Do you currently add an organism name(s)to focus your searches when using the BLAST standard nr database? You can now focus your searches by organism with the BLAST ClusteredNR database and get faster results with a better overview of protein homologs in a wider range of organisms. Your searches will be restricted to protein clusters that contain one or more sequences from the organism(s) you add.
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 (Figure 1). Simply select ClusteredNR in the database section of the BLAST form. You can even search standard nr at the same time to compare results.
Figure 1. Composite image from the BLAST search forms. The ClusteredNR database is available now for blastx and PSI-BLAST searches in addition to blastp. For all types of searches, you can choose to search both ClusteredNR and standard nr at the same time so you can 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. The two searches described below highlight these advantages of ClusteredNR.
As we previously announced, we are offering a ClusteredNR protein database on the web BLAST service that provides faster searches, greater taxonomic reach, and easier to interpret results than the traditional nr database. We’ve added some new features to the results that make the ClusteredNR even more useful by allowing analyses within each cluster including the ability to:
Align the query to the members of the cluster.
Display Tree View and MSA View the cluster alignment.
Submit the cluster to COBALT to generate a true multiple sequence alignment of the members.
Display a BLAST Taxonomy Report to see the taxonomic distribution of the sources of the members.
Figure 1 shows you how access these in-cluster analysis options. The new Cluster Taxonomy report is shown in Figure 2. Try ClusteredNR yourself — follow this link to set up a search!
Reduced redundancy. Faster searches. More diverse proteins and organisms in your BLAST results. Check out our new ClusteredNR database – derived from the default BLAST protein nr database by clustering sequences at 90% identity / 90% length (details below). Get quicker results and access to information about the distribution of your hits across a wider range of organisms and evolutionary distances.
You can choose the ClusteredNR database in the Choose Search Set section of the BLAST submission form where you normally pick the BLAST database. Simply select the Experimental databases radio button. You can also select the checkbox to search both ClusteredNR and the standard nr at the same time allowing you to compare results (Figure 1).