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Databases
Kazusa Genome DataBase
| Kazusa Genome DataBase | A portal site for the genome databases related to the plants whose genome sequences were determined or genome analyses were conducted mainly at Kazusa DNA Research Institute. |
Plant Genome Projects
| Strawberry GARDEN | Genome database for Fragaria × ananassa and wild strawberry (F. iinumae, F. nipponica, F. nubicola, and F. orientalis). This database contains sequence information (scaffolds, CDSs, translated genes, etc.) obtained by sequence assembly. Marker information, physical and genetic maps are available. Keyword and homology searches are available. |
| Sweetpotato GARDEN | Genome database for Ipomoea batatas. This database contains sequence information (scaffolds, CDSs, translated genes, etc.) obtained by sequence assembly. Keyword and homology searches are available. |
| Carnation DB | Genome database for Dianthus caryophyllus L. This database contains sequence information (scaffolds, CDSs, translated genes, etc.) obtained by sequence assembly. Keyword and homology searches are available. |
| Zoysia Genome Database | Genome database for zoysia grass. This database contains sequence information of Zoysia japonica (pseudomolecule, scaffolds, CDSs, translated genes, etc.), and Z. matrella and Z. pacifica (scaffolds, CDSs, translated genes, etc.) obtained by sequence assembly. Keyword and homology searches are available. |
| Eggplant Genome DataBase | Genome database for Solanum melongena L. This database contains sequence information (scaffolds, CDSs, translated genes, etc.) obtained by sequence assembly. Keyword and homology searches are available. |
| Raphanus sativus Genome DataBase | Genome database for Raphanus sativus L. This database contains sequence information (scaffolds, CDSs, translated genes, etc.) obtained by sequence assembly. SNP information for 7 cultivars of radish is available. Keyword and homology searches are available. |
| Buckwheat Genome DataBase (BGDB) | Genome database for Fagopyrum esculentum. This database contains sequence information (scaffolds, CDSs, translated genes, etc.) obtained by sequence assembly. Keyword and homology searches are available. |
| Eucalyptus camaldulensis Genome Database | Genome database of Eucalyptus camaldulensis: this database contains sequence information (contigs, CDS, and amino acid sequences) obtained by sequence assembly. Keyword and homology searches are available for predicted genes. |
| Jatropha Genome Database | Genome database of Jatropha curcas L.: this database contains sequence information (genome, scaffolds, CDS, amino acid sequences, GFF files, etc.) obtained by sequence assembly. Keyword and homology searches are available for predicted genes. |
| CloverGarden | Genome and marker database for subterraneum clover (Trifolium subterraneum), red clover (Trifolium pratense) and white clover (Trifolium repens). The database contains sequence, SNP and a linkage map information for subterranean clover. Keyword and homology searches are available. For Trifolium pratense, genetic maps, marker information, and EST information are available. On the page for EST information, the results of homology search against UniRef100 and the EST sequences are available. In the database for Trifolium repens, EST-SSR marker information and keyword search are available. The sequences of EST-SSR are available from the marker list. |
| CyanoBase | This database contains genetic information of ORFs (locations, sequences, and protein families) related to 39 strains of Cyanobacteria, including Synechocystis sp. PCC 6803, Anabaena sp. PCC 7120, and Chlorobium tepidum TLS. |
| RhizoBase | This database contains genetic information of ORFs (locations, sequences, and protein families) for 39 strains of Rhizobacteria, including Mesorhizobium loti MAFF303099, Bradyrhizobium japonicum USDA110, Sinorhizobium meliloti 1021, and closely related species. |
| Lotus japonicus Genome Sequencing Project | Genome database of Lotus japonicus, a model plant belonging to the family Leguminosae. Keyword search is available for predicted genes. This database provides a browser for the annotations on the genome sequences. The clone lists in each chromosome and information about RI lines between Miyakojima MG-20 and Gifu B-129 are also available. |
| Tomato SBM Database | Genome database of Selected BAC Mixture (SBM) assembly of Solanum lycopersicum, a model plant belonging to the family Solanaceae. This database contains contigs, scaffolds, BAC-end sequences, predicted genes, DNA markers, and linkage maps of three lines. Keyword and homology searches are also available for predicted genes. | Codon Usage Database | Database of codon usage. This database was constructed based on the codon usage of genes provided from NCBI GenBank. At present, this database contains the codon usages of 3,027,973 genes in 35,799 organisms. | TACWeb | Database of the transformation-competent bacterial artificial chromosome (TAC) vectors for Arabidopsis thaliana, a model plant. This database contains general information about TAC vectors, DNA libraries, and protocols. |
