Literature DB >> 29792119

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

Wataru Arai1, Takeaki Taniguchi2, Susumu Goto3, Yuki Moriya3, Hideya Uehara4, Kazuhiro Takemoto5, Hiroyuki Ogata6, Hideto Takami1.   

Abstract

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.

Entities:  

Keywords:  MAPLE 2.3.0; genomics; metabolic function; metagenomics

Mesh：

Substances：

Year:  2018        PMID： 29792119     DOI： 10.1080/09168451.2018.1476122

Source DB:  PubMed          Journal:  Biosci Biotechnol Biochem        ISSN： 0916-8451            Impact factor:   2.043


  10 in total

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Journal:  BMC Ecol Evol       Date:  2022-05-27

2.  Bodo saltans (Kinetoplastida) is dependent on a novel Paracaedibacter-like endosymbiont that possesses multiple putative toxin-antitoxin systems.

Authors:  Samriti Midha; Daniel J Rigden; Stefanos Siozios; Gregory D D Hurst; Andrew P Jackson
Journal:  ISME J       Date:  2021-01-15       Impact factor: 10.302

3.  Diversity of Bradyrhizobium in Non-Leguminous Sorghum Plants: B. ottawaense Isolates Unique in Genes for N2O Reductase and Lack of the Type VI Secretion System.

Authors:  Sawa Wasai-Hara; Shintaro Hara; Takashi Morikawa; Masayuki Sugawara; Hideto Takami; Junich Yoneda; Tsuyoshi Tokunaga; Kiwamu Minamisawa
Journal:  Microbes Environ       Date:  2020       Impact factor: 2.912

4.  The physiological potential of anammox bacteria as revealed by their core genome structure.

Authors:  Takashi Okubo; Atsushi Toyoda; Kohei Fukuhara; Ikuo Uchiyama; Yuhki Harigaya; Megumi Kuroiwa; Takuma Suzuki; Yuka Murakami; Yuichi Suwa; Hideto Takami
Journal:  DNA Res       Date:  2021-01-19       Impact factor: 4.458

5.  MicrobeAnnotator: a user-friendly, comprehensive functional annotation pipeline for microbial genomes.

Authors:  Carlos A Ruiz-Perez; Roth E Conrad; Konstantinos T Konstantinidis
Journal:  BMC Bioinformatics       Date:  2021-01-06       Impact factor: 3.169

6.  Metabolic potential of the imperfect denitrifier Candidatus Desulfobacillus denitrificans in an anammox bioreactor.

Authors:  Takashi Okubo; Hideto Takami
Journal:  Microbiologyopen       Date:  2021-08       Impact factor: 3.139

7.  Single-cell genomics of uncultured bacteria reveals dietary fiber responders in the mouse gut microbiota.

Authors:  Rieka Chijiiwa; Masahito Hosokawa; Masato Kogawa; Yohei Nishikawa; Keigo Ide; Chikako Sakanashi; Kai Takahashi; Haruko Takeyama
Journal:  Microbiome       Date:  2020-01-23       Impact factor: 14.650

8.  Carbon Use Efficiency and Its Temperature Sensitivity Covary in Soil Bacteria.

Authors:  Grace Pold; Luiz A Domeignoz-Horta; Eric W Morrison; Serita D Frey; Seeta A Sistla; Kristen M DeAngelis
Journal:  mBio       Date:  2020-01-21       Impact factor: 7.867

9.  FeGenie: A Comprehensive Tool for the Identification of Iron Genes and Iron Gene Neighborhoods in Genome and Metagenome Assemblies.

Authors:  Arkadiy I Garber; Kenneth H Nealson; Akihiro Okamoto; Sean M McAllister; Clara S Chan; Roman A Barco; Nancy Merino
Journal:  Front Microbiol       Date:  2020-01-31       Impact factor: 5.640

10.  Molecular Evolutionary Dynamics of Energy Limited Microorganisms.

Authors:  William R Shoemaker; Evgeniya Polezhaeva; Kenzie B Givens; Jay T Lennon
Journal:  Mol Biol Evol       Date:  2021-09-27       Impact factor: 16.240
  10 in total

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