Tutorial

Genomic variation data and phenotypic data are core data in SorGSD. Furthermore, practical tools for sorghum research, such as gene ID conversion, homologue search and genome browser, are also provided here. The data resources and tools mentioned above can be obtained directly from the Homepage or by 'Variation', 'Phonetype', 'ID Conversion', 'Homologue Search' and 'Genome Browser' functions.

1. Variation

A total of 39,547,621 genomic variations (including 33,825,236 SNPs and 5,722,385 small INDELs ) of 289 sorghum accessions were provided in SorGSD. You can search the variations on the page of Variation Search.

1.1 Variation Search

On this page, users can use advanced operations below to search variations:

  • Variation type: You can choose the type of variations (SNPs and INDELs) here.
  • Position: You can search through Variation ID directly. You can set the chromosome and start-stop site of a locus.
  • Gene Information: You can choose variations in one gene just by inputting a gene ID (V3.1) directly.
  • Consequence Type: You can also filter the variation by four levels of consequence types.
  • Minor Allele Frequency: You can set the minor allele frequency here.

The link of Variation Information Page and Gene Information Page will also be given in this page.

1.2 Variation Information
  • The Variation Information Page is used to display the whole information of a given variation site, which mainly contains Variation Detail, Individual Alleles, Gene Annotation and Genome Browser.
  • Variation Detail will list the Variation ID, Type, Position, Ref /Alleles, MAF, 5'-and 3'-flanking sequence.
  • In Individual Alleles, the SNP alleles of all samples at this position will be listed. A link of Phenotype Information Page of corresponding individual will also be given.
  • In Gene Annotation, the gene model table shows the gene list where SNP is located. The transcript and protein table will show the transcript and protein related to the reference SNP. Clicking on a Gene ID will redirect to the detail information of the gene in SorGSD.

The position of variation in genome will be displayed directly in Genome Browser.

1.3 Gene Information

The Gene Information Page shows Gene Detail, Gene Annotation (include transcript and peptide name, annotations, best hit gene and define in Arabidopsis and rice) and Variations Locating Gene.

2. Phenotype

Phenotypic data of 289 accessions are provided in SorGSD. The pictures of panicles are taken in our laboratory and the detail information of each individual is collected from GRIN-Global. You can search the phenotype on the page of Phenotype Search.

2.1 Phenotype Search

On this page, users can browse the profile information (include Panicle picture, Sample ID, Plant ID, Plant Name, Origin, Taxonomy and Usage) of each individual. You can search any key information of individual by Search. Click the picture to see the high-resolution image. The accessions without panicle pictures are indicated with cartoons. Click the Sample ID to see the detail Information.

2.2 Phenotype Detail

Here you can view the profile information of Phenotype Information and Phenotype Detail. Phenotype Detail includes Category, Descriptor, value and Study Environment.

3. ID Conversion

ID Conversion is a useful tool to convert gene accession from one to the other ID systems of V1.4, V2.1, V3.1, UniProt and PANTHER.

4. Homologue Search

Homologue Search is used for searching homologue of sorghum genes in maize, rice and Arabidopsis.

5. Genome Browser

SorGSD database uses Genome Browser to visualize several data types, including the variations, genes, transcripts and the density information of variations. Users would need to choose tracks and region of interest in the Select Tracks menu.