Plant cDNA Projects
| Chlamydomonas EST Index | EST database of Chlamydomonas reinhardtii. Keyword and homology searches are available. Clones can be ordered from the clone request site. |
| Lotus japonicus EST Index | EST database of Lotus japonicus. Keyword and homology searches are available. Information on cDNA arrays can be searched by accession numbers or keywords. |
| Arabidopsis EST Index | EST database of Arabidopsis thaliana. Keyword and homology searches are available. |
| Porphyra EST Index | EST database of Porphyra yezoensis. Keyword and homology searches are available. Clones can be ordered from the clone request site. |
| MiBASE Micro-Tom Database | Database of fruit- and leaf-derived EST sequences for 'Micro-Tom', a tomato cultivar. Keyword searches against the UniGene, EST sequences, GO, pathways, markers, and microarray data are available. Clones can be ordered from the clone request site. |
| Trifolium pratense EST Index | Database for EST sequence on Trifolium pratense. Keyword and homology searches are available. |
Markers
| Kazusa Marker DataBase | Database for DNA markers, genetic maps, and physical maps for 13 plant species, that were developed at the Kazusa DNA Research Institute. Keyword searches for the markers, sequence data, and experimental conditions are available. |
| KaTomicsDB | A portal website for databases related to DNA markers and SBM databases of tomato. |
| Tomato Marker Databese | Marker database of Solanum lycopersicum. Information on sequences including EST-SNP, EST-SSR, genome-SSR, intron-SNP markers, and linkage maps of three lines are available from the marker lists. Keyword searches are available for the markers. |
| Tomato Functional SNP DataBase | A database of SNP markers for 40 lines and SNP effects on gene functions of tomato. SNP position on protein 3D structure can be browsed. |
| Peanut Marker Databese | Marker database of Arachis hypogaea. Information on sequences including EST-SSR marker and transposable elements are available from the marker lists. Keyword search is available for the markers. |
| Daikon radish (Raphanus sativus) Marker Databese | Marker database of Raphanus sativus. Information on sequences including markers of EST-SSR, isozyme, R-EST, RAPD, RFLP, SSR, STS, and linkage maps are available from the marker lists. Keyword search is available for the markers. |
| Maker DB Glycine max/soybean | Marker database of Glycine max. Marker information is available from linkage maps. Keyword search is available for the markers. |
Portal website for integration of plant genome-related databases
| PGDBj | A portal website for general information, DNA markers, QTLs, DB links and genome analysis methods of plants including model plants and crops. Cross-search is available for the contents of PGDBj. |
Plant Genetic Information Projects
| KATANA | Arabidopsis thaliana Integrated Database. |
| KaPPA-View | Arabidopsis thaliana Metabolic Pathway Database. |
| MiBASE | Solanum lycopersicum (Tomato) EST and Unigene database. |
| KaFTom | Solanum lycopersicum (Tomato) Full-length sequence (HTC) and EST database. |
| CoP | Plant co-expressed gene network database. |
| RnR | Regulatory network research database for Arabidopsis thaliana T87 cultured cells. |
Metabolome Projects
| KOMICS | This is the portal that provides access to the databases and tools we have developed for metabolomics studies. |
| KomicMarket | Metabolite MS spectral annotation database. |
| MassBase | Metabolite MST database. |
| MS-MS Fragment Viewer | MS/MS spectral database for flavonoid compounds. |
Human cDNA Projects
| HUGE | Database of human unidentified gene-encoded large proteins. |
| NEDO(Kazusa) | Database of FLJ cDNA-encoded large proteins. |
| ROUGE | Database of unidentified rodent gene-encoded large proteins. |
| CREATE portal | This is the portal that allows access to the Collaboration of Regional Entities for the Advancement of Technological Excellence.
InGaP: a database of gene/protein expression profiles identified using mKIAA cDNA microarrays and anti-mKIAA antibodies. InCeP: a database of intracellular pathways based on mKIAA protein-protein interactions. |
| KOP | Database of human protein expression clones (Flexi ORF clones). |
Miscellaneous
| Mouse DNA Microarray | Database of mouse DNA Microarrays. |
| DAGViz | GO analysis database for genes in eukaryotic genomes. |
Others
| KaTomicsDB | KaTomicsDB is a portal website for the tomato genomics databases for DNA markers, SNP annotations, and genome sequences released from our research group. |
Software for genetic analysis
| Genotype Matrix Mapping (GMM) | A computer program for detecting QTL interactions. |
| Plant phenotyping software | Image analysis software programs for plant phenotyping |
| Polyans | Software program for the typing polymorphic bands on electrophoresis gel |
| KAGIANA | Excel-based tool for retrieving genomic information and co-expressed genes for Arabidopsis thaliana. |