BLASTFeed

A new feature was added to Primer-BLAST.

Tue, 23 Feb 2021 12:00:00 EST

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/.

A new version IgBLAST (1.17) is here.

Thu, 14 Jan 2021 12:00:00 EST

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.

New Columns added to the Description Table.

Tue, 17 Nov 2020 12:00:00 EST

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.

A new version BLAST+ (2.11.0) is here.

Tue, 05 Nov 2020 12:00:00 EST

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

BLAST now supports the new RefSeq Select databases.

Tue, 13 Oct 2020 12:00:00 EST

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.

A new feature was added to Primer-BLAST.

Tue, 29 Sep 2020 12:00:00 EST

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.

New BLAST Default Parameters and Search Limits.

Thu, 10 Sep 2020 12:00:00 EST

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

BLAST+ 2.10.1 is released – Fix for TBLASTN Multi-Threading issue.

Thu, 18 June 2020 12:00:00 EST

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.

Using new BLAST databases: Webinar on June 17, 2020.

Tue, 09 June 2020 12:00:00 EST

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.

Search Betacoronavirus Database.

Mon, 03 Feb 2020 10:00:00 EST

We have created a new BLAST database focused on the SARS-CoV-2 (Severe acute respiratory syndrome coronavirus 2) Sequences. For further detail please visit NCBI GenBank.

A new version IgBLAST (1.15.0) is here.

Wed, 22 Jan 2020 16:00:00 EST

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.

BLAST+ 2.10.0 is released - Improved Composition-based statistics

Mon, 23 Dec 2019 16:00:00 EST

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.

We have added 3 new fungal targeted loci databases to help you identify organisms.

Tue, 10 Dec 2019 16:00:00 EST

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:

  • On the BLAST home page select the Nucleotide BLAST suite.
  • Select rRNA/ITS as the Database set.
  • Select the appropriate database for your query.
  • End of updates for BLAST+ version 4 databases (dbV4)

    Fri, 27 Sep 2019 16:00:00 EST

    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.

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    A New version of Magic-BLAST(1.5.0) is here.

    Wed, 28 Aug 2019 17:00:00 EST

    The BLAST tool for mapping large next-generation RNA or DNA sequencing runs against a whole genome or transcriptome.

     

    Magic-BLAST, the BLAST tool that aligns next generation sequencing reads, has just been released with new user driven enhancements. :

    • Aligns nanopore sequences
    • Improved multithreading performance
    • Supports the new BLAST database version (BLASTDBv5) that allows you to limit your search by taxonomy (more information about database version 5 here: https://ftp.ncbi.nlm.nih.gov/blast/db/v5/blastdbv5.pdf)
    • More reliable placements of reads

    A new paper, published in BMC Bioinformatics (July, 2019), describes Magic-BLAST and compares it to other popular aligners.  It can be viewed at:  https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-019-2996-x

     The release notes are available at https://ncbi.github.io/magicblast/release/release.html

    The new executables are available on the NCBI FTP site at https://ftp.ncbi.nlm.nih.gov/blast/executables/magicblast/LATEST

    Read more here about Magic-BLAST here: https://ncbi.github.io/magicblast

     

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    New nr database available with fewer redundant titles

    Thu, 15 Aug 2019 17:00:00 EST

    ​We have made changes to the nr version 5 database, (nr_v5), to facilitate better search results and improved performance.

    We have reduced the number of redundant titles in the nr_v5 database used by webBLAST, which is also available for BLAST+ users.

    • The changes in nr preserve the taxonomic diversity of the entries in the database while reducing the number of titles for identical sequences. GenPept accessions are still accessible via www.ncbi.nlm.nih.gov/protein/$GENBANK_ACCESSION or the IPG website https://www.ncbi.nlm.nih.gov/ipg/. The "Identical Proteins" link in the alignments section of the webBLAST results takes you to a full list of all accessions associated with a sequence.
    • For BLAST+ users downloading nr_v5: the database is now approximately 50% smaller, resulting in faster downloads and BLAST searches, and smaller disk space requirements. The database is downloadable at: ftp://ftp.ncbi.nlm.nih.gov/blast/db/v5/
    • For BLAST+ there is a cleanup script to help you manage the transition to this smaller database. The script removes unused database volumes: ftp://ftp.ncbi.nlm.nih.gov/blast/temp/cleanup-blastdb-volumes.py

