[ Japanese | English ]

Search for Database Metadata

Search by Keyword
Search by Property
or
Showing 71 to 75 of 89 entries
Show entries
Database name DOI Database classification Organism Database description Features and manner of utilization of database Database maintenance site License
KOME
(Knowledge-based Oryza Molecular biological Encyclopedia)
10.18908/lsdba.nbdc00120-000
Plant databases - Rice
Oryza sativa (4530)

Information about approximately 38,000 full-length cDNA clones that were completely sequenced in the Rice full-length cDNA project is shown in the database. The full-length cDNA clones were collected from various tissues treated under various stress conditions. The database contains not only information about complete nucleotide sequences and encoded amino acid sequences, but also results of homology searches against public databases, mapping information, information about patterns of alternative splicing, protein domains and transmembrane structures, and information about cellular localizations and gene functions annotated with Gene Ontology.

The full-length cDNA libraries were constructed from randomly picked 170,000 clones derived from twenty types of stressed tissues of japonica rice. The clones were grouped into 28,000 independent classes according to their 3' terminal single-pass sequences. All of the representative clones were completely sequenced.

CC BY-SA
BodyParts3D
(3D structure database for anatomical concepts)
10.18908/lsdba.nbdc00837-000
Organ
Homo sapiens (9606)

Dictionary-type database for anatomy in which anatomical concepts are represented by 3D structure data that specify corresponding segments of a three-dimensional whole-body model for an adult human male

The biggest feature is that a three-dimensional whole-body model for an adult human male is available for free. The database is not only useful as an electronic atlas to three-dimensionally confirm the position and shape of human organ, but also useful in reusing the available data as the input data for human-body simulation and data mapping.
A tool called "Anatomogram" is also made available to the public (http://lifesciencedb.jp/bp3d/) to readily generate an anatomical image of human body by selecting body parts from BodyParts3D and setting desired viewpoint, zoom, color and opacity.

CC BY
Taxonomy Icon 10.18908/lsdba.nbdc00805-000
Images

Taxonomy Icon is a collection of icons (illustrations) of biological species that is free to use and distribute. More than 200 icons of various species including Bacteria, Fungi, Protista, Plantae and Animalia are available.

You can use the icons to create documents and websites. Also, you can look up the classification or scientific name of species.

CC BY
Society Catalog 10.18908/lsdba.nbdc00963-000
Catalog

Society Catalog provides information of the academic societies in Japan (organization name, website URL, contact address, etc.).

Users can easily find societies they need by using a category tree or a society website's thumbnail. This database is useful especially when the users are looking for societies they are not familier with.

National Bioscience Database Center
*The original website was terminated.

CC BY-SA
tRNADB-CE 10.18908/lsdba.nbdc00720-000
RNA sequence databases

This is the most accurate tRNA gene database curated manually by experts in the world. This database is the outcome of the model project to utilize the expertise of elderly researchers and to pass it down to the next generation, which was carried out at Nagahama Institute of Bio-Science and Technology. Specifically, the existing multiple tRNA gene search programs are used for automatic search of tRNA gene from sequenced prokaryote, eukaryote and virus genomes and envrironmental DNA sequences, and then the experts manually check those cases in which different results are generated by program.

- The database was constructed by performing a comprehensive search of tRNA genes on 1625 full-length genomes and 2993 draft genomes of bacteria and Archaea, 151 complete virus genomes, 121 complete chloroplast genomes, 12 complete eukaryote (Plant and Fungi) genomes and about 230 million environmental DNA sequences.
- Three prediction programs (tRNAScan-SE, Aragorn and tRNA finder) are used together to search tRNA genes. If the prediction results do not match, curation is carried out by experts.
- The relationship between the codon usage frequency and the number of tRNA genes can be browsed for each species to search the codon recognized by major isoaccepting tRNA (optimal codon) or minor tRNA (nonoptimal codon).

CC BY-SA
Database name DOI Database classification Organism Database description Features and manner of utilization of database Database maintenance site License