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Databases
Plant Genome Project
| Eucalyptus camaldulensis Genome Database | Genome database for Eucalyptus camaldulensis. This database contains sequence information (contigs, CDS, and amino acid sequences of genes) obtained by sequence assembly. Keyword and homology searches are available for predicted genes. |
| Jatropha Genome Database | Genome database for 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 | Marker database for red clover (Trifolium pratense) and white clover (Trifolium repens). In the database 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 (location, sequence, and protein family of ORF) for 39 strains (as of 2012) of Cyanobacteria, including Synechocystis sp. PCC 6803, Anabaena sp. PCC 7120, and Chlorobium tepidum TLS. This database also contains the results of homology searches between genes of the strains. |
| RhizoBase | This database contains genetic information (location, sequence, and protein family of ORF) for 39 strains (as of 2012) of Rhizobacteria, including Mesorhizobium loti MAFF303099, Bradyrhizobium japonicum USDA110, Sinorhizobium meliloti 1021, and closed species. This database also contains the results of homology searches between genes of the strains in this database. |
| Lotus japonicus Genome Sequencing Project | Genome database for Lotus japonicus, a model plant of family Leguminosae. Keyword search is available for predicted genes. This database contains a browser for chromosomes. The clone list of each chromosome and information on RI lines between Miyakojima MG-20 and Gifu B-129 are available. |
| Tomato SBM Database | Genome database for Selected BAC Mixture (SBM) assembly of Solanum lycopersicum, a model plant of family Solanaceae. This database contains contigs, scaffolds, BAC-end sequences, predicted genes, DNA markers, and linkage maps of 3 lines obtained by SBM assembly. Keyword and homology searches are available for predicted genes. |
| Codon Usage Database | Database of codon usage. This database was constructed on the basis of the NCBI GenBank and contains scientific names of species and a list of codon usage. At present, this database contains 35,799 species and CDS information on 3,027,973 species. |
| TACWeb | Database for the transformation-competent bacterial artificial chromosome (TAC) vectors for Arabidopsis thaliana, a model plant. This database contains general information on TAC vectors, DNA libraries, and protocols. |
Plant cDNA Project
| Chlamydomonas EST Index | Database for EST sequence on Chlamydomonas reinhardtii. Keyword and homology searches are available. Clones can be ordered from the clone request site. |
| Lotus japonicus EST Index | Database for EST sequence on Lotus japonicus. Keyword and homology searches are available. Information on cDNA arrays can be searched using accession numbers or keywords. Clones can be ordered from the clone request site. |
| Arabidopsis EST Index | Database for EST sequence on Arabidopsis thaliana. Keyword and homology searches are available. Clones can be ordered from the clone request site. |
| Porphyra EST Index | Database for EST sequence on Porphyra yezoensis. Keyword and homology searches are available. Clones can be ordered from the clone request site. This database is linked with other databases. |
| MiBASE Micro-Tom Database | Database for fruit- and leaf-derived EST sequence on 'Micro-Tom', a tomato cultivar. UniGene, EST, markers, and microarray data can be searched. Ontology and metabolic pathways can be searched based on homology with Arabidopsis thaliana. This database contains information on analytical programs, websites, and papers related to this cultivar. |
| Trifolium pratense EST Index | Database for EST sequence on Trifolium pratense. Keyword and homology searches are available. Clones can be ordered from the clone request site. |
| Trifolium repens EST Index | Database for EST sequence on Trifolium repens. Keyword and homology searches are available. Clones can be ordered from the clone request site. |
Marker
| Tomato Marker Databese | Marker database for Solanum lycopersicum. Information on sequences, which have been classified into EST-SNP, EST-SSR, genome-SSR, intron-SNP, etc., is available from the marker list. All markers listed on this site can be searched using keywords. This database contains information on linkage maps of 3 lines. |
| Peanut Marker Databese | Marker database for Arachis hypogaea. Marker sequences related to EST-SSR and transposable elements are available from the marker list. All markers on the site can be searched using keywords. |
| Daikon radish (Raphanus sativus) Marker Databese | Marker database for Raphanus sativus. Sequence information related to EST-SSR, isozyme markers, morphological markers, R-EST, RAPD, RFLP, SSR, and STS is available from the marker list. All markers listed on this site can be searched using keywords. This database contains information on linkage maps. |
| Maker DB Glycine max / soybean | Marker database for Glycine max. Marker information is available from linkage maps. Markers can be searched using keywords. |
Plant Genetic Information Project
| 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 Project
| KOMICS | This is the portal to the databases and tools we 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 Project
| HUGE | Database of human unidentified gene-encoded large proteins |
| NEDO(Kazusa) | Database of FLJ cDNA-encoded large proteins |
| ROUGE | Database of rodent unidentified gene-encoded large proteins |
| CREATE portal | This is the potal to the Collaboration of Regional Entities for the Advancement of Technological Excellence.
InGaP:A Database for Gene/Protein expression profiles using mKIAA cDNA microarray and anti-mKIAA antibodies. InCeP:A Database for Intracellular pathway based on mKIAA protein-protein interaction. |
| KOP | Database of human protein expression clones (Flexi ORF clones). |
Miscellaneousness
| Mouse DNA Microarray | Database of mouse DNA Microarray |
| DAGViz | GO analysis database for genes in eukaryotic genomes |
Computer software for genetic analysis
| Genotype Matrix Mapping | GMM Genotype Matrix Mapping: A Computer program for dedtection of QTL interactions |
| Polyans | Computer program for the typing polymorphic bands on electrophoresis gel |
| KAGIANA | Excel-based tool to retrieve genomic information and co-expressed genes in Arabidopsis thaliana |