SIGI: score-based identification of genomic islands.
SIGI: score-based identification of genomic islands.
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DOI：
10.1186/1471-2105-5-22
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发表时间：
2004-03-03
影响因子：
3
通讯作者：
Merkl R
中科院分区：
文献类型：
--
作者：
Merkl R
在许多微生物基因组中可以观察到基因组岛。这些DNA片段在序列或编码功能方面具有明显的组成。基因组岛通常被认为是通过水平基因转移获得的。对于基因组结构的分析和水平基因转移的研究，有必要可靠地识别和表征这些岛。使用密码子频率评分方案Score_G1G2（cdn）= log（f_G2（cdn）/ f_G1（cdn））。为了分析物种G1的基因并测试它们与物种G2的相关性，通过将公式应用于从两个基因组的平均密码子频率导出的对数几率来确定分数。一个非冗余的近400个密码子使用表，包括微生物物种的衍生;其成员交替使用在位置G2。进一步分析具有至少一个高于物种特异性和动态确定的截止值的评分值的基因。通过聚类分析，鉴定了包含具有统计学显著性大小的聚类的基因。这些簇被预测为基因组岛。最后，分别为这些基因，这些物种之间的分类关系负责显着的分数进行了解释。通过对天然基因和合成基因的广泛分析，旨在模拟基因改良的过程，这种方法的有效性及其局限性是合理的。该方法可靠地允许识别基因组岛和外来基因的可能起源。
Genomic islands can be observed in many microbial genomes. These stretches of DNA have a conspicuous composition with regard to sequence or encoded functions. Genomic islands are assumed to be frequently acquired via horizontal gene transfer. For the analysis of genome structure and the study of horizontal gene transfer, it is necessary to reliably identify and characterize these islands. A scoring scheme on codon frequencies Score_G1G2(cdn) = log(f_G2(cdn) / f_G1(cdn)) was utilized. To analyse genes of a species G1 and to test their relatedness to species G2, scores were determined by applying the formula to log-odds derived from mean codon frequencies of the two genomes. A non-redundant set of nearly 400 codon usage tables comprising microbial species was derived; its members were used alternatively at position G2. Genes having at least one score value above a species-specific and dynamically determined cut-off value were analysed further. By means of cluster analysis, genes were identified that comprise clusters of statistically significant size. These clusters were predicted as genomic islands. Finally and individually for each of these genes, the taxonomical relation among those species responsible for significant scores was interpreted. The validity of the approach and its limitations were made plausible by an extensive analysis of natural genes and synthetic ones aimed at modelling the process of gene amelioration. The method reliably allows to identify genomic island and the likely origin of alien genes.
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影响因子：
10.7
作者：
Koski, LB;Morton, RA;Golding, GB
通讯作者：
Golding, GB
影响因子：
3.9
作者：
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通讯作者：
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10.7
作者：
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Doolittle, WF
影响因子：
14.9
作者：
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通讯作者：
Bessières, P
影响因子：
12.3
作者：
Daubin V;Lerat E;Perrière G
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Perrière G