BLASTFeed

Starting with this release, we are including the blastn_vdb and tblastn_vdb executables in the BLAST+ distribution. These executables can directly search SRA and WGS projects without the need to build a BLAST database. See https://ftp.ncbi.nlm.nih.gov/blast/WGS_TOOLS/README_BLASTWGS.txt for information on using these executables with WGS projects.

We have also produced ARM LINUX executables and placed them on the FTP site (ncbi-blast-2.13.0+-x64-arm-linux.tar.gz). These executables have passed our normal QA, but this is our first release for this architecture. Please let us know if you find any issues.

Usage reporting - Help improve BLAST by sharing limited information about your search. Details on the information collected, how it is used, how to opt-out, and our privacy statement is found here: https://www.ncbi.nlm.nih.gov/books/NBK563686/

New features

• Blastn_vdb and tblastn_vdb included in the 2.13.0 release.
• Makeblastdb now produces a (JSON) metadata file about the database. This makes BLAST databases more Findable in the FAIR sense. See https://www.ncbi.nlm.nih.gov/books/NBK569839/#usrman_BLAST_feat.BLAST_database_metadat for details.

Improvements

• TBLASTN can now handle database sequences up to 2 billion bases (was 1 billion)
• Makeblastdb default volume size is now 3 billion bases (was 1 billion)
• Dustmasker has a new option to replace low complexity regions with N's (hard masking)
• Makeblastdb will issue an error message and exit if it encounters a sequence longer than the maximum supported size (2,147,483,647 letters).

Bug fixes

• Rare problem with mutex that caused BLAST to crash.
• Memory leaks.

See the release notes for more details at https://www.ncbi.nlm.nih.gov/books/NBK131777/

The new executables are at https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST

ElasticBLAST is a new cloud based tool to run your BLAST searches faster and make you more effective.

ElasticBLAST is ideal for users who have a large number (thousands to millions) of queries to BLAST or who prefer to use cloud infrastructure for their searches. It makes running BLAST on the cloud fast and easy and can run on Amazon Web Services and Google Cloud Platform.

To get started with ElasticBLAST, go to https://blast.ncbi.nlm.nih.gov/doc/elastic-blast/

We'll also have a webinar on ElasticBLAST on February 16. Register at https://attendee.gotowebinar.com/register/6641488258216124684?source=BLASTNews

Other resources:

• Our Poster from BOSC2021: https://f1000research.com/posters/10-920
• Our GitHub page: https://github.com/ncbi/elastic-blast

IgBLAST is now able to determine Ig isotypes.

We have added a new function to the NCBI IgBLAST webpage. Users can now search immunoglobulin (Ig) nucleotide sequences with the Constant region (C) gene database to determine the Ig isotypes including subtypes (IgM, IgG, IgA1, etc). The isotype information is reported in the rearrangement summary table.

Additionally the C gene region is displayed in the alignment section.

This feature is now available for human and mouse sequences with possible expansion to other organisms in the future.

We have made some improvements to how BLAST multi-threads and the amount of memory required by makeblastdb.

For this release, we have performed a major restructuring of the module that reads the BLAST databases. For multithreaded searches, these changes reduce the number of mutex calls, result in the use of fewer file pointers, and reduce the number of calls to memory map. These changes also allow us to support a different threading model (“threading by query”) that can be more efficient in some situations. See https://www.ncbi.nlm.nih.gov/books/NBK571452/ for more information.

NOTE: The NCBI is preparing to use a larger numerical range for its GI identifier. This release provides full support for these GI's that will appear in nucleotide databases later this year.

• Threading by query batch (for BLASTN, BLASTP, BLASTX, RPSBLAST, and RPSTBLASTN) may more efficiently BLAST large numbers of queries, especially if the database is small or the search is limited by taxid. Use "-mt_mode 1" to enable this option.
• Makeblastdb requires less virtual memory for smaller databases.
• Makeprofiledb creates multiple volumes for a CDD database, which allows RPSBLAST to handle a larger number of records. The number of SMP files included in a volume can be controlled with the new -new_smp_vol option.
• update_blastdb.pl now supports the "-showall pretty" option for databases hosted at the NCBI.
• update_blastdb.pl now reports the database timestamp in ISO8601 format.

