THE EFFECT OF CODON USAGE ON THE OLIGONUCLEOTIDE COMPOSITION OF THE ESCHERICHIA-COLI GENOME AND IDENTIFICATION OF OVERREPRESENTED AND UNDERREPRESENTED SEQUENCES BY MARKOV-CHAIN ANALYSIS
THE EFFECT OF CODON USAGE ON THE OLIGONUCLEOTIDE COMPOSITION OF THE ESCHERICHIA-COLI GENOME AND IDENTIFICATION OF OVERREPRESENTED AND UNDERREPRESENTED SEQUENCES BY MARKOV-CHAIN ANALYSIS
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DOI：
10.1093/nar/15.6.2627
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发表时间：
1987-03-25
影响因子：
14.9
通讯作者：
IVARIE, R
中科院分区：
文献类型：
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作者：
PHILLIPS, GJ;ARNOLD, J;IVARIE, R
如所附论文（5）所示，E.当从最高到最低丰度排序时，对于长度达6bp的序列，大肠杆菌基因组是高度不对称的。我们在这里表明，这在很大程度上反映了密码子的使用，因为大量使用的密码子被发现在高度丰富的寡聚体，而很少使用的密码子，有一些例外，发生在低丰度的序列。此外，线性回归分析揭示了每个三核苷酸的频率和它作为密码子的使用之间的强相关性。二核苷酸也不是随机分布在每个密码子位置上，并且转录但不翻译的基因（rRNA和tRNA基因）的二核苷酸组成与编码多肽的基因中所见的二核苷酸组成高度相关。然而，45个四，8个五，和6个六核苷酸显着过量或不足的马尔可夫链分析，不能占密码子的使用。在这些代表性不足的序列中，许多是回文序列，包括Dam甲基化位点
As shown in the accompanying paper (5), the oligonudeotide composition of the E. coli genome is highly asymmetric for sequences up to 6 bp in length when ranked from highest to lowest abundance. We show here that this largely reflects codon usage because heavily used codons were found in the highly abundant oligomers whereas rarely used codons, with some exceptions, occurred in sequences in low abundance. Furthermore, linear regression analysis revealed a strong correlation between the frequencies of each trinucleotide and its usage as a codon. Dinucleotides are also not randoo-ly distributed across each codon position and the dinucleotide composition of genes that are transcribed but not translated (rRNA and tRNA genes) was highly related to that seen in genes encoding polypeptides. However, 45 tetra-, 8 penta-, and 6 hexanucleotides were significantly over- or underabundant by Markov chain analysis and could not be accounted for by codon usage. Of these underrepresented sequences, many were palindromes, including the Dam methylation site