2023-08-16 カリフォルニア大学サンディエゴ校(UCSD)
◆UniAlignerは、セントロメアのような繰り返し配列において、有用な情報を提供する稀な部分文字列を優先して検出し、高速かつ正確に整列します。このアルゴリズムは、繰り返し配列が多い領域での進化や疾患の解析に新たな洞察をもたらす重要なツールとされています。
<関連情報>
- https://today.ucsd.edu/story/new-algorithm-reveals-extremely-high-mutations-rates-in-complex-genomic-regions
- https://www.nature.com/articles/s41592-023-01970-4
UniAligner:高速配列アライメントのためのパラメータフリーフレームワーク UniAligner: a parameter-free framework for fast sequence alignment
Andrey V. Bzikadze & Pavel A. Pevzner
Nature Methods Published14 August 2023
DOIhttps://doi.org/10.1038/s41592-023-01970-4
Abstract
Even though the recent advances in ‘complete genomics’ revealed the previously inaccessible genomic regions, analysis of variations in centromeres and other extra-long tandem repeats (ETRs) faces an algorithmic challenge since there are currently no tools for accurate sequence comparison of ETRs. Counterintuitively, the classical alignment approaches, such as the Smith–Waterman algorithm, fail to construct biologically adequate alignments of ETRs. We present UniAligner—the parameter-free sequence alignment algorithm with sequence-dependent alignment scoring that automatically changes for any pair of compared sequences. UniAligner prioritizes matches of rare substrings that are more likely to be relevant to the evolutionary relationship between two sequences. We apply UniAligner to estimate the mutation rates in human centromeres, and quantify the extremely high rate of large duplications and deletions in centromeres. This high rate suggests that centromeres may represent some of the most rapidly evolving regions of the human genome with respect to their structural organization.
