Adaptive seeds tame genomic sequence comparison

Szymon M. Kiełbasa, Raymond Wan, Kengo Sato, Paul Horton, Martin C. Frith

研究成果: Article同行評審

646 引文 斯高帕斯(Scopus)


The main way of analyzing biological sequences is by comparing and aligning them to each other. It remains difficult, however, to compare modern multi-billionbase DNA data sets. The difficulty is caused by the nonuniform (oligo)nucleotide composition of these sequences, rather than their size per se. To solve this problem, we modified the standard seed-and-extend approach (e.g., BLAST) to use adaptive seeds. Adaptive seeds are matches that are chosen based on their rareness, instead of using fixed-length matches. This method guarantees that the number of matches, and thus the running time, increases linearly, instead of quadratically, with sequence length. LAST, our open source implementation of adaptive seeds, enables fast and sensitive comparison of large sequences with arbitrarily nonuniform composition.

頁(從 - 到)487-493
期刊Genome Research
出版狀態Published - 2011 3月

All Science Journal Classification (ASJC) codes

  • 遺傳學
  • 遺傳學(臨床)


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