PAFFT: A new homology search algorithm for third-generation sequencers

Kazuharu Misawa, Ryo Ootsuki

Research output: Contribution to journalArticlepeer-review

1 Citation (Scopus)


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.

Original languageEnglish
Pages (from-to)265-267
Number of pages3
Issue number5
Publication statusPublished - 2015 Nov


  • Homology search
  • Third-generation sequencer

ASJC Scopus subject areas

  • Genetics


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