title: PAFFT: A new homology search algorithm for third-generation sequencers.
abstract: DNA sequencers that can conduct real-time sequencing from a single polymerase molecule are known as third-generation sequencers. Third-generation sequencers enable sequencing of reads that are several kilobases long. However, the raw data generated from third-generation sequencers are known to be error-prone. Because of sequencing errors, it is difficult to identify which genes are homologous to the reads obtained using third-generation sequencers. In this study, a new method for homology search algorithm, PAFFT, is developed. This method is the extension of the MAFFT algorithm which was used for multiple alignments. PAFFT detects global homology rather than local homology so that homologous regions can be detected even when the error rate of sequencing is high. PAFFT will boost application of third-generation sequencers.
authors.affiliation: Advanced Center for Computing and Communication, RIKEN, Hirosawa 2-1, Wako, Saitama 351-0198, Japan. Electronic address: misawa@megabank.tohoku.ac.jp.
authors.forename: Kazuharu
authors.initials: K
authors.lastname: Misawa
authors.affiliation: Faculty of Chemical and Biological Sciences, Japan Women's University, Tokyo, Japan; Department of Natural Sciences, Faculty of Arts and Sciences, Komazawa University, 1-23-1 Komazawa, Setagaya-ku, Tokyo 154-8525, Japan.
authors.forename: Ryo
authors.initials: R
authors.lastname: Ootsuki
mesh_terms: D000465:Algorithms; D017422:Sequence Analysis, DNA / Q000379:methods*; D012689:Sequence Homology, Nucleic Acid
keywords: Homology search; Third-generation sequencer