an integrated resource for domestic Dog

How to use Dog Genome Database (DogGD) ?
1. Browse data

DogGD includes two assembly genomes that are dhole and wolf. DogGD only load the scaffold which longer than 500kb and the according annotated data information.

1.1 Scaffold

When users open “Assembly Data” menu, a statistical web page for dhole and wolf appears. Click the number in “>500k”, a scaffold list will be opened. The field in the result table describes as follows.

#Gene the number of gene annotated in the scaffold

#Aligned Reference Length (bp) the length of scaffold can aligned to the reference

#Coverage Reference Rate which equal to the aligned reference length/ aligned reference chromosome length

1.2 Gene

When click the gene number in the scaffold will open a gene list page.

Click the gene name will open the detail information of gene. There are two display ways for gene, including Custom and GenBank format.

For custom format, the data information will mainly display as table. While for GenBank format, the data information arrange as different parts as NCBI GenBank.

There annotated information for Gene has provided, that are Ensembl Gene, SwissProt and Trembl.

2. Search data

2.1 Simple Search

When uses click “search”, a basic search page shows as follows. Currently, users can search annotated information by scaffold name and gene, and they can also search scaffold by annotated information, such as KEGG, SwissProt ACC, Trembl ACC.

A gene list shows as search result.

2.2 Blast

DogGD provides Scaffold, CDS, pep sequence for users to do blast with own data. It supports four blast functions that are blastn, blastp, blastx and tblastn.

Users can upload own data or give a sequence in the input box, and then set several parameters. After wait a minute, then a result page will be shown.

A balstn result page shows as follows.

3. Genome View

3.1 Genome Syn

Genome Synteny Browse provides a synteny among dhole, wolf and reference dog. Users can view the synteny information by choose each chromosome of dog reference.

4. Download

DogGD provides genome file, peptipe file ,CDS file as well as annotation file for users to download. Users can retrieve these data from Link.