title: Adaptive seeds tame genomic sequence comparison.
abstract: 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.
authors.affiliation: Department of Computational Biology, Max Planck Institute for Molecular Genetics, Berlin D-14195, Germany.
authors.forename: Szymon M
authors.initials: SM
authors.lastname: Kiełbasa
authors.forename: Raymond
authors.initials: R
authors.lastname: Wan
authors.forename: Kengo
authors.initials: K
authors.lastname: Sato
authors.forename: Paul
authors.initials: P
authors.lastname: Horton
authors.forename: Martin C
authors.initials: MC
authors.lastname: Frith
mesh_terms: D000465:Algorithms; D001483:Base Sequence; D019295:Computational Biology / Q000379:methods*; D004247:DNA / Q000737:chemistry; D016678:Genome; D008969:Molecular Sequence Data; D016415:Sequence Alignment / Q000379:methods*; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software
chemical_list: D004247:DNA