BACKGROUND Genomic DNA frequently undergoes rearrangement of the gene order that can be localized by comparing the two DNA sequences. In mitochondrial genomes different mechanisms are likely at work, at least some of which involve the duplication of sequence around the location of the apparent breakpoints. We hypothesize that these different mechanisms of genome rearrangement leave distinctive sequence footprints. In order to study such effects it is important to locate the breakpoint positions with precision. RESULTS We define a partially local sequence alignment problem that assumes that following a rearrangement of a sequence F, two fragments L, and R are produced that may exactly fit together to match F, leave a gap of deleted DNA between L and R, or overlap with each other. We show that this alignment problem can be solved by dynamic programming in cubic space and time. We apply the new method to evaluate rearrangements of animal mitogenomes and find that a surprisingly large fraction of these events involved local sequence duplications. CONCLUSIONS The partially local sequence alignment method is an effective way to investigate the mechanism of genomic rearrangement events. While applied here only to mitogenomes there is no reason why the method could not be used to also consider rearrangements in nuclear genomes.

中文翻译：

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部分局部三向比对和线粒体基因组重排的序列特征。

背景技术基因组DNA经常经历可以通过比较两个DNA序列来定位的基因顺序的重排。在线粒体基因组中，不同的机制可能在起作用，至少其中一些涉及明显断点位置周围的序列重复。我们假设这些不同的基因组重排机制会留下独特的序列足迹。为了研究这种影响，精确定位断点位置很重要。结果 我们定义了一个部分局部序列比对问题，假设在序列 F 重排后，产生了两个片段 L 和 R，它们可能完全吻合以匹配 F，在 L 和 R 之间留下缺失 DNA 的间隙，或重叠彼此。我们表明，这种对齐问题可以通过立方空间和时间的动态规划来解决。我们应用新方法来评估动物有丝分裂基因组的重排，并发现这些事件中有很大一部分涉及局部序列重复。结论部分局部序列比对方法是研究基因组重排事件机制的有效方法。虽然这里仅适用于有丝分裂基因组，但没有理由不能将该方法也用于考虑核基因组中的重排。结论部分局部序列比对方法是研究基因组重排事件机制的有效方法。虽然这里仅适用于有丝分裂基因组，但没有理由不能将该方法也用于考虑核基因组中的重排。结论部分局部序列比对方法是研究基因组重排事件机制的有效方法。虽然这里仅适用于有丝分裂基因组，但没有理由不能将该方法也用于考虑核基因组中的重排。