Parallelization of MAFFT for large-scale multiple sequence alignments

Tsukasa Nakamura; Kazunori D. Yamada; Kentaro Tomii; Kazutaka Katoh

doi:10.1093/bioinformatics/bty121

Parallelization of MAFFT for large-scale multiple sequence alignments

Tsukasa Nakamura, Kazunori D. Yamada, Kentaro Tomii, Kazutaka Katoh

情報科学研究科

研究成果: Article › 査読

156 被引用数 (Scopus)

抄録

Summary: We report an update for the MAFFT multiple sequence alignment program to enable parallel calculation of large numbers of sequences. The G-INS-1 option of MAFFT was recently reported to have higher accuracy than other methods for large data, but this method has been impractical for most large-scale analyses, due to the requirement of large computational resources. We introduce a scalable variant, G-large-INS-1, which has equivalent accuracy to G-INS-1 and is applicable to 50 000 or more sequences.

本文言語	English
ページ（範囲）	2490-2492
ページ数	3
ジャーナル	Bioinformatics
巻	34
号	14
DOI	https://doi.org/10.1093/bioinformatics/bty121
出版ステータス	Published - 2018 7 15

ASJC Scopus subject areas

Statistics and Probability
Biochemistry
Molecular Biology
Computer Science Applications
Computational Theory and Mathematics
Computational Mathematics

文献へのアクセス

10.1093/bioinformatics/bty121

フィンガープリント「Parallelization of MAFFT for large-scale multiple sequence alignments」の研究トピックを掘り下げます。これらがまとまってユニークなフィンガープリントを構成します。

引用スタイル

@article{a93fb450fb6f4c2aabc516027aff43fb,

title = "Parallelization of MAFFT for large-scale multiple sequence alignments",

abstract = "Summary: We report an update for the MAFFT multiple sequence alignment program to enable parallel calculation of large numbers of sequences. The G-INS-1 option of MAFFT was recently reported to have higher accuracy than other methods for large data, but this method has been impractical for most large-scale analyses, due to the requirement of large computational resources. We introduce a scalable variant, G-large-INS-1, which has equivalent accuracy to G-INS-1 and is applicable to 50 000 or more sequences.",

author = "Tsukasa Nakamura and Yamada, {Kazunori D.} and Kentaro Tomii and Kazutaka Katoh",

note = "Funding Information: This work was supported by JSPS KAKENHI [grant numbers JP16K07464 (to K.D.Y., K.T. and K.K.) and JP17J06457 (to T.N.)] and Platform Project for Supporting Drug Discovery and Life Science Research [grant numbers JP17am0101110 (to T.N., K.D.Y. and K.T.) and JP17am0101108 (to K.K.)] from AMED, Japan.",

year = "2018",

month = jul,

day = "15",

doi = "10.1093/bioinformatics/bty121",

language = "English",

volume = "34",

pages = "2490--2492",

journal = "Bioinformatics",

issn = "1367-4803",

publisher = "Oxford University Press",

number = "14",

}

TY - JOUR

T1 - Parallelization of MAFFT for large-scale multiple sequence alignments

AU - Nakamura, Tsukasa

AU - Yamada, Kazunori D.

AU - Tomii, Kentaro

AU - Katoh, Kazutaka

N1 - Funding Information: This work was supported by JSPS KAKENHI [grant numbers JP16K07464 (to K.D.Y., K.T. and K.K.) and JP17J06457 (to T.N.)] and Platform Project for Supporting Drug Discovery and Life Science Research [grant numbers JP17am0101110 (to T.N., K.D.Y. and K.T.) and JP17am0101108 (to K.K.)] from AMED, Japan.

PY - 2018/7/15

Y1 - 2018/7/15

N2 - Summary: We report an update for the MAFFT multiple sequence alignment program to enable parallel calculation of large numbers of sequences. The G-INS-1 option of MAFFT was recently reported to have higher accuracy than other methods for large data, but this method has been impractical for most large-scale analyses, due to the requirement of large computational resources. We introduce a scalable variant, G-large-INS-1, which has equivalent accuracy to G-INS-1 and is applicable to 50 000 or more sequences.

AB - Summary: We report an update for the MAFFT multiple sequence alignment program to enable parallel calculation of large numbers of sequences. The G-INS-1 option of MAFFT was recently reported to have higher accuracy than other methods for large data, but this method has been impractical for most large-scale analyses, due to the requirement of large computational resources. We introduce a scalable variant, G-large-INS-1, which has equivalent accuracy to G-INS-1 and is applicable to 50 000 or more sequences.

UR - http://www.scopus.com/inward/record.url?scp=85055056401&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=85055056401&partnerID=8YFLogxK

U2 - 10.1093/bioinformatics/bty121

DO - 10.1093/bioinformatics/bty121

M3 - Article

C2 - 29506019

AN - SCOPUS:85055056401

VL - 34

SP - 2490

EP - 2492

JO - Bioinformatics

JF - Bioinformatics

SN - 1367-4803

IS - 14

ER -