MBGD/Introduction/References

MBGD Documents

Introduction to MBGD†

References†

Please cite the following references when you refer to MBGD in your published work:

1. Uchiyama I, Mihara M, Nishide H, Chiba H, Takayanagi M, Kawai M, Takami H.
   MBGD: Microbial Genome Database for Comparative Analysis Featuring Enhanced Functionality to Characterize Gene and Genome Functions Through Large-scale Orthology Analysis
   J Mol Biol. 2025 Jan 16:168957.
   
   
2. Uchiyama I, Mihara M, Nishide H, Chiba H, Kato M.
   MBGD update 2018: microbial genome database based on hierarchical orthology relations covering closely related and distantly related comparisons
   Nucleic Acids Res. 47, D382-D389, 2019.
   
   
3. Uchiyama I, Mihara M, Nishide H, Chiba H.
   MBGD update 2015: microbial genome database for flexible ortholog analysis utilizing a diverse set of genomic data
   Nucleic Acids Res. 43, D270-276, 2015.
   
   
4. Uchiyama I, Mihara M, Nishide H, Chiba H.
   MBGD update 2013: the microbial genome database for exploring the diversity of microbial world.
   Nucleic Acids Res. 41, D631-D635, 2013.
   
   
5. Uchiyama, I, Higuchi, T., Kawai, M.
   MBGD update 2010: toward a comprehensive resource for exploring microbial genome diversity
   Nucleic Acids Res. 38, D361-D365, 2010.
   
   
6. Uchiyama, I
   MBGD: a platform for microbial comparative genomics based on the automated construction of orthologous groups
   Nucleic Acids Res. 35, D343-D346, 2007.
   
   
7. Uchiyama, I
   MBGD: microbial genome database for comparative analysis
   Nucleic Acids Res. 31, 58-62, 2003.
   

Data sources and programs†

Data for constructing MBGD were mostly taken from NCBI RefSeq genome entries. See MBGD data sources for detail. In addition, the following programs/databases are used in MBGD.

• BLAST2 [homology search/motif search] (Altschul et al. 1997)
• HMMER3 [homology search] (Robert et al. 2011)
• MMseqs2 [homology search] (Steinegger et al. 2017)
• DIAMOND [homology search] (Buchfink et al. 2021)
• DomClust [clustering] (Uchiyama 2006)
• DomRefine [refinement of clustering] (Chiba et al. 2014)
• CoreAligner [multiple genome alignment] (Uchiyama 2008)
• ClustalW ver. 1.8 [multiple alignment] (Thompson et al. 1994)
• Clustal Omega [multiple alignment] (Sievers et al. 2014)
• MAFFT [multiple alignment] (Katoh et al. 2013)
• PHYLIP/drawtree [phylogenetic tree drawing] (Felsenstein 1993)
• FastTree [phylogenetic tree] (Price et al. 2010)
• InterPro [domain prediction] (Hunter et al. 2011)
• CGAT [comparing genome] (Uchiyama et al. 2006)
• CDD [motif dictionary] (Marchler-Bauer et al. 2002)
• GOLD [genome metadata] (Liolios et al. 2010)

Contact address:†

For questions and comments, please contact to:

Ikuo Uchiyama
National Institute for Basic Biology, Okazaki National Research Institutes
Email: uchiyama@nibb.ac.jp

Acknowledgements†

This database is supported by Grant-in-Aid for Publication of Scientific Research Results from Japan Society for the Promotion of Science (JSPS).

(For the initial version)
I am grateful to Prof. Toshihisa Takagi (Human Genome Center, Univ. Tokyo) for his advice and help in initiating this project as well as continuous support, and to Prof. Naotake Ogasawara (Nara Inst. Sci. Tech.) for helpful suggestions and comments. I also thank Toshio Higuchi (Intec W&G) for programming help, and Yoichi Hashimoto and Kagehiko Kitano (Intec W&G) for their contributions at the initial stage of this project. This work was partly supported by Grant-in-Aid for Scientific Research on Priority Areas from Ministry of Education, Culture, Sports, Science and Technology of Japan. The software development was initially supported by Human Genome Center, University of Tokyo.

Overview of MBGD

Introduction

• Overview
• Functions
• References

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