SilkDB v2.0: a platform for silkworm (Bombyx mori ) genome biology

Abstract

The SilkDB is an open-access database for genome biology of the silkworm (Bombyx mori). Since the draft sequence was completed and the SilkDB was first released 5 years ago, we have collaborated with other groups to make much remarkable progress on silkworm genome research, such as the completion of a new high-quality assembly of the silkworm genome sequence as well as the construction of a genome-wide microarray to survey gene expression profiles. To accommodate these new genomic data and house more comprehensive genomic information, we have reconstructed SilkDB database with new web interfaces. In the new version (v2.0) of SilkDB, we updated the genomic data, including genome assembly, gene annotation, chromosomal mapping, orthologous relationship and experiment data, such as microarray expression data, Expressed Sequence Tags (ESTs) and corresponding references. Several new tools, including SilkMap, Silkworm Chromosome Browser (SCB) and BmArray, are developed to access silkworm genomic data conveniently. SilkDB is publicly available at the new URL of http://www.silkdb.org.

Figure 1.

Example of searching and browsing of SilkDB. (A) Snapshot of the tool of SilkMap. This tool enables users to anchor protein or nucleotide sequence on silkworm chromosomes. (B) An example of search result for SilkMap. The pentagrams indicate the position on chromosome for query sequence, and provide the hyperlink to corresponding GBrowse view. (C) Snapshot of the tool of SCB. This tool enables users to click on any part of chromosome to access the page of detailed view by GBrowse. (D) Visualization of genome annotation by GBrowse. (E) An example of Gene Page.