群体基因型的有限语言表示索引
Indexing Finite Language Representation of Population Genotypes
摘要：
随着DNA测序的最新进展，现在有可能对个体的完整基因组进行测序和组装。这些丰富而集中的基因型信息可以用于进行不同群体范围的研究，现在首次直接在全基因组水平上进行。我们提出了一种方法来索引人口基因型信息与完整的基因组序列，以便人们可以使用该索引来有效地将给定的序列与基因组进行比对，并考虑到所有可能的基因型重组。这是通过将单个基因组的多重比对转换成有限自动机来实现的，该有限自动机通过随时切换序列来识别可以从比对中读取的所有字符串。有限自动机用Burrows-Wheeler变换的扩展来索引，以允许在合理的重组序列内进行模式搜索。由于个体基因组的高度相似性，索引的大小仍然有限。该指数发现在变异调用和引物设计中的应用。在变异调用实验中，我们发现仅精确匹配约1.0%的新重组体匹配，而近似匹配高达2.4%。
英文摘要：
With the recent advances in DNA sequencing, it is now possible to have complete genomes of individuals sequenced and assembled. This rich and focused genotype information can be used to do different population-wide studies, now first time directly on whole genome level. We propose a way to index population genotype information together with the complete genome sequence, so that one can use the index to efficiently align a given sequence to the genome with all plausible genotype recombinations taken into account. This is achieved through converting a multiple alignment of individual genomes into a finite automaton recognizing all strings that can be read from the alignment by switching the sequence at any time. The finite automaton is indexed with an extension of Burrows-Wheeler transform to allow pattern search inside the plausible recombinant sequences. The size of the index stays limited, because of the high similarity of individual genomes. The index finds applications in variation calling and in primer design. On a variation calling experiment, we found about 1.0% of matches to novel recombinants just with exact matching, and up to 2.4% with approximate matching.
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