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Links tagged with 'japan'

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DDBJDatabase Content

http://www.ddbj.nig.ac.jp [open in a new window]

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DNA > Databases

The DNA Data Bank of Japan (DDBJ) provides a nucleotide sequence archive database and accompanying database tools for sequence submission, entry retrieval and annotation analysis. A new archive for quantitative genomics data, the DDBJ Omics aRchive (DOR). The DOR stores quantitative data both from the microarray and high-throughput new sequencing platforms. Other improvements include improved content of the DDBJ patent sequence, released a new submission tool of the DDBJ Sequence Read Archive (DRA) which archives massive raw sequencing reads, and enhanced a cloud computing-based analytical system from sequencing reads, the DDBJ Read Annotation Pipeline.

links directory index: 49
TitlePublication YearGoogle Scholar Citation Count
The DNA Data Bank of Japan launches a new resource, the DDBJ Omics Archive of functional genomics experiments20123
DDBJ progress report201115
DDBJ launches a new archive database with analytical tools for next-generation sequence data201031
NAR Database Issue 2010NAR Database Issue 2011
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tagsalgorithms amino acid sequence animals bacterial genome computational biology genetic databases genomics humans japan molecular sequence annotation nucleic acid databases patents as topic protein databases

GenomeNetTool Content

http://www.genome.ad.jp/ [open in a new window]

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DNA > Sequence Retrieval and Submission
Human Genome > Other Resources
Protein > Networks & Interactions, Pathways and Enzymes
Protein > Sequence Retrieval

Network of database and computational resources including KEGG (pathways, interactions, etc.) and DBGET/LinkDB (an integrated database retrieval system). It also hosts several web-based tools for sequence analysis (ie. Blast, Motif, Clustal W)

links directory index: 285
TitlePublication YearGoogle Scholar Citation Count
The KEGG database2002182
DBGET/LinkDB: an integrated database retrieval system1998103
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tagsamino acid sequence animals biological models computer simulation factual databases genetic models genome humans information systems japan ligands molecular biology molecular sequence data protein binding proteome

IMCB - Fugu Genome ProjectTool Content

http://www.fugu-sg.org/ [open in a new window]

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Model Organisms > Databases
Model Organisms > Fish

Lots of information on fugu including complete draft sequence, annotations, comparative vertebrate genomics, phylogenies, publications, and information about the fugu genome project; has some very useful tools including annotation tools, an Ensembl mirror, and BLAST.

links directory index: 1759
TitlePublication YearGoogle Scholar Citation Count
Whole-genome shotgun assembly and analysis of the genome of Fugu rubripes20021097
Fugu: a compact vertebrate reference genome2000108
Generation and analysis of 25 Mb of genomic DNA from the pufferfish Fugu rubripes by sequence scanning199980
Characterization of the pufferfish (Fugu) genome as a compact model vertebrate genome1993474
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tagsanimals base sequence biological evolution computational biology conserved sequence cosmids dna dna sequence analysis dna transposable elements exons factual databases fish proteins fishes gene duplication gene library gene order genetic models genome genomics human genome humans introns japan mammals microsatellite repeats molecular evolution molecular sequence data nucleic acid repetitive sequences open reading frames phylogeny physical chromosome mapping poisonous fishes proteins proteome research satellite dna sequence alignment synteny takifugu vertebrates

KEGGDatabase Content

http://www.genome.ad.jp/kegg [open in a new window]

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Model Organisms > Databases

The KEGG PATHWAY database contains pathway maps for the molecular systems in both normal and perturbed states. In the KEGG DISEASE database, each disease is represented by a list of known disease genes, any known environmental factors at the molecular level, diagnostic markers and therapeutic drugs, which may reflect the underlying molecular system. The KEGG DRUG database contains chemical structures and/or chemical components of all drugs in Japan, including crude drugs and TCM (Traditional Chinese Medicine) formulas, and drugs in the USA and Europe. The new disease/drug information resource named KEGG MEDICUS can be used as a reference knowledge base for computational analysis of molecular networks, especially, by integrating large-scale experimental datasets.

