Cassis: detection of genomic rearrangement breakpoints
Cassis: detection of genomic rearrangement breakpoints
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DOI：
10.1093/bioinformatics/btq301
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发表时间：
2010-08-01
期刊：
影响因子：
5.8
通讯作者：
Sagot, Marie-France
中科院分区：
文献类型：
--
作者：
Baudet, Christian;Lemaitre, Claire;Sagot, Marie-France
基因组经历了改变其组织的大的结构变化。受这些重排影响的染色体区域称为断点，而那些没有重排的区域称为同线性块。Lemaitre等人提出了一种新的方法，通过与相关物种的基因组进行比较来精确地界定基因组中的重排断点。该方法接收两个物种基因组中发现的一个21个直链基因的列表作为输入，建立一组可靠的和非重叠的同线性块，并细化不包含在其中的区域。通过将每个断点序列与其他物种中特定的正向序列进行比对，我们可以寻找断点内部的弱相似性，从而扩展共线性块并缩小断点。窄化断点的识别依赖于分割算法，并进行统计评估。在这里，我们提出了实现这种方法的基因组重排断点的精确检测的软件包CNOPS。
Genomes undergo large structural changes that alter their organization. The chromosomal regions affected by these rearrangements are called breakpoints, while those which have not been rearranged are called synteny blocks. Lemaitre et al. presented a new method to precisely delimit rearrangement breakpoints in a genome by comparison with the genome of a related species. Receiving as input a list of one2one orthologous genes found in the genomes of two species, the method builds a set of reliable and non-overlapping synteny blocks and refines the regions that are not contained into them. Through the alignment of each breakpoint sequence against its specific orthologous sequences in the other species, we can look for weak similarities inside the breakpoint, thus extending the synteny blocks and narrowing the breakpoints. The identification of the narrowed breakpoints relies on a segmentation algorithm and is statistically assessed. Here, we present the package Cassis that implements this method of precise detection of genomic rearrangement breakpoints.