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Database name DOI Database classification Organism Database description Features and manner of utilization of database Database maintenance site License
Trypanosomes Database 10.18908/lsdba.nbdc01243-000
Protein sequence databases
Homo sapiens (9606)
Trypanosoma (5690)

The Trypanosomes database is a database providing the comprehensive information of proteins that is effective targets for drug development that can control trypanosomiasis. Trypanosome is a parasitic protozoan of the genus Trypanosoma that infects a variety of hosts and causes various diseases, including African sleeping sickness and South American chagas disease, that is, trypanosomiasis. Every year more than 100 thousands of people suffer from trypanosomiasis. It also infects livestock, and more than 100 thousands of cattle have died per year. So far, it has been found effective targets for drug development that can control trypanosomiasis. One of such targets is a group of enzymes that control trypanosome DNA/RNA biosynthetic pathway. Another target is a group of enzymes that control trypanosome oxidation/reduction pathway. Actually, in case of trypanosomes, these enzymes are involved in both reaction pathways, and greatly affect lives of trypanosomes.

This trypanosomes database system provides keyword search and several narrowing retrieval functions for browsing data. In the original database, it also provides the list of papers related to trypanosomes.

National Institute of Genetics, Research Organization of Information and Systems (ROIS)

CC BY-SA
Q-TARO
(QTL Annotation Rice Online database)
10.18908/lsdba.nbdc01234-000
Nucleotide Sequence Databases
Oryza sativa (4530)

This is a database of Rice QTL information extracted from published research papers.
From 1214 reports, we selected 5096 QTLs. The positions of these QTLs were estimated from the physical positions of either two flanking markers (the genomic positions of the distal ends of the two markers) or a co-segregated single marker (between the start and end positions on the genome). If the QTLs were isolated by map-based cloning, the position of the BAC/PAC clone or gene locus was used. By screening for redundancy of traits at the same physical positions, as of March 31 of 2008, we selected 1051 QTLs extracted from 463 reports as representative QTLs. To arrange QTL information, we constructed QTL database (QTL Annotation Rice Online database; Q-TARO, http://qtaro.abr.affrc.go.jp/) consists of two web interfaces. One interface is a table containing information on the mapping of each QTL and its genetic parameters. The other interface is a genome viewer for viewing genomic locations of the QTLs. Currently, update of QTL information is not continued.
 

Over the past two decades, genetic dissection of complex phenotypes of economic and biological interest has revealed the chromosomal locations of many quantitative trait loci (QTLs) in rice and their contributions to phenotypic variation. Mapping resolution has varied considerably among QTL studies, owing to differences in population size and number of DNA markers used. Additionally, the same QTLs have often been reported with different locus designations. This situation has made it difficult to determine allelic relationships among QTLs and to compare their positions. To facilitate reliable comparisons of rice QTLs, we extracted QTL information from published research papers and constructed a database of 1051 representative QTLs, which we classified into 21 trait categories. Q-TARO clearly displays the co-localization of QTLs and distribution of QTL clusters on the rice genome.

CC BY-SA
AT Atlas
(Advanced Technologies Atlas)
10.18908/lsdba.nbdc01162-000
Other Molecular Biology Databases
Experimental Methodology

AT Atlas will make you familiar with the accomplishments by research groups of "Protein Production", "Structural Analysis" and "Chemical Regulation" in the Targeted Proteins Research Program. AT Atlas is composed of graphical abstract (flow chart) , information in text including actual application of the method and link to PRotein Experimental Information Management System (PREIMS). You will be able to find experimental methods used to elucidate the structure and/or functions of proteins that you are interested in. Further, you will be able to reproduce the experimental process to study corresponding entries of PREIMS. (Most of the graphical abstracts have been drawn by use of Cell Illustrator that is a pathway-drawing software developed by Prof. Satoru Miyano and his colleagues at the U. Tokyo)

The database provides techniques in protein production (hardly-soluble proteins, membrane proteins, protein complexes etc.), structural analysis of proteins and chemical library for protein regulation technology, which were worked in Targeted Proteins Research Program (TPRP). It is a practical database including graphical abstracts and links to detailed protocols in PREIMS (Protein Experimental Information Management System).

Platform for Drug Discovery, Informatics, and Structural Life Science

Research Organization of Information and Systems

National Institute of Genetics

CC BY-SA
TP Atlas
(Targeted Proteins Atlas)
10.18908/lsdba.nbdc01161-000
Metabolic and Signaling Pathways

TP Atlas is a comprehensive "Targeted Proteins Research achievements database" in which you can access a variety of information on the target proteins, their structures, published papers and press releases by navigating the network diagram drawn by Cell Illustrator for each TP Research project. It covers all 35 TP projects ranging from signal transduction networks to enzymatic reaction pathways in the three fields of fundamental biology, medicine/pharmacology and food/environment. (Cell Illustrator is a pathway drawing software developed by Prof. Satoru Miyano and his colleagues at the U. Tokyo)

In this database, the background, highlight and outline of each project in "Targeted Proteins Research Program" are summarized. The relationships of proteins or signaling pathways are shown diagrammatically in each project. The diagrams are downloadable. You can also get information of proteins (sequences and structures), genes, and published papers in each project.

National Institute of Genetics, Research Organization of Information and Systems (ROIS)

CC BY-SA
RMG
(Rice Mitochondrial Genome)
10.18908/lsdba.nbdc00193-000
Nucleotide Sequence Databases
Oryza sativa Japonica Group (39947)

This database contains information on the rice mitochondrial genome. You can refer entire sequence of rice mitochondrial genome and information on the analysis results.

The mitochondrial genome information can be used as standard for analysis of the mitochondria of major cereal crops such as corn and wheat as well as other monocotyledonous plants.

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