also discussed). (b) The inhomogeneity rule-coding and non-coding ORFs differ in inhomogeneity of base composition in the three codon positions. By use of the inhomogeneity index (IHI), one can make a distinction between coding (IHI > 14) and non-coding (IHI < or = 14) ORFs at 95% accuracy. We find that 'spurious' ORFs (with IHI < or = 14) are distributed mainly in three classes of ORFs, namely, those with 'similarity to unknown proteins', those with 'no similarity', or 'questionable ORFs'. The total number of spurious ORFs (which are unlikely to be regarded as coding ORFs) is estimated to be 470. (c) The evaluation of ORF length distribution shows that below 200 amino acids the occurrence of ATG initiator ORFs is close to random.

摘要

通过对序列数据的统计分析，揭示了酿酒酵母基因组中基因识别和开放阅读框（ORF）组织的一些规律。本研究包括：（a）随机框架规则——双链基因组中的六个阅读框W1、W2、W3、C1、C2和C3被ORF随机占据（还讨论了ORF重叠的相关现象）。（b）不均匀性规则——编码和非编码ORF在三个密码子位置的碱基组成不均匀性方面存在差异。通过使用不均匀性指数（IHI），可以以95%的准确率区分编码（IHI>14）和非编码（IHI≤14）ORF。我们发现“假”ORF（IHI≤14）主要分布在三类ORF中，即那些“与未知蛋白质相似”、“无相似性”或“可疑ORF”。估计假ORF（不太可能被视为编码ORF）的总数为470个。（c）ORF长度分布评估表明，在200个氨基酸以下，ATG起始ORF的出现接近随机。