mbgd.genome.ad.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.genome.ad.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.genome.ad.jp Reviews

https://mbgd.genome.ad.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.genome.ad.jp

1

MBGD: MBGD Archive

http://mbgd.genome.ad.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.

2

CGAT: Comparative Genome Analysis Tool

http://mbgd.genome.ad.jp/CGAT

A Comparative Genome Analysis Tool. Client; a Java application) and DataServer. A set of Perl scripts). The DataServer package contains data construction scripts and CGI scripts and the AlignmentViewer program visualizes the alignment data obtained from the server thorough the HTTP protocol. Uchiyama, I., Higuchi, T., Kobayashi, I.: CGAT: a comparative genome analysis tool for visualizing alignments in the analysis of complex evolutionary changes between closely related genomes.

3

DomRefine: Domain-based Ortholog Clustering Refinment Pipeline

http://mbgd.genome.ad.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

DomClust: Hierarchical Clustering Program for Orthologous Protein Domain Classification

http://mbgd.genome.ad.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.

5

Gene Name List

http://mbgd.genome.ad.jp/htbin/GeneNameList

The number of gene names assigned by the original depositors.

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funcmetabol.com

건국대학교 생명공학과 기능대사체 연구실

http://www.funcmetabol.com//link/link.html

Http:/ www.metabolomicssociety.org. The Koreaan Society of Microbiology and Biotechnology. Http:/ www.kormb.or.kr. Korean Society for Mass Spectrometry. Http:/ www.ksms.org. Korean Society for biochemistry and Molecular Biology. Http:/ www.biochem.or.kr. Http:/ pubchem.ncbi.nlm.nih.gov. CAS (A division of the American Chemical Society). Http:/ www.cas.org. CCD (The Combined Chemical Dictionary). Http:/ ccd.chemnetbase.com. Http:/ www.chemindustry.com/. Http:/ chemdb.kisti.re.kr. Http:/ www.gdb.org. GEM (...

species.wikimedia.org

Archaea - Wikispecies

https://species.wikimedia.org/wiki/Archaea

Candidati*: Aenigmarchaeota Diapherotrites Micrarchaeota Nanohaloarchaeota Pacearchaeota Parvarchaeota Woesearchaeota. Group: Archaea incertae sedis. Candidati*: DUSEL4 group NAG2 group Bathyarchaeota Geoarchaeota Lokiarchaeota Thorarchaeota. The taxa 'Regnum' and 'Phylum' are in use, but not covered by the Rules of Bacteriologocal Code (1990 Revision). Sources: NCBI, Bacterio.net). The category 'Candidatus' is not covered by the Rules of Bacteriologocal Code (1990 Revision). Williams, T.A.

virology.biken.osaka-u.ac.jp

Links - Ikuta Lab

http://virology.biken.osaka-u.ac.jp/links.html

Back to Home Page. Protein Data Bank Japan. The American Journal of Human Genetics. Cell Host and Microbe. Trends in Biochemical Sciences. Trends in Cell Biology. Trends in Cognitive Sciences. Trends in Ecology and Evolution. Trends in Endocrinology and Metabolism. Trends in Molecular Medicine. Trends in Pharmacological Sciences. Trends in Plant Science. Nat Struct. Mol. Biol. PLoS Neglected Tropical Diseases. The Lancet Diabetes and Endocrinology. The Lancet Global Health. The Lancet Infectious Diseases.

v2.pseudomonas.com

Pseudomonas Genome Database - Related Links

http://v2.pseudomonas.com/related_links.jsp

Please note that we will be retiring this old site on Tuesday, August 25th, 2015. At that point, the URL for www.pseudomonas.com will bring you to our new site currently hosted at beta.pseudomonas.com. We encourage you to visit the new site now and see a more recent set of updated gene annotations and MANY more. Sequence analysis, gene annotation and functional pathway analysis are listed below. We encourage researchers to contact us. With suggestions for additional items that should be listed. Transposo...

cybionix.com

bioinformatics

http://www.cybionix.com/bioinformatics/databases

Genomic Databases of Model Organisms. Human and Mouse Genome Comparisons. Gene and Genome Relationship and Proteome Analysis. Metabolism and Regulation,Functional Genomics. Gene Nomenclature, Functional Characterization,and Genome Database Development. Immunogenic and Receptor Databases. Database of Patterns and Sequence of Protein Families. A computerized store house of data that provide a standardized way for locating, adding, and changing data. Protein Nucleic acid Complex Database. MAGPIE: Multipurpo...

environbiotechnology.com

Resource – Environmental Biotechnology

http://environbiotechnology.com/resource

Microbial Solutions to Environmental Challenges. Applied and Environmental Microbiology. Environmental Science and Technology. Antimicrobial Agents and Chemotherapy. Journal of Antimicrobial Chemotherapy. International Journal of Antimicrobial Agents. How to Be a Good Graduate Student. How to Get the Most out of Conferences. A Guide to Ethical Writing Avoiding plagiarism. How to Write A Paper in Scientific Journal Style and Format. Guide for Writing a Funding Proposal. Ribosomal Database Project II (RDP).

fesb.ch.a.u-tokyo.ac.jp

Link集

http://fesb.ch.a.u-tokyo.ac.jp/link.html

The RCSB Protein Data Bank. Kyoto Encyclopedia of Genes and Genomes (KEGG). Human Genome Sequencing Data. US National Agricultural Library. REBASE Restriction Enzyme Database. The cloning vector collection.

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mbgd.genome.ad.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

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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