TY - JOUR
T1 - PAFFT
T2 - A new homology search algorithm for third-generation sequencers
AU - Misawa, Kazuharu
AU - Ootsuki, Ryo
N1 - Funding Information:
We thank Dr. Marcelo Bento Soares and anonymous reviewers for valuable suggestions and comments. We also thank Dr. Ryutaro Himeno for his encouragement and support. This work was supported by JSPS KAKENHI Grant Number 26650146.
Publisher Copyright:
© 2015 Elsevier Inc.
Copyright:
Copyright 2020 Elsevier B.V., All rights reserved.
PY - 2015/11
Y1 - 2015/11
N2 - 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.
AB - 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.
KW - Homology search
KW - Third-generation sequencer
UR - http://www.scopus.com/inward/record.url?scp=84944904408&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=84944904408&partnerID=8YFLogxK
U2 - 10.1016/j.ygeno.2015.09.005
DO - 10.1016/j.ygeno.2015.09.005
M3 - Article
C2 - 26387926
AN - SCOPUS:84944904408
VL - 106
SP - 265
EP - 267
JO - Genomics
JF - Genomics
SN - 0888-7543
IS - 5
ER -