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!
Figure 1. Accessing in-cluster analysis options. Shown: the Cluster Member view of a cluster. These results are from search against ClusteredNR with the human B-type creatine kinase (NP_001814.2) as a query. Using the menu bar at the top of this display, you can now also perform analyses within the cluster: generate a BLAST alignment with the query sequence against the individual sequences in the cluster, display the aligned cluster members in a BLAST-based Tree View or the MSA Viewer or launch COBALT to create a Multiple alignment. You can also download the cluster members in various formats as previously described.
Figure 2. The Cluster Taxonomy tab for the cluster members shown in Figure 1. The Cluster Ancestor in the BLAST results is Amniotes as shown at the top of the report. The taxonomy report reveals the diversity of land-based vertebrates — including lizards, snakes, and some mammals — that have proteins in this cluster.
We are always working to improve the ClusteredNR database and BLAST to help you identify protein sequences and find homologs. We welcome your feedback! If you have any questions or input on improvements, please write to email@example.com.
The BLAST ClusteredNR database is part of the NIH Comparative Genomics Resource (CGR), an NLM project to establish an ecosystem to facilitate reliable comparative genomics analyses for all eukaryotic organisms.
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