Rogozin Igor B, Makarova Kira S, Wolf Yuri I, Koonin Eugene V
NCBI/NLM/NIH, 8600 Rockville Pike, Bldg. 38A, Bethesda, MD 20894, USA.
Brief Bioinform. 2004 Jun;5(2):131-49. doi: 10.1093/bib/5.2.131.
Gene order in prokaryotes is conserved to a much lesser extent than protein sequences. Only some operons, primarily those that encode physically interacting proteins, are conserved in all or most of the bacterial and archaeal genomes. Nevertheless, even the limited conservation of operon organisation that is observed provides valuable evolutionary and functional clues through multiple genome comparisons. With the rapid growth in the number and diversity of sequenced prokaryotic genomes, functional inferences for uncharacterized genes located in the same conserved gene neighborhood with well-studied genes are becoming increasingly important. In this review, we discuss various computational approaches for identification of conserved gene strings and construction of local alignments of gene orders in prokaryotic genomes.
原核生物中的基因顺序保守程度远低于蛋白质序列。只有一些操纵子，主要是那些编码物理上相互作用蛋白质的操纵子，在所有或大多数细菌和古菌基因组中是保守的。然而，即使是观察到的操纵子组织的有限保守性，通过多个基因组比较也能提供有价值的进化和功能线索。随着已测序原核生物基因组数量的快速增长和多样性的增加，对于与已充分研究的基因位于相同保守基因邻域的未表征基因进行功能推断变得越来越重要。在这篇综述中，我们讨论了用于识别保守基因串和构建原核生物基因组中基因顺序局部比对的各种计算方法。