    Here are the new rules on how we keep titles in nr_v5:

    • We keep all refseq, swissprot, pir and PDB titles.
    • We keep any GenPept titles with a TAXID that has not already been seen in the record.
    • We keep at least five GenPept titles regardless of whether the TAXIDS have been seen before or not in this record.
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    New BLAST Results is now the default view

    Wed, 31 Jul 2019 16:00:00 EST

    Based on user feedback the New Results page is an overwhelming success.

     

    The new BLAST results page that has been available for testing since April is now the default results page.  Thank you for your comments and feedback on this new output. We have made several changes to the page that address issues or problems that you have pointed out and are also working on adding several additional features that you have suggested in future releases. We will still provide access to the old results for some time to allow people who have workflows or teaching materials to adjust to the new display..

    The BLAST programs and databases are now cloud ready

    Thu, 27 Jun 2019 17:00:00 EST

    ​NCBI now provides a dockerized version of BLAST that you can use on the cloud.

    BLAST workloads often come in bursts. You may want to search a large number of sequences all at once and need the results as soon as possible to enable further analysis. Often the number of sequences and rapid turnaround needed preclude using a web service.   In many situations like this you also don’t have a continuous need that would justify an investment in your own dedicated server.  Using BLAST in the cloud environment cloud is an ideal solution to this dilemma.  The BLAST databases have also been moved to the cloud allowing you to run computations close to where the data is, eliminating the time and resources needed to download large data files to your local network.  In the cloud, you are not restricted by your local compute resources or limits on public web services and don’t have to buy compute power that sits idle most of the time.   

    This implementation of BLAST has been tested on the Google Cloud environment, however by using open and de facto standards such as Docker and Linux commands, it should be easy to port to other cloud platforms and operating environments.  Instruction have been created to get started using BLAST in the Cloud and for database information.

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    New BLAST Results to become default on Aug 1, 2019

    Thu, 30 May 2019 14:00:00 EST

    To help instructors integrate the new design into their lesson plans, we are making the change before the fall semester.

     

     The new BLAST results page that has been available for testing since April will become the default results page for everyone on Aug 1, 2019.   Thank you for your comments and feedback on this new output. We have made several changes to the page that address issues or problems that you have pointed out and are also working on adding several additional features that you have suggested in future releases. We will still provide access to the old results for some time to allow people who have workflows or teaching materials to adjust to the new display.

     

    NCBI Insights:

    https://ncbiinsights.ncbi.nlm.nih.gov/2019/05/20/new-blast-results-to-become-the-default-view-august-1-2019/

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    A new version IgBLAST (1.14.0) is here.

    Wed, 15 May 2019 15:00:00 EST

    We’ve released a new version of IgBLAST with three new improvements.

     

     The new version of IgBLAST is now available with three new features:

    1. Implementation of AIRR format is more consistent with AIRR specs including changing undefined type (NON, N/A) to empty string, not appending "reversed" to seqid when query is in reversed orientation, using standard locus names such as IGH, TRB instead of traditional VH, VB etc.
    2. Improved logic for showing CDR3 end.
    3. Restoring seqid for no result case.

    The new release is available on https://ftp.ncbi.nih.gov/blast/executables/igblast/release/LATEST

    The new manual is on GitHub  https://ncbi.github.io/igblast/

    lgBLAST facilitates the analysis of immunoglobulin and T cell
    receptor variable domain sequences. Read more here:  https://ncbi.github.io/igblast/   and here:  https://www.ncbi.nlm.nih.gov/pubmed/23671333

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    Webinar on May 15, 2019

    Wed, 08 May 2019 16:00:00 EST

    Using organism (taxonomy) information in your BLAST search.

    Limiting a BLAST search to particular organism or group is important for efficient BLAST searches and results that are easier to interpret especially as the databases continue to grow in size. The latest standalone BLAST databases, DBv5, have built-in taxonomy information and provide faster sequence access through identifiers. Using Taxonomy limits in your searches is easier than ever when you use these new databases with the current BLAST programs. Through this webinar you will learn how to download and use BLASTDBv5 and the latest BLAST programs to limit searches to taxonomic groups and to retrieve sequences from the database by taxonomy without the often difficult step of first downloading an identifier list.

