Tag: Nucleotide BLAST (blastn)

Updated bacterial and archaeal reference genomes collection now available!

Updated bacterial and archaeal reference genomes collection now available!

An updated bacterial and archaeal reference genome collection is available! This collection of 17,163 genomes was built by selecting exactly one genome assembly for each species among the 272,000+ prokaryotic genomes in RefSeq, except for E. coli for which two assemblies were selected as reference.

A total of 497 species are included in this collection for the first time. In addition, comparing to the October 2022 set, 174 species are represented by a better assembly and 15 species were removed because of changes in NCBI Taxonomy or uncertainty in their species assignment. The criteria for selecting one assembly for a given species from all assemblies available in RefSeq for the species include assembly contiguity and completeness and quality of the RefSeq annotation. See the documentation for details.

We have updated the nucleotide BLAST RefSeq reference genomes database (fourth in the menu) as well as the database on the Microbial Nucleotide BLAST page to reflect these changes. You can also run BLAST searches against the proteins annotated on these reference genomes (RefSeq Select proteins database, second in the menu).

Re-evaluating the BLAST Nucleotide Database (nt)

Re-evaluating the BLAST Nucleotide Database (nt)

The ongoing sequencing revolution has resulted in exponential growth of the NCBI BLAST databases. The default BLAST nucleotide database (nt), the most popular Web BLAST database, is currently 903 billion letters and continues to grow rapidly – doubling in size in the last year. This growth will cause longer search times, reduced capacity, and more delays in updating the database. In the not-too-distant future, searching the entire nt database on the web will no longer be possible unless we modify the database scope and composition.

Because of the above concerns, we want to make the default Web BLAST nucleotide database smaller and more efficient. Some options are to:

    • Change its composition to improve the quality of sequence entries included
    • Take steps to slow its growth rate
    • Divide it into several databases by biological or functional categories

Continue reading “Re-evaluating the BLAST Nucleotide Database (nt)”

Now available: Updated prokaryote representative genomes collection

Now available: Updated prokaryote representative genomes collection

An updated bacterial and archaeal representative genomes collection is available! We selected a total of 16,665 of the 262,000 prokaryotic assemblies in RefSeq to represent their respective species. For the first time, more complete assemblies (as calculated by CheckM) were ranked higher than less complete assemblies. See the ranked list of criteria for selecting representative assemblies here. Continue reading “Now available: Updated prokaryote representative genomes collection”

Announcing an updated prokaryotic representative genomes collection with 706 new species!

Announcing an updated prokaryotic representative genomes collection with 706 new species!

An updated bacterial and archaeal representative genomes collection is available! A total of 16,105 assemblies among the 249,000 prokaryotic assemblies in RefSeq were selected to represent their respective species. The collection has grown by 3.7% since January 2022. A total of 706 species are represented for the first time. In addition, 186 species are represented by a better assembly, and 124 species were removed because of changes in NCBI Taxonomy or uncertainty in their species assignment.

We updated the database on the Microbial Nucleotide BLAST page as well as the basic nucleotide BLAST RefSeq Representative genomes database (fourth in the menu) to reflect these changes. Finally, remember that you can now run BLAST searches against the proteins annotated on representative genomes (second in the menu). See more info here.

BLAST+ 2.13.0 now available with SRA BLAST, ARM Linux executables, and database metadata

BLAST+ 2.13.0 now available with SRA BLAST, ARM Linux executables, and database metadata

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.

New features

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.

ARM Linux executables

This release also includes executables compiled under ARM Linux for the first time. Please let us know if you find any issues with ARM Linux programs.

Database metadata in JSON format

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.

Updated prokaryotic representative genomes collection includes 685 new species!

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.

We updated the database on the Microbial Nucleotide BLAST page as well as the basic nucleotide BLAST RefSeq Representative genomes database (fourth in the menu) to reflect these changes. Finally, remember that you can now run BLAST searches against the proteins annotated on representative genomes (second in the menu). Find more information here.

Updated prokaryotic representative genome collection

The bacterial and archaeal representative genome collection has been updated!  We selected a total of 14,912 of the 224,000 prokaryotic RefSeq assemblies to represent their respective species. The collection has grown by 8% since April 2021 and now includes Candidatus and endosymbiont species (Figure 1), which constitute 303 and 140 respectively of the 1,077 newly added species. In addition, 719 species are represented by a better assembly, and 70 species were removed because of changes in NCBI Taxonomy or uncertainty in their species assignment.

Figure 1. Graphical view of a portion of the RefSeq Representative assembly for the bedbug endosymbiont Candidatus Wolbachia massiliensis isolate PL13.

Continue reading “Updated prokaryotic representative genome collection”

BLAST+ 2.12.0 now available with more efficient multithreaded searches

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.

Continue reading “BLAST+ 2.12.0 now available with more efficient multithreaded searches”

Prokaryotic representative genomes update–over 900 new species!

We are happy to announce an updated bacterial and archaeal representative genome collection! We have selected 13,835 among 214,000 prokaryotic RefSeq assemblies to represent their respective species. The collection has increased by 6% since December 2020. About 950 species are represented for the first time, 476 species are represented by a better assembly, and 170 species were removed because of changes in NCBI Taxonomy or uncertainty in their species assignment.

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April 7 Webinar: Recent and upcoming enhancements to NCBI BLAST and Primer-BLAST services!

April 7 Webinar: Recent and upcoming enhancements to NCBI BLAST and Primer-BLAST services!

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
  • Register

After registering, you will receive a confirmation email with information about attending the webinar. A few days after the live presentation, you can view the recording on the NCBI webinars playlist on the NLM YouTube channel. You can learn about future webinars on the Webinars and Courses page.