ClusteredNR, the new protein database that provides results with a better overview of protein homologs in a wider range of organisms, is now available for blastx (translated nucleotide query) and PSI-BLAST (Position Specific Iterative BLAST) searches. Simply select ClusteredNR in the database section of the BLAST form. You can even search standard nr at the same time to compare results.
ClusteredNR is especially useful with blastx for finding more distant homologs when searching with queries from over-represented groups. For PSI-BLAST, the greater taxonomic scope of ClusteredNR database allows you to work more effectively with the default number target sequences in the first round. For more details and examples see our NCBI Insights post.
Try it out!
PeterC_NCBI Is there a plan/ETA when the clustered db indexes may be made available for download for local searches?
GenoMax I heard back from the development team. It will probably take at least six months before the ClusteredNR database is available for download. For it to be useful you'd need to have access to the contents of each cluster. Right now the web service queries an SQL database to get that information. We'll need to include a new app and some sort of LMDB file to make a portable / usable version of ClusteredNR.
Thanks for asking. That's a good question. Let me check with the development team and I'll get back to you,