SilkDB
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Analysis & Tools

BLAST
SilkMap
Wego
BmArraymap
Clustalw
Cap3
SMS

Publications

• Science 306, 1937-1940 (2004)( PDF )

• Nucleic Acids Research 33, 399-402 (2005)( PDF )

Quick Start Guide

1. Introduction

SilkDB is an integrated database for genome biology of silkworm. This database provides not only information of genomic data including sequences, genes, functional annotation and chromosome mapping, but also biological information such as expression data and corresponding references. In addition, previously and newly developed bioinformatics tools provided in the database will facilitate users to easily exploit information they wanted. SilkDB will be useful for the research of the silkworm functional and comparative genomics.

2. Database Searches

A. Quick Search

The Quick Search is available in the toolbar located at the left of most pages. User could perform a Quick Search by entering keywords, gene symbol, scaffold ID, or position of scaffold.

Examples of search terms:

* BGIBMGA012615 (Gene ID)

* BGIBMGA01261* (Batch of Gene IDs)

* nscaf1071 (Scaffold ID)

* nscaf1071:63000..80184 (Genome Position)

* pheromone (Keyword)

The under picture is an example of searching result by Keyword of "pheromone".

Clicking on an individual item within a track will link to Gbrowse reprot of this gene.

B. SCB Tool

Silkworm Chromosome Browser (SCB) is a tool to provide the position of scaffolds on 28 chromosomes, which are fully interactive and enable the user to click on any region of chromosome to access the page of detailed view by Gbrowse. Before using this tool, please download the SVG plugin from Adobe SVG plugin download page and install it.

 

C. BLAST Tool

User could use the BLAST to search against scaffolds, genes, ESTs, repeat sequences, other genomes and genes of model organisms. On the result page of a BLAST search, each hit is linked to the GBrowse view of the sequence.

D. SilkMap Tool

SilkMap is a tool to map protein or nucleotide sequence on silkworm chromosomes. Through SilkMap, user could not only know location of the query sequence on chromosomes, but also know the copies of the query sequence in silkworm genome.

 

3. Gene Page

Gene Page is the heart of SilkDB. Gene Page is available for each gene, containing all the related information, including gene symbol, position, definition, EST evidence, corresponding microarray probes, domain assignment, GO annotation, gene family (orthologs and paralogs), refseq ID, reference information (title, author, and PubMed ID), BLAST homolog, genome sequence, CDS sequence, as well as deduced protein sequence.