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

     Webinar to be held on May 15th at 12 noon EST.

     Register here:              https://attendee.gotowebinar.com/register/1368017163849201420?source=BLASTNews

     

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    New BLAST Results Page in Beta

    Tue, 23 Apr 2019 08:00:00 EST

    A user driven experiment to improve the BLAST solution.

     

    The design of this new Results page is based on feedback and interviews, and the goal is better usability and an attempt to better expose desired features that were mostly hidden from users. 

    This new Results page may eventually be incorporated in BLAST, in its current or a revised form, based on your input. Please try this experiment and let us know what you think via the feedback button.

    To access the new Results page, select it from the BLAST Search page or the current Results page.

     

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    BLAST+ 2.9.0 is here.

    Tue, 02 Apr 2019 17:00:00 EST

    BLAST+ 2.9.0 is released - enhanced support for the new database format.

    This version enhances support for the new BLAST database version (BLASTDBv5). This includes:

    1.)   Support for the RCSB Protein Data Bank (PDB) changes. Specifically, the PDB now permits individual biopolymer chains to have identifiers up to four-characters long. Formerly, only single-character chain identifiers could be assigned.  Additional details about NCBI’s 3D structure resources and how they can be used are available at: https://www.ncbi.nlm.nih.gov/Structure/MMDB/mmdb.shtml.

    2.)   Bug fixes

    See the release notes are 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

    We will continue to update the BLAST databases in their current version (BLASTDBv4) until September 2019.

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    ​A new version IgBLAST (1.13) is here.

    Fri, 08 Mar 2019 17:00:00 EST

     Your tool to facilitate the analysis of immunoglobulin and T cell receptor variable domain sequences.

     

     

    The new version of IgBLAST is now available with three new features:

    1. Determining the V gene reading frame from the end of FWR3 region instead of end of V gene.  This is to allow proper determination of the frames for rearrangements that have insertions or deletions near the V gene end.
    2. The packaging of the IgBlast standalone program and files has been modified to make it easier for users to install.
    3. Increase allowed distance between V gene end and J gene start to 225 bp to allow detection of ultra long D/N region.

     The release notes are available at https://ncbi.github.io/igblast/ https://ncbi.github.io/igblast/rel/Release-notes.html
    The new executables are available on the NCBI FTP site at https://ftp.ncbi.nih.gov/blast/executables/igblast/release/LATEST

    lgBLAST facilitates the analysis of immunoglobulin and T cell
    receptor variable domain sequences. Read more here:  https://ncbi.github.io/igblast/   and here:  https://www.ncbi.nlm.nih.gov/pubmed/23671333

     

     

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    Are you identifying organisms? The 16S database may be your best choice.

    Fri, 22 Feb 2019 14:00:00 EST

    For initial searches, the 16S database contains the data that most people need to identify organisms.

    Using the 16S database will speed up your searches and provide you the results that you are most likely looking for.  Please go to our new "How To" video to get more information (external site). 

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    Understanding BLAST+ parameters

    Mon, 28 Jan 2019 17:00:00 EST

    Having a basic understanding of  BLAST+ parameters is essential to getting the results that meet your needs.

     

    A recent Bioinformatics letter(external link) clears up some confusion and misunderstanding about how BLAST+ works.  More information on this topic can be found in the BLAST+ documentation.

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    BLAST+ 2.8.1 is released

    Wed, 19 Dec 2018 17:00:00 EST

    New databases, better performance.

     

    This is the first production release to support the new BLAST database version (BLASTDBv5). This is a taxonomically aware version of the BLAST database that:
    1.) Allows you to limit your search by taxonomy using information built into the BLAST databases.
    2.) Has improved performance when limiting BLAST search with accessions.
    3.) Can retrieve sequences by taxonomy from a BLAST database with blastdbcmd.
    There are additional enhancements:
    4.) A new option (-subject_besthit) culls HSPs on a per subject sequence basis by removing HSPs that are completely enveloped by another HSP. This is an experimental option and is subject to change.
    5.) Use of the -max_target_seqs option for formats 0-4 is allowed. The number of alignments and descriptions will be set to max_target_seqs.
    6.) A warning is issued if -max_target_seqs is set to less than five.


