Gene Structure Display Server 2.0

BioCodeKb - Bioinformatics Knowledgebase

Visualizing genes structure and annotated features helps biologists to investigate their function and evolution intuitively. The Gene Structure Display Server 2.0 has been widely used by more than 60,000 users since its first publication in 2007. This server of newly designed interface, supports for more types of annotation features and formats, as well as an integrated visual editor for editing the generated figure. Gene Structure Display Server (GSDS) is designed for the visualization of gene features, such as the composition and position of exons, introns, and conserved elements etc. To facilitate evolutionary analysis, a phylogenetic tree can be uploaded and added on the figure.


Features

Compared with version 1.0, GSDS 2.0 has a newly designed user-interface and several new features as following:

  • Support for multiple widely-used gene feature description formats including BED, GTF/GFF3 has been added.

  • Besides exons and introns, more types of annotation features such as conserved-elements, binding sites and other functional elements can be displayed with customizable shapes/colors.

  • The figure can be modified in feature display after its first generation, and sent to a built-in interactive editor for further refining.

  • To facilitate evolutionary analysis, a phylogenetic tree can be uploaded and added to the side of the gene structure.

  • Moreover, extra features such as conserved elements and binding sites can also be uploaded and displayed along with the main features.

  • The generated figures can be further modified by users. With the purpose to generate suitable, high-quality figures for publication, GSDS 2.0 provides types of functionality on their further modification. By setting the parameters on the result page, users can turn on/off the display of specified features and adjust their size, shape and color. Intron lengths can also be rescaled to display large introns properly.

  • Moreover, the generated figure can be sent to a built-in online SVG editor for further modification interactively after clicking the ‘Edit figure interactively’ button.


A web server GSDS (Gene Structure Display Server) has been developed for drawing gene structure schematic diagrams. Users can submit three types of data of CDS and genomic sequences, NCBI GenBank accession numbers or GIs, exon positions on a gene. GSDS uses this information to obtain the gene structure and draw diagram for it. Users can also designate some special regions to mark on the gene structure diagram. The output result will be PNG or SVG format picture. The corresponding sequence will be shown in a new window by clicking the picture in PNG format.


Get the GenBank gff annotation with your GenBank accession number by yourself and input the gff file to GSDS 2.0. For example, your GenBank accession number is NG_008935.1

  1. Go to the GenBank entry https://www.ncbi.nlm.nih.gov/nuccore/NG_008935.1

  2. Download the GFF3 file by clicking "send to" on the upper right corner then click "File" and then choose GFF3 format and click "Create File".

  3. Use the GFF3 file as input to GSDS.

  4. If the introns in the resulted plot are displayed too long. At the result page of GSDS 2.0, use the Change the Intron rescale option to Shrink, adjust the shrink factor and click redraw, then you will get a nice plot.

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