- Bombyx mori comprehensive gene set : This gene set was constructed from 11,104 full-length cDNAs, 408,172 expressed sequence tags (ESTs), 2,089 publicly available mRNA sequences and 16,625 gene models, aiming at improvement of gene coverage. The details of the gene set is fully described in our paper entitled "Large scale full-length cDNA sequencing reveals a unique genomic landscape in a lepidopteran model insect, Bombyx mori". Please wait until the paper is accepted for publication.
- KAIKOGAAS : The database integrates the annotation of genome scaffolds generated from the silkworm genome sequencing efforts of Japan and China. The database provides detailed annotation of a total of 192 scaffolds anchored to the 28 silkworm chromosomes (total length - 417.7 Mb) as well as 4,615 scaffolds which are more than 1kb in length but with unknown position in the chromosomes. In addition, the database also includes the annotation of 55 BAC clones that were used to check the quality of the WGS assembly.
- Linkage Map : Using 190 segregants from a backcross of a p50T female x an F1 (p50T x C108T) male, a toltal of 1,755 SNPs linkage map was constructed with Mapmaker/exp (version 3.0; LOD score 3.0 ) . The SNP markers segregated into 28 linkage groups, with a total recombination length of 1413 cM.
- Full-length cDNA database (KAIKOcDNA) : The search function for clone / keyword in the silkworm full-length cDNA sequences submitted to public database. A list of silkworm full-length cDNA sequences was provided, too. These were derived from various cDNA libraries constructed using different strain, organ / tissue, developmental stage etc.
- EST database (KAIKOcDNA) : The search function for clone / keyword in the silkworm partial cDNA sequences submitted to public database. A list of silkworm partial cDNA sequences was provided, too. These were derived from various cDNA libraries constructed using different strain, organ / tissue, developmental stage etc.
- Bombyx Trap DataBase : Information on reporter expressions and positions of transposon vectors (mutators) in transposon insertion lines (enhancer trap strains, or gene trap strains) is presented with this database. This database is integrated into silkworm genome database, KAIKObase.
- KAIKO 2D DataBase : A two-dimensional polyacrylamide gel electrophoresis federated database for analysis of silkworm proteins from various organs/tissues and developmental stages. In analysis, EST and gene models obtained from the joint collaboration of Japan and China are used. The organs/tissues include midgut, fatbody, middle silkgland, posterior silkgland, malpighian tube, ovary and hemolymph at various developmental stages such as larva, spinning and pupation. This database is integrated into silkworm genome database, KAIKObase.
The query interface of KAIKO 2DDB utilizes the Make2D-DB II tool from the Swiss Institute of Bioinformatics.
- BombMap : Bomoyx mori genome Map information system is a database mainly for the silkworm linkage map using RAPD (Randomly Amplified Polymorphic DNA), STS (Sequence-Tagged Site) markers.
- Transposons : A list of silkworm Transposons submitted to public databases. These data were collected using Sequence Retrieved System (SRS) version 8, a network browser for molecular biology databanks. One of the main features of SRS is its ability to link data from one source to related information in another and analyses of the search using many bioinformatic analysis tools or applications. For further information, please refer to the SRS version 8 site which can be accessed through the NIAS DNA Bank.
- Genomic Sequences : Scaffold, contig, repeat, BAC, BAC end, Fosmid end, and gene model sequences can be downloaded.