    There are also some bug fixes. See the release notes are 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

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    IgBLAST version 1.12 available

    Thu, 06 Dec 2018 09:00:00 EST

    IgBLAST facilitates the analysis of immunoglobulin and T cell receptor variable domain sequences.

    The new version increases the allowed distance between V gene end and J gene start positions (from 90 bp to 150 bp) as well as between V gene end and D gene start positions (from 55 bp to 120 bp) to accommodate extremely long VDJ junctions found in some antibodies. This version better supports the new AIRR Rearrangement Schema (https://docs.airr-community.org/en/latest/datarep/rearrangements.html).  Also, it includes fixes for minor bugs found in previous versions.

     The release notes are available at https://ncbi.github.io/igblast/rel/Release-notes.html
    The new executables are available on the NCBI FTP site at https://ftp.ncbi.nih.gov/blast/executables/igblast/release/LATEST

    lgBLAST facilitates the analysis of immunoglobulin and T cell
    receptor variable domain sequences. Read more here:  https://ncbi.github.io/igblast/   and here:  https://www.ncbi.nlm.nih.gov/pubmed/23671333

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    Learn how to use BLAST

    Wed, 17 Oct 2018 15:00:00 EST

    See our collection of webinars and tutorials designed to help you

    • Improved standalone BLAST database and programs: now with taxonomic information
    • Getting the most out of Web BLAST tabular format
    • Using BLAST well, How to maximize your search efforts
    • 5 teaching examples on how to use NCBI BLAST

    The complete collection is on YouTube

    Using BLAST Well, How to Maximize Your Search Efforts: Webinar on October 3, 2018

    Thu, 27 Sep 2018 11:00:00 EST

    In this webinar, the NCBI BLAST team lead will show you how to be more effective with BLAST.

     

    You will learn how to:

    • Choose the most appropriate BLAST databases based on size and conten
    • Select and customize BLAST output formats
    • Generate any format from the BLAST archive format
    • Take advantage of the new BLAST DBv5 built-in taxonomic information to get clearer results
    • Use Magic-BLAST NCBI's splice-aware next-generation sequence alignment program

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

    Webinar to be held on October 3, 2018 at 12 noon EDT.

    Register here!              

     

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    A new version (1.4.0) of the BLAST RNA-seq mapping tool, Magic-BLAST, is now available

    Tue, 21 Aug 2018 16:00:00 EST

    ​Magic-BLAST version 1.4.0 is released.

     

    The new version provides an option for strand-specific alignments, improved mapping sensitivity, better alignments in presence of higher sequencing error rates, and better splice site detection in compositionally biased genomes.

     The release notes are available at https://ncbi.github.io/magicblast/release/release.html
    The new executables are available on the NCBI FTP site at ftp://ftp.ncbi.nlm.nih.gov/blast/executables/magicblast/LATEST
    Magic-BLAST is a tool for mapping large next-generation RNA or DNA sequencing runs against a whole genome or transcriptome. Read more here: https://ncbi.github.io/magicblast and read our Magic-BLAST paper here: https://www.biorxiv.org/content/early/2018/08/13/390013

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    Introducing the BLAST widget - integrating your BLAST results into NCBI’s Genome Data Viewer!

    Tue, 31 Jul 2018 18:00:00 EST

    Want to analyze your BLAST results in the context of a genome browser and compare those results against other genome assembly annotations? Introducing the Genome Data Viewer (GDV) and the BLAST widget.

    We have good news! NCBI has been listening and is pleased to introduce the BLAST widget, a new browser feature that seamlessly integrates your BLAST results as a track within the GDV genome browser. This widget provides direct access, within GDV, to execute and manage BLAST queries (BLASTN, TBLASTN) aligned to specific assembly displayed in GDV.

    Learn more about the BLAST widget by viewing a short introductory tutorial. Click here to learn more about GDV. 

