MBGD/Introduction/References
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[[MBGD Documents]]
* Introduction to MBGD [#qfeba334]
** References [#d6d2b8ff]
Please cite the following references when you refer to MB...
> Uchiyama, I ~
MBGD: microbial genome database for comparative analysis ~
Nucleic Acids Res. 31, 58-62, 2003.
> Uchiyama, I ~
MBGD: a platform for microbial comparative genomics based...
Nucleic Acids Res. 35, D343-D346, 2007.
> Uchiyama, I, Higuchi, T., Kawai, M. ~
MBGD update 2010: toward a comprehensive resource for exp...
Nucleic Acids Res. 35, D361-D365, 2010.
> Uchiyama I, Mihara M, Nishide H, Chiba H. ~
MBGD update 2013: the microbial genome database for explo...
Nucleic Acids Res. 41, D631-D635, 2013.
** Data sources and programs [#t0ef825c]
Data for constructing MBGD were mostly taken from NCBI Re...
In addition, the following programs/databases are used in...
- BLAST2 [homology search/motif search] (Altschul et al. ...
- HMMER3 [homology search] (Robert et al. 2011)
- 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....
- Clustal Omega [multiple alignment] (Sievers et al. 2014)
- MAP [multiple alignment] (Huang 1992)
- MAFFT [multiple alignment] (Katoh et al. 2013)
- PHYLIP/drawtree [phylogenetic tree drawing] (Felsenstei...
- 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: [#s5c5af88]
For questions and comments, please contact to:
> Ikuo Uchiyama ~
National Institute for Basic Biology, Okazaki National Re...
Email: uchiyama@nibb.ac.jp
** Acknowledgements [#x943507b]
This database is supported by Grant-in-Aid for Publicatio...
(For the initial version) ~
I am grateful to Prof. Toshihisa Takagi (Human Genome Cen...
End:
[[MBGD Documents]]
* Introduction to MBGD [#qfeba334]
** References [#d6d2b8ff]
Please cite the following references when you refer to MB...
> Uchiyama, I ~
MBGD: microbial genome database for comparative analysis ~
Nucleic Acids Res. 31, 58-62, 2003.
> Uchiyama, I ~
MBGD: a platform for microbial comparative genomics based...
Nucleic Acids Res. 35, D343-D346, 2007.
> Uchiyama, I, Higuchi, T., Kawai, M. ~
MBGD update 2010: toward a comprehensive resource for exp...
Nucleic Acids Res. 35, D361-D365, 2010.
> Uchiyama I, Mihara M, Nishide H, Chiba H. ~
MBGD update 2013: the microbial genome database for explo...
Nucleic Acids Res. 41, D631-D635, 2013.
** Data sources and programs [#t0ef825c]
Data for constructing MBGD were mostly taken from NCBI Re...
In addition, the following programs/databases are used in...
- BLAST2 [homology search/motif search] (Altschul et al. ...
- HMMER3 [homology search] (Robert et al. 2011)
- 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....
- Clustal Omega [multiple alignment] (Sievers et al. 2014)
- MAP [multiple alignment] (Huang 1992)
- MAFFT [multiple alignment] (Katoh et al. 2013)
- PHYLIP/drawtree [phylogenetic tree drawing] (Felsenstei...
- 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: [#s5c5af88]
For questions and comments, please contact to:
> Ikuo Uchiyama ~
National Institute for Basic Biology, Okazaki National Re...
Email: uchiyama@nibb.ac.jp
** Acknowledgements [#x943507b]
This database is supported by Grant-in-Aid for Publicatio...
(For the initial version) ~
I am grateful to Prof. Toshihisa Takagi (Human Genome Cen...
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