Islander: a database of integrative islands in prokaryotic genomes, the associated integrases and their DNA site specificities
Islander: a database of integrative islands in prokaryotic genomes, the associated integrases and their DNA site specificities
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DOI：
10.1093/nar/gkh059
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发表时间：
2004-01-01
影响因子：
14.9
通讯作者：
Williams, KP
中科院分区：
文献类型：
--
作者：
Mantri, Y;Williams, KP
前体染色体通常含有由位点特异性整合酶递送的岛，例如温带致病性岛或致病性岛。整合通常发生在tRNA或tmRNA基因内，分裂基因，然而岛内的序列恢复被破坏的基因。因此，再生的RNA基因和该基因的移位片段标志着岛的端点。我们应用这一原理来寻找基因组DNA序列中的岛。我们的算法生成一个tRNA和tmRNA基因的列表，使用每个作为起始DNA的BLAST搜索的查询，并通过一系列过滤器删除不太可能的命中。在106个完整的细菌基因组中搜索岛屿产生了143个候选者，搜索本身提供了其中三个错误候选者的估计。相关的整合酶的初步系统发育分析减少了这一组89例独立进化的位点特异性，这表明强烈的偏见的tmRNA基因。网站Islander（hftp：www.indiana.edu/similar toislander）以GenBank风格的文件呈现候选岛，并将整合酶基因型与位点特异性相关联。
Prokaryotic chromosomes often contain islands, such as temperate phages or pathogenicity islands, delivered by site-specific integrases. Integration usually occurs within a tRNA or tmRNA gene, splitting the gene, yet sequences within the island restore the disrupted gene. The regenerated RNA gene and the displaced fragment of that gene thus mark the endpoints of the island. We applied this principle to search for islands in genomic DNA sequences. Our algorithm generates a list of tRNA and tmRNA genes, uses each as the query for a BLAST search of the starting DNA and removes unlikely hits through a series of filters. A search for islands in 106 whole bacterial genomes produced 143 candidates, with the search itself providing an estimate of three false candidates among these. Preliminary phylogenetic analysis of the associated integrases reduced this set to 89 cases of independently evolved site specificity, which showed strong bias for the tmRNA gene. The website Islander (hftp://www.indiana.edu/similar toislander) presents the candidate islands in GenBank-style files and correlates integrase phylogeny with site specificity.