Mauve: Multiple alignment of conserved genomic sequence with rearrangements
Mauve: Multiple alignment of conserved genomic sequence with rearrangements
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DOI：
10.1101/gr.2289704
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发表时间：
2004-07-01
期刊：
影响因子：
7
通讯作者：
Perna, NT
中科院分区：
文献类型：
--
作者：
Darling, ACE;Mau, B;Perna, NT
随着基因组的进化，它们经历了大规模的进化过程，这对序列比较提出了挑战，而不是由短序列构成。扩增导致频繁的基因组重排，水平转移将新序列引入细菌染色体，而缺失则移除基因组的片段。因此，每个基因组都是独特的谱系特异性片段的马赛克，与其他基因组的子集共享的区域和在所有考虑的基因组中保守的片段。此外，这些片段的线性顺序可能在基因组之间被打乱。我们提出了在存在重排和水平转移的情况下鉴定和比对保守基因组DNA的方法。我们的方法已经在一个软件包中实现，称为Mauve。Mauve已应用于九个肠细菌基因组的比对，并确定了三种哺乳动物基因组的全局重排结构。我们已经评估了Mauve比对的质量，并通过对基因组进化的广泛模拟与其他方法进行了比较。
As genomes evolve, they undergo large-scale evolutionary processes that present a challenge to sequence comparison not posed by short sequences. Recombination causes frequent genome rearrangements, horizontal transfer introduces new sequences into bacterial chromosomes, and deletions remove segments of the genome. Consequently, each genome is a mosaic Of unique lineage-specific segments, regions shared with a subset of other genomes and segments conserved among all the genomes under consideration. Furthermore, the linear order of these segments may be shuffled among genomes. We present methods for identification and alignment of conserved genomic DNA in the presence of rearrangements and horizontal transfer. Our methods have been implemented in a software package called Mauve. Mauve has been applied to align nine enterobacterial genomes and to determine global rearrangement structure in three mammalian genomes. We have evaluated the quality of Mauve alignments and drawn comparison to other methods through extensive simulations of genome evolution.