MAPLE 2.3.0: an improved system for evaluating the functionomes of genomes and metagenomes

被引：39

作者：

Arai, Wataru ^{[1
]}

Taniguchi, Takeaki ^{[2
]}

Goto, Susumu ^{[3
]}

Moriya, Yuki ^{[3
]}

Uehara, Hideya ^{[4
]}

Takemoto, Kazuhiro ^{[5
]}

Ogata, Hiroyuki ^{[6
]}

Takami, Hideto ^{[1
]}

机构：

[1] JAMSTEC, Yokohama Inst, Microbial Genome Res Grp, Yokohama, Kanagawa, Japan

[2] Mitsubishi Res Inst, Healthcare & Wellness Div, Tokyo, Japan

[3] Res Org Informat & Syst, Database Ctr Life Sci, Kashiwa, Chiba, Japan

[4] Hewlett Packard Japan Ltd, HPE SGI Business Unit, Tokyo, Japan

[5] Kyushu Inst Technol, Dept Biosci & Bioinformat, Fukuoka, Fukuoka, Japan

[6] Kyoto Univ, Inst Chem Res, Bioinformat Ctr, Uji, Kyoto, Japan

来源：

BIOSCIENCE BIOTECHNOLOGY AND BIOCHEMISTRY | 2018年 / 82卷 / 09期

关键词：

MAPLE; 2; 3; 0; metabolic function; metagenomics; genomics;

D O I：

10.1080/09168451.2018.1476122

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

070307 [化学生物学]; 071010 [生物化学与分子生物学];

摘要：

MAPLE is an automated system for inferring the potential comprehensive functions harbored by genomes and metagenomes. To reduce runtime in MAPLE analyzing the massive amino acid datasets of over 1 million sequences, we improved it by adapting the KEGG automatic annotation server to use GHOSTX and verified no substantial difference in the MAPLE results between the original and new implementations.

引用

页码：1515 / 1517

页数：3

共 6 条

[1]

KEGG for linking genomes to life and the environment [J].

Kanehisa, Minoru ;

Araki, Michihiro ;

Goto, Susumu ;

Hattori, Masahiro ;

Hirakawa, Mika ;

Itoh, Masumi ;

Katayama, Toshiaki ;

Kawashima, Shuichi ;

Okuda, Shujiro ;

Tokimatsu, Toshiaki ;

Yamanishi, Yoshihiro .

NUCLEIC ACIDS RESEARCH, 2008, 36 :D480-D484

[2]

KAAS: an automatic genome annotation and pathway reconstruction server [J].

Moriya, Yuki ;

Itoh, Masumi ;

Okuda, Shujiro ;

Yoshizawa, Akiyasu C. ;

Kanehisa, Minoru .

NUCLEIC ACIDS RESEARCH, 2007, 35 :W182-W185

[3]

GHOSTX: An Improved Sequence Homology Search Algorithm Using a Query Suffix Array and a Database Suffix Array [J].

Suzuki, Shuji ;

Kakuta, Masanori ;

Ishida, Takashi ;

Akiyama, Yutaka .

PLOS ONE, 2014, 9 (08)

[4]

An automated system for evaluation of the potential functionome: MAPLE version 2.1.0 [J].

Takami, Hideto ;

Taniguchi, Takeaki ;

Arai, Wataru ;

Takemoto, Kazuhiro ;

Moriya, Yuki ;

Goto, Susumu .

DNA RESEARCH, 2016, 23 (05) :467-475

[5]

Evaluation method for the potential functionome harbored in the genome and metagenome [J].

Takami, Hideto ;

Taniguchi, Takeaki ;

Moriya, Yuki ;

Kuwahara, Tomomi ;

Kanehisa, Minoru ;

Goto, Susumu .

BMC GENOMICS, 2012, 13

[6]

Environmental genome shotgun sequencing of the Sargasso Sea [J].

Venter, JC ;

Remington, K ;

Heidelberg, JF ;

Halpern, AL ;

Rusch, D ;

Eisen, JA ;

Wu, DY ;

Paulsen, I ;

Nelson, KE ;

Nelson, W ;

Fouts, DE ;

Levy, S ;

Knap, AH ;

Lomas, MW ;

Nealson, K ;

White, O ;

Peterson, J ;

Hoffman, J ;

Parsons, R ;

Baden-Tillson, H ;

Pfannkoch, C ;

Rogers, YH ;

Smith, HO .

SCIENCE, 2004, 304 (5667) :66-74

← 1 →