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.
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.
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。
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