e.g. 1:1246..9423
How to use DoGSD database?

1.Browse

1.1 SNP tables

DoGSD database summarizes SNP number by chromosome of 77 samples (8 wolves and 69 dogs) and dbSNP(version 139) both on individual and nonredundant resolutions. Click the number, you will see the whole SNP list at a given chromosome.

 

Chrom: the chromosome of dog/wolf.
#Reference SNP: refers to the unique SNP number in this database.
From the third to the thirteenth columns refers to the Individual SNP lists of all our samples.

1)Reference SNP list

The #Reference SNP would lead users to a reference SNP table which shows general SNP information of all samples. In this page, users will see the colored genotype of all samples at a given position which identified by individuals name. If this position hit in a gene, the gene name and the located region will be shown. Click RSNP ID will go to the detail information page of this position, and click GBrowse link will open a GBrowse view panel.

2)The reference SNP detail information

The detail information of reference SNP is used to exhibit the detail SNP information of a given SNP in DoGSD. The page mainly includes three parts that are general information, gene information and SNPs of other individuals in this position. General Information lists gene ID, version number, chromosome and position and SNP class of a given SNP. In gene information part, the gene model shows the gene list in which SNP located. The transcript and the protein part will show the transcript and protein related to the reference SNP. Click Gene ID will go to the detail information of gene in DoGSD, and click transcript or protein accession will go the Ensembl database. In SNPs of other individuals part,the SNP of all samples at this position will be listed.

3)Individual SNP list

The #sample_id list represents individual SNP list which shows general information about SNPs of the individual. Click SNP ID will go to the detail information page of this SNP.

4)SNP detail information

The SNP detail information is used to view the SNP information of a specific individual at the given position. Users can see 6 parts of information.

The General Information part will show SNP ID, individual, SNP loaded time and NCBI rs id of a SNP.

The Allele Information part will show the individuals genotype information, 30bp of 3 flank and 5 flank sequence.

The Reference Map Information will show the position, derived and reference alleles.

The Gene Information will show the information about related gene, transcript and protein of a SNP.

The SNPs of other individuals in this position will show the genotype information in other individuals.

The Fasta information will show 50 bps sequence of upstream and downstream of this SNP.

5)Gene detail information

The gene detail information shows SNPs located in the corresponding gene.

1.2 SNPs in Gene

SNP in Gene Statistics lists SNPs located in gene and coding regions. According to the protein sequence, we divided the SNP list into synonymous and non-synonymous ones. Click the number in the statistical column, you will see the whole SNP list.

1)SNP hit in gene

The #SNP Hit in Gene list is used to view SNP information located in different gene region, that is 3 UTR, 5 UTR, intron, CDS,splice_site,NON_CDS. Click SNP ID will go to the detail information page of this SNP.

2)Coding SNP information

The #SNP coding, #Coding Synonymous, #Coding NonSynonymous lists are used to view SNP located in gene CDS region, annotated as synonymous and nonsynonymous, the residue change column gives residue change which derived by this SNP.

1.3 Browse on Chromosome

DoGSD database use GBrowse to visualize several data types, including the indel, SNP, gene, transcript and the density information of SNP/300kb, allele frequency. At first, users need to choose the interested tracks in the Select Tracks page, and a region, then you can see what you choose in the GBrowse page.

2.Search

DoGSD provides SNP search function, including search SNPs in single individual and comparison of SNPs in two or more individuals. Users can set several parameters to search through this database, including location in chromosome, SNP class (mainly SNP), SNP location in gene region and genotype. The search result page of single individual is a little different from compared individuals.

2.1 Single individual search

Use this search,user can view SNP data of each individual.To do this,uses must choose the "Show SNP information in individuals" in the search page.In single search result page, users can see the search condition set in the search page, and the total number of SNP is also returned. Below the search condition, uses can see the SNP list, the information including SNP ID, position, location (if SNP is located in gene, the gene name will be show) and flank sequence (upstream and downstream of 30bp at this position).Users also can click GBrowse link to see the SNP in GBrowse panel.And if you click the SNP ID link, a detail information will be showed.

2.2 Compared individuals search

Use this search,users can view SNP information of two or more individuals.To do this, users must choose "Show SNP information by individuals comparisons" in the search page.In compared individuals search result page, the SNP list shows SNP in selected individuals according to SNP location of referred individual. Therefore, the UniSNP ID referred to the reference SNP, and the order of individuals behind the Ref genotype column correspond to the order of selected individuals.

Users also can download the search result. To download the result, first choose the SNP, and then click the download button. Two download models are supported. The Text model will list the selected items in a web page, and the File model will save the selected items in a file.

 

3.Download

Users can download the SNP file and bam file and fastq file of specific samples in this database.The ftp site is ftp://pub.big.ac.cn/pub/dogsd/

4. General search

DoGSD database provides general search function towards two data types ,that are gene and SNP. General search is used to search the information in all individuals, which is different from SNP search function. Several types of keyword are supported; a detail description will be given in the following part.

Region search: users can set a region to search the SNP information in all individuals, the format is chromosome: start position.. end position, such as 1:3000246..3003423
SNP search: users can set the genotype to search the SNP information in all individuals, the format is snp: genotype, such as snp:W. The genotype can be lower or upper word.

Individual search: users can search the SNP of one given individual of DoGSD database, such as KM2

Gene name search: users can set the gene name to search the gene information.

Any word search: users can set any word to search, if the word matches any of the following column that are gene name, SNP id, SNP local id, SNP chromosome and SNP position, a search result will be returned.