legumeSSRdb Tutorial


Help section page of legumeSSRdb, here you will find a step by step guide to search microsatellites (SSR) in 13 legume species and design markers for crop improvement. Users can also check cross species transferability of designed markers. If you have any questions that are not covered in this page please refer to FAQ page or send an email to naveen.duhan@usu.edu. For this tutorial we will use the Demo , so if you want to replicate the results obtained in this tutorial just follow the steps.


Major features implemented in legumeSSRdb.

  1. Advanced SSR querying
  2. Real time visualization of SSR query statistics
  3. SSR sequence extraction based on custom flanking region
  4. Custom primer design and validation
  5. Cross species transferability (ePCR)
  6. SSR predictor tool (SSR-web)
  7. Visualization of SSRs using JBrowse
  8. Local NCBI blast

Search Microsatellites

Select a species from the species dropdown menu or click any species on home page. This will open a search page for the selected species.

  • SSR can be searched in three different regions: Genic, Non-genic, and Genomic
  • Select a chromosome number or select all
  • Select a motif type or enter repeat motif type to search

You can also search based on motif frequency, genomic region using advanced search options

Result page will display the SSR and their information based on the search query. Select design primers to design markers.

Design Primers

On this page you can design custom primers for the markers

The designed markers are displayed in the genome. Select a marker from left side table to view the markers.

Run ePCR

Run ePCR option can be used for a marker to check cross species transferabilty

Amplification of selected markers can be viewed in other species either selecting genome from the dropdown menu or providing a FASTA file.


SSR can be visualize on reference genome with annotation using Jbrowse.

User can also run standalone blast against the legume species.

User can also predict SSR in a given sequence using our prediction tool.

Browser Compatibility

legumeSSRdb have been tested in the following setups.

OS Version Chrome Firefox Safari Opera
Linux Ubuntu 20.04 87.0.4280.88 84.0.2 n/a 58.0.3135.53
MacOS Mojave 10.14.2 72.0.3626.121 65.0.1 12.0.2 not tested
Windows 10 72.0.3626.121 63.0.3 not tested 45.0.2552.888