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.
A search of the ClusteredNR database (results) using human myoglobin (NP_005359.1) as a query and limited to Cetacea (whales & dolphins) returns clusters containing all the whale myoglobin matches present in a search of standard nr, as well as matches to clusters containing cytoglobin (Figure 1 A). These significant cytoglobin matches are not shown in the standard nr results with the Cetacea limit, which are dominated by matches to proteins from a single species, Physeter catodon (sperm whale) (Figure 1 B).
Figure 1. Comparison of search results for ClusteredNR and standard nr. Both searches used a human myglobin (NP_005359.1) query and Cetacea as an organism limit. A. The complete Descriptions section from the ClusteredNR search results. The results show many myoglobin clusters containing only cetacean sequences, including a 14-member cluster containing proteins from 11 different whale species. The results also show significant matches to cytoglobin proteins including a 46-member cluster that has proteins from a wide range of mammals including whales. B. First and last four matches in the Descriptions table from standard nr results. All matches are Cetacean myoglobins and lack the cytoglobin matches shown in the ClusteredNR results.
How do I add an organism to my search?
Add an organism (or multiple) to your search by following these quick and easy steps:
- Select ClusteredNR in the database section of the BLAST form.
- Enter an organism from NCBI’s taxonomy in the organism box and select the matching name from the autocomplete list.
Note: If you’d like to add multiple organisms, click on the Add Organism button, and repeat previous steps. You can also choose to exclude organisms.
We want to hear from you!
As an ongoing effort to improve the BLAST service, including the ClusteredNR database, we want your feedback! If you have any questions or input on improvements, please write to us!
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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