SilkDB 3.0

https://academic.oup.com/view-large/figure/190996505/gkz919fig2.jpg

Methods

linear multiple view multiple scale multiple focus contiguous no abstraction linear parallel arrangement linear orthogonal arrangement within interconnection segment sparse type segment contiguous type point sparse type point contiguous type

Tool

Access Format web application
Supported Files other
License Creative Commons Attribution License
Tool name

SilkDB 3.0
Tool Link https://silkdb.bioinfotoolkits.net/main/species-info/BMSK0008583
Documentation https://silkdb.bioinfotoolkits.net/main/help/-1#h-9

Paper

SilkDB 3.0: visualizing and exploring multiple levels of data for silkworm

Fang Lu, Zhaoyuan Wei, Yongjiang Luo, Hailong Guo, Guoqing Zhang, Qingyou Xia, Yi Wang, SilkDB 3.0: visualizing and exploring multiple levels of data for silkworm, Nucleic Acids Research, Volume 48, Issue D1, 08 January 2020, Pages D749–D755, https://doi.org/10.1093/nar/gkz919

Abstract

SilkDB is an open-accessibility database and powerful platform that provides comprehensive information on the silkworm (Bombyx mori) genome. Since SilkDB 2.0 was released 10 years ago, vast quantities of data about multiple aspects of the silkworm have been generated, including genome, transcriptome, Hi-C and pangenome. To visualize data at these different biological levels, we present SilkDB 3.0 (https://silkdb.bioinfotoolkits.net), a visual analytic tool for exploring silkworm data through an interactive user interface. The database contains a high-quality chromosome-level assembly of the silkworm genome, and its coding sequences and gene sets are more accurate than those in the previous version. SilkDB 3.0 provides a view of the information for each gene at the levels of sequence, protein structure, gene family, orthology, synteny, genome organization and gives access to gene expression information, genetic variation and genome interaction map. A set of visualization tools are available to display the abundant information in the above datasets. With an improved interactive user interface for the integration of large data sets, the updated SilkDB 3.0 database will be a valuable resource for the silkworm and insect research community.