links directory index: 653
TitlePublication YearGoogle Scholar Citation Count
KEGG for integration and interpretation of large-scale molecular data sets201235
KEGG for representation and analysis of molecular networks involving diseases and drugs2010618
NAR Database Issue 2010
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external linksLink on Wikipedia
tagsalgorithms animals biotransformation carbohydrate sequence chemical phenomena chemistry computational biology computer communication networks disease environment enzymes factual databases genes genetic databases genome genomics human genome human genome project humans information storage and retrieval internet japan knowledge bases ligands metabolism molecular biology molecular sequence annotation molecular sequence data nucleic acid databases pharmaceutical preparations pharmacological phenomena protein binding protein databases protein interaction mapping proteins signal transduction software systems biology systems integration tertiary protein structure user-computer interface

KEGG: Kyoto Encyclopedia of Genes and GenomesDatabase Content

http://www.genome.ad.jp/kegg/ [open in a new window]

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Expression > Networks
Protein > Networks & Interactions, Pathways and Enzymes
Protein > Proteomics

Pathway maps, molecular catalogs, genome maps and gene catalogs that capture knowledge about interactions in terms of information pathways. KEGG comprises several databases, including BRITE (protein-protein interactions), PATHWAY (interaction networks for cellular processes), and LIGAND (chemical compounds and chemical reactions). KEGG Atlas is a new tool for the global analysis of metabolic pathways.

links directory index: 5191
TitlePublication YearGoogle Scholar Citation Count
KEGG for linking genomes to life and the environment20081156
KEGG Atlas mapping for global analysis of metabolic pathways2008146
The KEGG database2002182
KEGG: Kyoto Encyclopedia of Genes and Genomes19993707
NAR Web Server Issue 2008
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tagsamino acid sequence animals biological models computational biology computer simulation disease factual databases gene expression genes genetic models genome genomics humans japan ligands metabolic networks and pathways metabolism molecular sequence data molecular structure pharmaceutical preparations protein binding proteome sequence homology systems biology systems integration

NBRP resourcesDatabase Content

http://www.nig.ac.jp/database/index-e.html [open in a new window]

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Literature > Databases

The National BioResource Project (NBRP) is a system for collecting, preserving and providing bioresources for use as experimental materials for life science research. Thirty databases and an integrated database-retrieval system (BioResource World: BRW) have been created. BRW provides access to a collection of 4.5-million records on bioresources including wild species, inbred lines, mutants, genetically engineered lines, DNA clones, etc. BRW supports summary browsing, keyword searching, and searching by DNA sequences or gene ontology. The results of searches provide links to online requests for distribution of research materials.

links directory index: 11
TitlePublication YearGoogle Scholar Citation Count
NBRP databases: databases of biological resources in Japan201011
NAR Database Issue 2010
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tagsalgorithms animals computational biology gene expression profiling genetic databases humans japan nucleic acid databases plant genome protein databases viral genome

Short Read ArchivesDatabase Content

http://www.ncbi.nlm.nih.gov/Traces/trace.cgi [open in a new window]

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DNA > Databases

The Sequence Read Archive (SRA) database provides the scientific community with an archival destination for next generation data sets. Partners of the International Nucleotide Sequencing Database Collaboration, include the National Center for Biotechnology Information (NCBI), the European Bioinformatics Institute (EBI), and the DNA Data Bank of Japan (DDBJ) have all established the SRA. Users of these resources can obtain data sets deposited in any of the three SRA instances.

links directory index: 38
TitlePublication YearGoogle Scholar Citation Count
Archiving next generation sequencing data201038
NAR Database Issue 2010
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tagsanimals computational biology dna sequence analysis europe genetic databases genomics humans japan national library of medicine (u.s.) nucleic acid databases united states

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