Faster, Better Results for Protein BLAST Searches

Effective August 2025, ClusteredNR will become the protein BLAST default database 

We are excited to announce that the default database for protein BLAST searches will soon be the NCBI ClusteredNR database! Introduced in 2022, ClusteredNR is a collection of protein sequence clusters built from the current default database, nr. The representative sequence for each cluster is chosen based on its title and reflects the function of the proteins in the cluster, helping you focus on meaningful biological insights and decreasing redundant results.  

What’s better about ClusteredNR?

• Faster searches 
• Decreased redundancy in results 
• Broader taxonomic coverage in results 

Searching ClusteredNR

The example below uses the human major prion protein, NP_000302, against ClusteredNR. The results table shows the first cluster contains 132 sequences, reducing redundancy in the results, and providing broader taxonomic coverage overall compared with the search against the nr database.

Tested with BLAST users

We tested this with users and found strong support for ClusteredNR as the new protein BLAST default database. The feedback from educators, researchers, students, and bioinformaticians emphasized its clarity, speed, and usefulness in research and teaching. 

Try it out!

Search the ClusteredNR database and let us know what you think. Share your feedback using the yellow feedback button on the BLAST webpage or email us directly.

Note: Later this summer ClusteredNR will become the default database for protein BLAST. The standard nr database will still be available as an option in the database selection list.

Stay up to date

BLAST is part of the NIH Comparative Genomics Resource (CGR). CGR facilitates reliable comparative genomics analyses for all eukaryotic organisms through the NCBI Toolkit and community collaboration. Connect with NLM on social media to stay up to date with BLAST and other CGR news.