Parallelization of MAFFT for large-scale multiple sequence alignments

被引：585

作者：

Nakamura, Tsukasa ^{[1
,2
]}

Yamada, Kazunori D. ^{[2
,3
]}

Tomii, Kentaro ^{[1
,2
,4
,5
]}

Katoh, Kazutaka ^{[2
,6
]}

机构：

[1] Univ Tokyo, Grad Sch Frontier Sci, Dept Computat Biol & Med Sci, Chiba 2778562, Japan

[2] Natl Inst Adv Ind Sci & Technol, AIRC, Tokyo 1350064, Japan

[3] Tohoku Univ, Grad Sch Informat Sci, Sendai, Miyagi 9808579, Japan

[4] AIST, Biotechnol Res Inst Drug Discovery BRD, Tokyo 1350064, Japan

[5] AIST, Tokyo Tech Real World Big Data Computat Open Lab, Tokyo 1528550, Japan

[6] Osaka Univ, Res Inst Microbial Dis, Suita, Osaka 5650871, Japan

来源：

BIOINFORMATICS | 2018年 / 34卷 / 14期

关键词：

SECONDARY STRUCTURE PREDICTION;

D O I：

10.1093/bioinformatics/bty121

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

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.

引用

页码：2490 / 2492

页数：3

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