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    Five Teaching Examples on how to use NCBI BLAST.

    Wed, 18 Jul 2018 09:00:00 EST

    ​Learn how to easily incorporate BLAST into your undergraduate biology courses with cut and paste examples. Webinar to be held on July 25, 2018 at 12 noon EDT.

    Sequence similarity search tools such as BLAST are fundamental to modern biology and are now taught to students in undergraduate biology classes or earlier. We have many standard demonstrations that we use to highlight the features of BLAST. These examples are also useful for teaching biology principles and techniques including evolution, taxonomy, homology, multiple sequence alignment, phylogenetic trees, primer design and gene expression analysis. This webinar will provide you with examples using NCBI BLAST that explore these principles and techniques that you can readily adapt to your classrooms.

    Register here: BLAST in the classroom

     

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    Introducing the BLAST widget - integrating your BLAST results into NCBI’s Genome Data Viewer!

    Tue, 19 Jun 2018 14:00:00 EST

    Want to analyze your BLAST results in the context of a genome browser and compare those results against other genome assembly annotations? Introducing the Genome Data Viewer (GDV) and the BLAST widget.

    We have good news! NCBI has been listening and is pleased to introduce the BLAST widget, a new browser feature that seamlessly integrates your BLAST results as a track within the GDV genome browser. This widget provides direct access, within GDV, to execute and manage BLAST queries (BLASTN, TBLASTN) aligned to specific assembly displayed in GDV.

    Learn more about the BLAST widget by viewing a short introductory tutorial. Click here to learn more about GDV. 



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    Getting the Genomic Context for BLAST Protein Matches

    Thu, 07 Jun 2018 08:00:00 EST

    Do you ever want to see the flanking genes of a protein match from a BLAST search?  A webinar on June 20 will teach you how to find this information.​  Read more and sign up at: 

    https://attendee.gotowebinar.com/register/8738679115251447041?source=BLAST_News

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    IgBLAST 1.9.0 released

    Fri, 18 May 2018 08:00:00 EST

    IgBLAST now supports AIRR rearrangement reports.

    With an increasing amount of repertoire studies using next generation sequencing (NGS) technology to generate very large sets of Ig/TCR rearrangement analysis data, it became clear a common standard was needed for sequence analysis result. This drove the adaptive immune receptor repertoire (AIRR) community to develop the AIRR standard so they can easily share their data.  Details on the standard at https://docs.airr-community.org/en/latest/

    This format is available on web IgBlast page as well as in standalone IgBlast tool (with the -outfmt 19 option).

    The new release is available on https://ftp.ncbi.nih.gov/blast/executables/igblast/release/1.9.0, along with a new manual on GitHub  https://ncbi.github.io/igblast/

    IgBLAST facilitates the analysis of immunoglobulin and T cell receptor variable domain sequences.


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    May 16 webinar

    Mon, 07 May 2018 15:00:00 EST

    ​Improved BLAST+ and BLAST databases: now with taxonomic information.

    Find out about easier taxonomic limits in the latest BLAST+ release.  Read more and sign up at https://ncbiinsights.ncbi.nlm.nih.gov/2018/05/07/may-16-webinar-improved-standalone-blast-databases-programs-taxonomic-information/

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    BLAST+ 2.8.0-alpha released

    Wed, 28 Mar 2018 18:00:00 EST

    BLAST+ now has a better database.

    We have made some recent enhancement to the BLAST+ applications that allow you to:

    1.)   Limit your search by taxonomy using information built into the BLAST databases.

    2.)   Improved performance when limiting BLAST search with accessions.

    3.)   Use blastdbcmd to retrieve sequences by taxonomy from a BLAST database.

    We've introduced a new version of the BLAST databases (version 5) to support the items listed above

    The new executables are at ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.8.0alpha/

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

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

    The release notes are at https://www.ncbi.nlm.nih.gov/books/NBK131777/

    This is an alpha release to allow users to test and comment on new features.

     

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    QuickBLASTP webinar video

    Tue, 16 Jan 2018 09:00:00 EST

    NCBI insights lists new videos that are available.

    QuickBLASTP is a new way to search large sets of proteins quickly for the most similar matches.

     

     

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