New tool for sequence similarity searches in Coronaviruses

New tool for sequence similarity searches in Coronaviruses

5 Jun 2020 - 12:23

RNAcentral has launched a new tool to help scientists studying Coronaviruses to search thousands of viral genomes and explore results by virus, host, country, and more.

The new search uses nhmmer and enables the users to explore the results using facets powered by the EBI Search. For example, it is possible to search for a fragment of a SARS-CoV-2 genome, select similar sequences identified in COVID-19 patients, and browse sequence variants from different countries.

Betacoronavirus sequence similarity search interface

The viral sequences are regularly extracted from the NCBI BLAST database and the metadata is retrieved from the associated INSDC entries. While the search uses the same sequences as NCBI BLAST, there are several important differences:

  • Support for facets and keyword searches for exploring results
  • Use nhmmer as the search engine
  • Explore up to 1,000 top hits (compared to 100 in BLAST)
  • Integration with Rfam to annotate structured RNA elements

The search is produced and maintained by the RNAcentral team, repurposing the infrastructure of the RNAcentral sequence similarity search to query betacoronavirus sequences instead of non-coding RNAs.

Try the new search at https://covid19sequencesearch.github.io and get in touch with feedback.

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