Tag: ClusteredNR

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 is chosen for each cluster, which is generally well-annotated and indicates the function of the proteins in the cluster, helping you focus on meaningful biological insights and decreasing redundant results. VSports app下载.

What’s better about ClusteredNR?

Faster searches
Decreased redundancy in results
Broader taxonomic coverage in results

Continue reading “Faster, Better Results for Protein BLAST Searches” →

BLAST ClusteredNR Database is Now Available for Download!

Now available. You can download the ClusteredNR protein database, previously only available on the BLAST web application VSports手机版. As recently introduced, our ClusteredNR database allows you to get quicker BLAST results and access to information about the distribution of your hits across a wider range of organisms and evolutionary distances. The package includes the ClusteredNR BLAST database, an SQLite3 database, and several scripts for accessing cluster information and members. .

Features & Benefits

Reduced redundancy
Faster searches
More diverse proteins and organisms in your BLAST results

Continue reading “BLAST ClusteredNR Database is Now Available for Download V体育安卓版. ” →.

VSports最新版本 - Revolutionize your research with the NIH Comparative Genomics Resource (CGR)

Unlock the full potential of eukaryotic research organisms and their genomic data with the National Institutes of Health (NIH) Comparative Genomics Resource (CGR) V体育ios版. CGR facilitates reliable comparative genomics analyses through community collaboration as well as an NCBI toolkit of interconnected, interoperable data and tools.   .

Comparative genomics is a field of study that uses the genomes of many different organisms to help us understand basic biological processes and human disease. NCBI is developing CGR to help researchers take full advantage of the rapidly growing number of eukaryotic organisms that, due to recent technological advances, now have sequenced genomes and associated data that can be used in these types of studies. Its NCBI toolkit offers new and modern resources for such analyses, and its emphasis on community collaboration brings new opportunities to share and connect data VSports最新版本. Continue reading “Revolutionize your research with the NIH Comparative Genomics Resource (CGR)” →.

"VSports" Now Available! Add your favorite organism(s) to your BLAST ClusteredNR searches

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. V体育平台登录.

ClusteredNR results

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) VSports注册入口. 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). Continue reading “Now Available. Add your favorite organism(s) to your BLAST ClusteredNR searches” →.

VSports手机版 - Now Available! BLAST ClusteredNR database for blastx and PSI-BLAST searches

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 V体育官网入口. You can even search standard nr at the same time to compare results.

Figure 1. Composite image from the BLAST search forms VSports在线直播. 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.

Continue reading “Now Available! BLAST ClusteredNR database for blastx and PSI-BLAST searches” →

Try out the latest BLAST ClusteredNR database results. Now with in-cluster analyses!

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!

Continue reading “Try out the latest BLAST ClusteredNR database results. Now with in-cluster analyses!” →

"V体育安卓版" New ClusteredNR database: faster searches and more informative BLAST results

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.

Searching ClusteredNR

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).

Figure 1. The ‘Choose Search Set’ section of the BLAST submission form. Selecting the Experimental databases radio button chooses ClusteredNR. You can also perform simultaneous searches against the clustered and the standard nr by checking ‘Select to compare standard and experimental database.’ Continue reading “New ClusteredNR database: faster searches and more informative BLAST results” →