Tag: Protein BLAST (BLASTp)

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.

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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.

Protein BLASTDBs are accession-based

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.

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.

The new BLAST results are now the default view

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.

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New BLAST results for specialized searches now available for testing

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.

  1. PSI-BLAST
  2. PHI-BLAST
  3. DELTA-BLAST
  4. Align two or more sequences

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Have you tried BLAST+ (2.9.0) and version 5 BLAST databases (dbV5)?

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.

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.

May 15, 2019 Webinar: Using taxonomic information and other improvements in standalone BLAST+ (2.9.0) and the v5 databases

May 15, 2019 Webinar: Using taxonomic information and other improvements in standalone BLAST+ (2.9.0) and the v5 databases

Next Wednesday, May 15, 2019 at 11AM, NCBI staff will show you how to use the latest version of standalone BLAST+ (2.9.0) and the new accession-based DBv5 databases with built-in taxonomy information. You will learn how to limit searches to taxonomic groups and to retrieve sequences from the database by taxonomy without having to download an identifier list. You will also learn about additional improvements in the BLAST databases and programs that make them compatible with the new PDB identifiers and gi-less proteins from the Pathogen Detection Project.

Date and time: Wed, May 15, 2018 11:00 AM – 11:30 AM 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 YouTube channel. You can learn about future webinars on the Webinars and Courses page.

New videos on YouTube: NCBI resources, QuickBlastP, update to API keys for E-Utils, and advanced use of API keys

Need a refresher of what NCBI offers? Or just feel you aren’t taking full advantage of NCBI resources? Check out some of NCBI’s most recent recordings of NCBI Minute webinars up on the NCBI YouTube channel.

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January 10 NCBI Minute: QuickBLASTP — a program for rapidly finding high-scoring protein matches in large databases

January 10 NCBI Minute: QuickBLASTP — a program for rapidly finding high-scoring protein matches in large databases

In the next NCBI Minute on Wednesday, January 10, 2018, NCBI staff will demonstrate the new QuickBLASTP service that can search large databases at least 10X faster than traditional protein-protein BLAST (blastp). You will learn about the strategy QuickBLASTP uses to speed up the search. You will also see how to use the new QuickBLASTP service on the NCBI web BLAST site and how to access and run the standalone kblastp demonstration release.

Date & time: Wed, Jan 10, 2018 12:00 PM – 12:30 PM EST

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 YouTube channel. You can learn about future webinars on the Webinars and Courses page.