• Fixed phiblast core dump when -subject option is used.
• Fixed memory leak in setup procedures.

See the release notes for more details at https://www.ncbi.nlm.nih.gov/books/NBK131777/

The new executables are at https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST

We now offer the ability for user to run primer-blast from NCBI assembly page.

This new feature allows users to design primers using additional eukaryote genome database that are not offered on NCBI Primer-Blast page. To use this feature, simply click "Run Primer-BLAST" link in the right column on the NCBI assembly page. For more information, please go to: https://ncbiinsights.ncbi.nlm.nih.gov/2021/02/18/assembly/.

We’ve added a new field “V frame shift” to the IgBLAST output to indicate if there is an internal frame shift in the normal V gene translation frame.

IgBLAST is a popular NCBI package for classifying and analyzing immunoglobulin (IG) and T cell receptor (TCR) variable domain sequences. Improvements are:

• 1. New field “V frame shift” to the IgBLAST output to indicate if there is an internal frame shift in the normal V gene translation frame. Such frame shifts can arise due to the nucleotide deletion/insertion events introduced by somatic mutations; they can be found in some pseudogenes in germline configuration.
• 2. Updated the definition for whether a sequence is productive or not to reflect this new field. Previously, a sequence is considered to be productive if the V(D)J rearrangement frame is in-frame and no stop codon is found. Now the definition for a productive sequence includes no internal frame shift in V gene, in addition to previous requirement of V(D)J rearrangement frame being in-frame and no stop codon.

IgBLAST 1.17 is available for download from the BLAST FTP area. See the new manual on GitHub for information about setting up and running IgBLAST.

A user driven enhancement to improve the BLAST solution.

Through the BLAST survey and user feedback we received multiple requests to add additional columns to the Description table. We have added Scientific Name, Common Name, Taxid, and Accession Length. We are adding Common Name and Accession Length to the default list displayed. Click 'Select Columns' or 'Manage Columns' to add or delete columns. Your preferences will be saved for your next visit to BLAST.

When you download, only the columns displayed will be saved.

This version supports a new usage reporting service and a new multi-theading feature.

Usage reporting - Help improve BLAST by sharing limited information about your search. Details on the information collected, how it is used, how to opt-out, and our Privacy statement is found here: https://www.ncbi.nlm.nih.gov/books/NBK563686/

Threading by query batch for rpsblast/rpstblastn works for BLAST'ing large numbers of queries. For large numbers of queries, use the -mt option to more efficiently multi-thread the search.

Bug fixes:

• Fix slowdown in TBLASTN searches run without composition-based statistics on long database sequences.
• Remove necessity of a network connection for blast_formatter. This also speeds up blast_formatter if the database can be found locally.
• A core dump for RPSBLAST and RPSTBLASTN has been fixed.
• Makeblastdb for windows has been fixed to not require as much virtual memory and to not produce overly large LMDB files.

See the release notes for more details at https://www.ncbi.nlm.nih.gov/books/NBK131777/

The new executables are at https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST

The RefSeq Select data-set consists of a representative or “Select” transcript for every protein-coding gene.

To apply these new databases, use the pull down selector with Standard Databases selected in BLASTn and BLASTp. These database are also available on FTP/GCP/AWS sites for BLAST+ and BLAST+Docker users.

For in-depth information on the contents of these database go to this site https://www.ncbi.nlm.nih.gov/refseq/refseq_select/ for details.

We have added a new function to Primer-BLAST that helps users design primers common for a group of highly similar sequences.

Many users want to test if a gene is expressed but they don’t know or they don't care which transcripts are expressed. However, they do want primers to cover all transcript variants. Additionally, some users would like to have primers to cover a group of highly related bacteria strains.

Given a group of highly similar sequences, Primer-BLAST attempts to generate primers that are common for all sequences in this group. To find such primers, it uses BLAST to align the longest sequence among the group to the rest to find common regions which are then used to limit the locations of primers. The longest sequence is also used as the representative template sequence.

