mbgd.nibb.ac.jp

MBGD: Microbial Genome Database for Comparative Analysis

Beginning of this page. Skip to main content. MBGD : Microbial Genome Database for Comparative Analysis. Microbial Genome Database for. Is a database for comparative analysis of completely sequenced microbial genomes, the number of which is now growing rapidly. The aim of MBGD. Is to facilitate comparative genomics from various points of view such as ortholog identification, paralog clustering, motif analysis and gene order comparison. References: Nucleic Acids Res. Genomes, Last update 2016/05/19 ).

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MBGD: Microbial Genome Database for Comparative Analysis | mbgd.nibb.ac.jp Reviews

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Beginning of this page. Skip to main content. MBGD : Microbial Genome Database for Comparative Analysis. Microbial Genome Database for. Is a database for comparative analysis of completely sequenced microbial genomes, the number of which is now growing rapidly. The aim of MBGD. Is to facilitate comparative genomics from various points of view such as ortholog identification, paralog clustering, motif analysis and gene order comparison. References: Nucleic Acids Res. Genomes, Last update 2016/05/19 ).

<META> KEYWORDS

1 comparative analysis

2 about mbgd

3 introduction

4 ortholog

5 classification

6 ortholog table

7 organism selection

8 my mbgd mode

9 cluster tables

10 searching mbgd

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comparative analysis,about mbgd,introduction,ortholog,classification,ortholog table,organism selection,my mbgd mode,cluster tables,searching mbgd,advanced search,homology search,function categories,gene names,downloads and programs,data archive,domclust

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MBGD: Microbial Genome Database for Comparative Analysis | mbgd.nibb.ac.jp Reviews

https://mbgd.nibb.ac.jp

Beginning of this page. Skip to main content. MBGD : Microbial Genome Database for Comparative Analysis. Microbial Genome Database for. Is a database for comparative analysis of completely sequenced microbial genomes, the number of which is now growing rapidly. The aim of MBGD. Is to facilitate comparative genomics from various points of view such as ortholog identification, paralog clustering, motif analysis and gene order comparison. References: Nucleic Acids Res. Genomes, Last update 2016/05/19 ).

INTERNAL PAGES

mbgd.nibb.ac.jp

1

MBGD: List of Clusters

http://mbgd.nibb.ac.jp/htbin/list_clusttab.pl

List of Cluster Tables. The list of clusters that you have made. Note that these tables might be deleted witout notice in the future. [Return to the top page]. O1 -HO -S -c60 -p0.5 -V0.6 -C80 -ao0.8 -ai0.95 -ne1. Return to the top page].

2

Gene Name List

http://mbgd.nibb.ac.jp/htbin/GeneNameList

The number of gene names assigned by the original depositors.

3

DomRefine: Domain-based Ortholog Clustering Refinment Pipeline

http://mbgd.nibb.ac.jp/domrefine

Domain-based Ortholog Clustering Refinment Pipeline. Identification of ortholog groups is a crucial step in comparative analysis of multiple genomes. Although several computational methods have been developed to create ortholog groups, most of those methods do not evaluate orthology at the sub-gene level. In our method for domain-based ortholog clustering, DomClust. By optimizing the DSP score. Chiba, H. and Uchiyama, I.

4

MBGD: MBGD Archive

http://mbgd.nibb.ac.jp/htbin/view_arch.cgi

Each file contains an ortholog table and is named as "mbgd ReleaseNo. Is in the form of Year. Such as "mbgd 2008-01.default.tab". Right-click on the link and choose "Download linked file as" (or equivalent) to download and save the file. A cluster table generated by the DomClust program using the default set of organisms. A cluster table extended from the default table that covers all organisms stored in the database. Each cluster ID is same as that of the default table. Alignments and phylogenetic trees.

5

DomClust: Hierarchical Clustering Program for Orthologous Protein Domain Classification

http://mbgd.nibb.ac.jp/domclust

Hierarchical Clustering Program for Orthologous Protein Domain Classification. DomClust has been used for classifying hundreds of mocrobial genomes in MBGD (Microbial genome database for comparative analysis). Which itself provides currently the most user-friendly interface for DomClust. The readme file for the program. The program source code. The readme file for the dataset. The COG02 dataset used in the DomClust paper (including all-all similarities, 65MB). You can also download homology data from MBGD.

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hgc.jp

Databases | Human Genome Center

http://hgc.jp/english/database.html

JSNP database is a collection of approximately 200,000 gene-based SNP information that includes their location, methods to genotype them, their allele frequencies in Japanese general population. This project was one of the Prime Minister's National Millennium Projects in Japan, with the collaboration of Human Genome Center (HGC), Institute of Medical Science (IMS), The University of Tokyo, and Japan Science and Technology Agency (JST). Database of transcription factors and promoters of Bacillus subtilis.

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MBGD: Microbial Genome Database for Comparative Analysis

Beginning of this page. Skip to main content. MBGD : Microbial Genome Database for Comparative Analysis. Microbial Genome Database for. Is a database for comparative analysis of completely sequenced microbial genomes, the number of which is now growing rapidly. The aim of MBGD. Is to facilitate comparative genomics from various points of view such as ortholog identification, paralog clustering, motif analysis and gene order comparison. References: Nucleic Acids Res. Genomes, Last update 2016/05/19 ).

mbgd.nibb.ac.jp

MBGD: Microbial Genome Database for Comparative Analysis

Beginning of this page. Skip to main content. MBGD : Microbial Genome Database for Comparative Analysis. Microbial Genome Database for. Is a database for comparative analysis of completely sequenced microbial genomes, the number of which is now growing rapidly. The aim of MBGD. Is to facilitate comparative genomics from various points of view such as ortholog identification, paralog clustering, motif analysis and gene order comparison. References: Nucleic Acids Res. Genomes, Last update 2016/05/19 ).

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