Comparative DNA sequence features in two long Escherichia coli contigs.
Comparative DNA sequence features in two long Escherichia coli contigs.
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两个长大肠杆菌重叠群的 DNA 序列特征比较。
DOI：
10.1093/nar/21.16.3875
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发表时间：
1993
影响因子：
14.9
通讯作者：
Karlin,S
中科院分区：
文献类型：
--
作者：
Cardon,LR;Burge,C;Schachtel,GA;Blaisdell,BE;Karlin,S
最近对大肠杆菌的两个相对较长（约 100 kb）重叠群的测序为研究大肠杆菌染色体的异质性和基因组组织提供了独特的机会。我们评估了两个新重叠群中的许多常见和对比序列特征，并与所有可用的大肠杆菌序列（> 1.6 Mb）进行了比较。我们的分析包括评估：(i) 限制性位点、特殊寡核苷酸（例如 Chisites、Daman 和 Dcm 甲基酶靶标）和其他标记阵列的计数和分布； (II)显着的远近正向和反向重复序列； (ill) 长重叠群和其他大肠杆菌序列之间的序列相似性； (iv)稀有和常见寡核苷酸的表征和鉴定； (v) 成分偏差 简而言之，寡核苷酸； (vl)序列组成中位置依赖性波动。这两个重叠群揭示了许多独特的特征，包括：五个重复/二元元素的簇，其间隔非常规则，类似于其中一个重叠群中的转录衰减子； REP 元件、ERIC 和其他长重复序列； Chi序列作为最常见的寡核苷酸的区别；某些限制性位点和短回文的聚集、过度分散和规律性区域；以及两个长重叠群中不均匀性的比较域。这些和其他特征都与大肠杆菌染色体的组织有关。
The recent sequencing of two relatively long(approximately 100 kb) contigs ofE.colipresentsunique opportunities for Investigating heterogeneity and genomic organization of theE.colichromosome.We have evaluated a number of common and contrasting sequence features In the two new contigs with comparisons to all availableE.colisequences (>1.6 Mb). Our analyses Include assessments of: (i)counts and distributions of restriction sites, special ollgonucleotides (e.g.,Chisites,DamandDcmmethylase targets), and other marker arrays; (II)significant distant and close direct and inverted repeat sequences; (ill) sequence similarities between the long contigs and otherE.colisequences; (Iv)characterization and identification ofrareandfrequentoligonucleotides; (v) compositional biases In short oligonucleotides; and (vl) position-dependent fluctuations in sequence composition. The two contigs reveal a number of distinctive features, including: a cluster of five repeat/dyad elements with very regular spacings resembling a transcription attenuator In one of the contigs; REP elements, ERICs, and other long repeats; distinction of theChisequence as the most frequent ollgonucleotlde; regions of clustering, overdisperslon, and regularity of certain restriction sites and short palindromes; and comparative domains of inhomogeneities In the two long contigs. These and other features are discussed In relation tothe organization of theE.colichromosome.