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Introduction

This page will help you get a quick overview of the site

Introduction

For the development of the BSVDB web resource, a total of 25 barley varieties were compared for structural variation between each chromosome of the genome and the reference genome Morex.

The web server contains six tabs. Home, Search, Tools, Introduction and About Us.

  • On the Home page, you can see an introduction and location information for the reference genome and each genome.
  • The Search page provides information about the selected breed in the upper part and search options in the lower part. You can search for structural variant information by selecting the genome or genomes and chromosomes as well as the pattern type, repeat type, length and position in the genome.
  • On the Tools page, you can enter a sequence to compare query sequence to the genome using local blast, or use JBrowse to visualise and annotate variation information on the genome.

    • After selecting the barley variety to be searched for, the web page provides a detailed description of the selected variety and an analysis of the data annotated with structural variants.

  • Search for structural variants in the interval of interest
  • Search for structural variants in gene id of interest

    • Based on the search query, the result page will display the structural variants and information.

  • You can see the statistics of the structural variants for the relevant interval or gene location.
  • You can click the Download button to download the structural variation annotation information file for the selected species.
  • Click the "Go to JBrowse" button in each row to view it in JBrowse.

    • Basic Local Alignment Search Tool

    You can use the BLAST tool for local sequence alignment

    Visualizing and exploring genomic data

    You can use JBrowse to visualise genomic information and to find regions of interest.

    Search featured region by annotation score

    By scoring the number of genomes containing structural variants at the same location, you get a score value for structural variants in each interval, and you can find and download featured regions by their scores.