See the NCBI Insights post for an example search and more details.

To provide a more useful BLAST output, maximize performance, and to make search time more consistent, webBLAST is updating some of the default parameters and search limits.

As previously announced, we have just made the following changes:

• 1. Expect Value default will be 0.05
• 2. Max target sequences limit will be no more than 5,000
• 3. Max query sequence size for BLASTn, blastx and tblastx and will be 1,000,000
• 4. Max query sequence size for BLASTp and tblastn will be 100,000
• 5. Max query/subject sequence size for blast2Sequences mode will be 10,000,000

If you have any questions or concerns, please email us at blast-help@ncbi.nlm.nih.gov

This version supports pulling databases from our FTP site as well from cloud providers or our BLAST+Docker solution.

See the release notes for more details at: https://www.ncbi.nlm.nih.gov/books/NBK131777/.

The new executables are at https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST.

In this webinar, the NCBI BLAST team will show you how to be more effective using new BLAST databases to help identify organisms and explore their diversity.

NCBI updated BLAST rRNA Databases: RefSeq Ribosomal RNA Sequences for Identification and Phylogenetic Analysis of Fungi, Bacteria.

NCBI produces a set of curated marker rRNA sequences (targeted loci) for Bacteria and Archaea (16S) and Fungi (18S, 28S and ITS). We now have 41,000 markers, which are available as a distinct set of BLAST databases. These sequences are largely from type strains and are useful for identifying organisms. You will learn about the scope of the targeted loci projects and see practical examples of using these data and NCBI BLAST to help identify organisms and explore their diversity. You will also learn about and see how to avoid pitfalls of assigning identities only from the BLAST results from a single locus.

While the webinar will focus on NCBI web BLAST, you can also use many of these strategies to make the standalone programs(BLAST+) searches more efficient.

Webinar to be held on June 17th at 12 noon EDT.

Register here.

We’ve released a new version of IgBLAST with four new improvements. IgBLAST is a popular NCBI package for classifying and analyzing immunoglobulin (IG) and T cell receptor (TCR) variable domain sequences. Improvements are:

    1. Support for the new FWR4 annotation feature in the AIRR format, both in standard format and in the AIRR alignment format.

    2. The previous “-penalty” parameter was renamed as -V_penalty to be consistent with other IgBLAST penalty options.

    3. Restored constant internal BLAST search parameters for domain annotation (i.e., FWR/CDR) such that this process is not influenced by user parameters.

    4. Corrected FWR/CDR annotations for certain mouse VK and rat VH germline genes.

IgBLAST 1.15 is available for download from the BLAST FTP area. See the the new manual on GitHub for information about setting up and running IgBLAST.

We have updated the BLAST process to improve the stability of BLAST results against changes in the number of results requested. We have also added an experimental option which increases the likelihood of finding novel results. To enable: set the environment variable ADAPTIVE_CBS to 1. Your feedback on this option is is welcome.

In addition, the new version fixes several bugs. See the release notes for more details at: https://www.ncbi.nlm.nih.gov/books/NBK131777/

The new executables are at https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST

New version 5 databases are at https://ftp.ncbi.nlm.nih.gov/blast/db/v5

Read more about the version 5 database at https://ftp.ncbi.nlm.nih.gov/blast/db/v5/blastdbv5.pdf

As a reminder, we will discontinue updates to the older BLAST databases format (BLASTDBv4) in early 2020.

For initial searches, the 16S and targeted loci databases contains the data that most people need to identify these organisms.

Using these databases will speed up your searches and provide you the results that you are most likely looking for. To search these databases, follow these steps:

Start moving to the new version 5 databases!

We recently updated the version 5 BLAST protein and nucleotide databases, (dbV5), on our FTP site to be 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 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.

Beginning with BLAST 2.10.0 -- due out in October 2019, the program makeblastdb will produce dbV5 databases by default.

For more information on the new database version and BLAST+ (2.9.0), see the previous NCBI Insights article and the recording of our recent webinar.