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).
BLAST+ 2.13.0 includes several important new features including SRA BLAST programs, ARM Linux executables, and the ability to produce database metadata as well as some important improvements, and a few bug fixes. You can download the new BLAST release from the FTP site.
SRA / WGS BLAST (blastn_vdb, tblastn_vdb)
Beginning with this release, the BLAST distribution now includes the SRA BLAST programs blastn_vdb and tblastn_vdb that can directly search SRA and WGS projects without the need to build a BLAST database. See the BLAST documentation on how to use these programs with WGS projects.
Starting with BLAST+ 2.13.0, the makeblastdb program generates an additional file with the file extension .njs for nucleotide databases or .pjs for protein databases. These files contain BLAST database metadata in JSON format. See the BLAST database metadata section in the BLAST User Manual for an example. This file can be easily read by many tools and makes the BLAST database more compliant with FAIR principles.
See the release notes for more details on improvements and bug fixes for the release.
Important reminder about usage reporting
As we announced previously, BLAST can report limited usage information back to NCBI. This information shows us whether BLAST+ is being used by the community, and therefore is worth being maintained and developed. It also allows us to focus our development efforts on the most used aspects of BLAST+. Please help us improve BLAST by allowing BLAST to share information about your search. The BLAST privacy statement provides details on the information collected, how it is used, and how to opt-out of reporting if you don’t want to participate.
We are happy to announce an updated bacterial and archaeal representative genomes collection. The current collection contains a total of 15,507 assemblies selected from 236,000 prokaryotic RefSeq assemblies to represent their respective species. The collection has grown by five percent since August 2021. A total of 685 species are represented for the first time. In addition, 370 species are represented by a better assembly, and 84 species were removed because of changes in NCBI Taxonomy or uncertainty in their species assignment.
BLAST+ 2.12.0 programs feature better multithreaded searches and support a different threading model, threading by query, that can be more efficient in some situations. The new release is also fully compatible the increase in the numeric range for the GI identifier, which will take effect in the nucleotide database later this year. The list below shows details of the new features and bug fixes. You can download the new BLAST release from the FTP site.
Join us on April 7, 2021 at 12PM eastern time to learn about new web BLAST and Primer-BLAST enhancements that improve your BLAST experience. You’ll also see a preview of some planned improvements to the databases that make it easier to find relevant matches.
Recent changes to web BLAST include added data columns on the descriptions table, so you can quickly find and sort your matches. Primer-BLAST now offers direct links from genome assembly pages, so you can easily select the specificity database. Primer-BLAST also now accepts multiple target templates making it easy to design primers that can amplify several similar sequences such as all splice variants of gene or the same target (16S, COI) from different strains or species.
Date and time: Wed, April 7, 2021 12:00 PM – 12:45 PM EDT
The version 5 BLAST (dbV5) protein databases are now accession-based. You can access these databases and the nucleotide BLASTDBs on our FTP site.
As we described in a previous post, this means they now contain the GI-less proteins from the NCBI Pathogen Project and other high-throughput projects. The v5 databases are also compatible with proteins from PDB structures with multi-character chain identifiers and will include these as they become available in our other protein systems. Only the latest version of BLAST+ (2.9.0, download) will work with the updated v5 databases and allow you to access all of the most recent protein and nucleotide data. In the winter of 2019, we will stop updating the version 4 BLAST databases and offer the v5 databases as the default for download.
In addition, makeblastdb will be updated in BLAST 2.10.0, due out in October 2019, so by default it creates dbV5 formatted databases.
As you may know, we have been offering a new BLAST results (Figure 1) as a test page since April. In response to your positive reception and after incorporating many improvements that you suggested, we made the new results the default today, August 1, 2019.
You will still be able to access to the traditional results for a several months. This will provide you additional time if you need it to adjust your workflows or teaching materials to the new display.
As you probably know, BLAST has been offering a new results page as an option for standard BLAST for you to test and provide feedback since April. See our post from earlier this spring for more details. We have just added new results pages (Figure 1) for the following four specialized BLAST services for you to test.
We recently updated the version 5 BLAST protein databases, (dbV5), on our FTP site to be completely accession-based. As we described in a previous post, this means they now contain the gi-less proteins from the NCBI Pathogen Project and other high-throughput projects. The v5 databases are also compatible with proteins from PDB structures with multi-character chain identifiers and will include these as they become available in our other protein systems. Only the latest version of BLAST+ (2.9.0, download) will work with the updated v5 databases and allow you to access all of the most recent protein data. At the end of September 2019, we will stop updating the version 4 BLAST databases and offer the v5 databases as the default for download.