Recently, an international collaboration has been launched to assemble a complete silkworm genome sequence, which is based on the 6× and 3× draft genome sequences created by Chinese group and Japanese group in 2004 (Mita et al., 2004; Xia et al., 2004), respectively. The genome assembly quality has been greatly improved. Base on a high density SNP genetic map, over 80% of genome sequence could be mapped on 28 chromosomes of the silkworm.
The first version of SilkDB was released in 2004. Since that time, the silkworm has become a focus in insect research community and the study of silkworm has been greatly accelerated. Now, we are happy to announce the release of a new version of SilkDB, which updated all of the data, added new information of genome sequence and genes, and provides new tools to facilitate use of the genome database. In sum, the following areas have been improved:
•Updated the new genome assembly data
•Updated the new gene prediction data
•Provided the ncRNA data, such as miRNA gene, tRNA genes, rRNA gene.
•New genome browser New SilkDB now provides a new genome browse to navigate the genome information, which was based on the chromosomes. Click on anywhere on a chromosome, it links to the GBrowse browser to visit the genome sequence or gene information.
•New SilkMap tool In order to provide a convenience browser, we have developed a new tool, SilkMap. By using this tool, users could map any protein sequences or nucleotide sequences on silkworm chromosomes. It will provide a visualization picture of the locations. Through it, user could know locations of query sequences on chromosomes, and the number of gene copies in the silkworm genome.
•New annotation data The SilkDB has been updated for all of the annotation of all the genes, including:
- Gene ontology annotation
- Links to silkworm microarray database BmMDB for expression data
- Links to refseq of NCBI
- Links to PubMed references