BLASTFeed
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
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:
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.
.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.
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.
.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:
.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:
- 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.
- Improved logic for showing CDR3 end.
- 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
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.
.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:
- 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.
- The packaging of the IgBlast standalone program and files has been modified to make it easier for users to install.
- 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).
.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.
.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
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
Learn how to use BLAST
Wed, 17 Oct 2018 15:00:00 EST
See our collection of webinars and tutorials designed to help you
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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
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.
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.
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
.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.
.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/
.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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IgBLAST 1.8.0 released
Wed, 15 Nov 2017 16:00:00 EST
A new version of IgBLAST is now available.
This release has the following improvements:
- The igblastn executable can now multi-thread much more efficiently for large sets of queries. The default number of threads is now four, but can be changed with the -num_threads option.
- The igblastn executable can now take an SRA accession as the query input. The search runs on the local machine, but the queries are retrieved from the SRA repository at the NCBI. Use the -sra rather than the -query option to enable.
- A lower default nucleotide mismatch penalty values for finding D and J genes (from -4 to -2 and from -3 to -2, respectively). This improves accuracy in finding the best D and J gene hits for moderately mutated sequences.
The new release is available on FTP, along with a new manual on GitHub.
The IgBLAST webpage also uses the new default nucleotide mismatch penalty values (i.e., -2 for finding both D and J genes).
IgBLAST facilitates the analysis of immunoglobulin and T cell receptor variable domain sequences.
.BLAST+ 2.7.1 released
Mon, 23 Oct 2017 08:00:00 EST
A new version (2.7.1) of the BLAST+ executables is now available.
In this new version, blastdbcmd can look up taxonomic names (e.g., scientific or common name) faster. We have also made some low-level improvements that allow BLAST to multithread more efficiently, especially when available memory is not sufficient for the database.
The release notes are at https://www.ncbi.nlm.nih.gov/books/NBK131777/
The new executables are available on the NCBI FTP site at https://ftp.ncbi.nlm.nih.gov/blast/executables/LATEST
Note: some LINUX and MacOSX users may find that they need to increase the number of open file descriptors allowed for a process. The number of allowed open file descriptors can be easily changed with "ulimit -n" (under bash). We suggest setting the limit to at least 1024.
Magic-BLAST 1.3.0 released
Thu, 28 Sep 2017 16:00:00 EST
A new version (1.3.0) of the BLAST RNA-seq mapping tool, Magic-BLAST, is now available.
The new version provides improved sensitivity, reports unaligned reads, does not cache SRA sequences in local files, and fixes issues with SAM format. 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
.QuickBLASTP
Tue, 23 May 2017 13:00:00 EST
Try QuickBLASTP for a fast protein search of nr.
Read about QuickBLASTP at the NCBI Insights blog or just try it here.
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Magic-BLAST 1.2.0 released
Mon, 27 Feb 2017 14:00:00 EST
A new version of the BLAST mapping tool is now available.
The new version handles multiple SRA accessions, offers improved splice site detection and multi-threading performance, and fixes issues with macOS installation. The release notes are available at ftp://ftp.ncbi.nlm.nih.gov/blast/executables/magicblast/LATEST/ChangeLog
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..
BLAST+ 2.6.0 released
Tue, 10 Jan 2017 12:00:00 EST
A new version (2.6.0) of the BLAST+ executables is now available.
This new version offers improved support for use of accession.version as the primary NCBI identifier. The speed of blastdbcmd when dumping information from a database (e.g., all GIs or all accessions) has been improved. A number of other bug fixes and improvements are also included. Future releases will continue to improve the support for accession.version as the main NCBI identifier.
The release notes are at https://www.ncbi.nlm.nih.gov/books/NBK131777/
The new executables are available on the NCBI FTP site at ftp://ftp.ncbi.nlm.nih.gov/blast/executables/LATEST
Magic-BLAST 1.1.0 available
Mon, 07 Nov 2016 09:00:00 EST
The new version offers support for HTTPS, accession.version as the primary sequence identifier, and fixes problems with SAM flag values.
The release notes are at ftp://ftp.ncbi.nlm.nih.gov/blast/executables/magicblast/LATEST/ChangeLog
Access to the NCBI SRA repository (-sra option) requires access to the NCBI website (and HTTPS). You should update your Magic-BLAST executables by November 9, 2016 to ensure that this feature continues to work. More information about the HTTPS transition is available at https://www.ncbi.nlm.nih.gov/home/develop/https-guidance.shtml
The new executables are available on the NCBI FTP site at ftp://ftp.ncbi.nlm.nih.gov/blast/executables/magicblast/LATEST
.HTTPS and BLAST API calls
Wed, 26 Oct 2016 18:00:00 EST
BLAST API calls must use HTTPS by November 9, 2016.
For more information, please see https://www.ncbi.nlm.nih.gov/news/07-27-2016-new-guidance-https/
.October 26th NCBI Minute
Fri, 07 Oct 2016 18:00:00 EST
NCBI staff will introduce two new BLAST databases: the RefSeq Representative Genomes database and the Model Organisms or Landmark protein database.
Read more about this October 26 webinar (and learn how to register) at https://www.ncbi.nlm.nih.gov/news/10-11-2016-ncbi-minute-new-blast-dbs/
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BLAST+ 2.5.0 released
Fri, 23 Sep 2016 17:00:00 EST
A new version (2.5.0) of the BLAST+ executables is now available.
The new version offers support for HTTPS, accession.version as the primary sequence identifier, support for composition-based statistics with RPSTBLASTN, and a new taxonomic organism report. The release notes are at https://www.ncbi.nlm.nih.gov/books/NBK131777/
Two BLAST+ features require communication with the NCBI website (and HTTPS). First, the –remote flag sends the search to the NCBI for processing. Second, BLAST can take a sequence ID as a query and retrieve the sequence from the NCBI. You should update your BLAST+ executables by November 9, 2016 to ensure that these features continue to work. More information about the HTTPS transition is available at https://www.ncbi.nlm.nih.gov/home/develop/https-guidance.shtml
Improved support for accession.version as the primary identifier affects a number of BLAST+ executables. Blastdbcmd now produces FASTA from BLAST databases that has accession.version as the identifier rather than the traditional bar-delimited FASTA ID. See https://www.ncbi.nlm.nih.gov/news/03-02-2016-phase-out-of-GI-numbers for more information. Makeblastdb can now guess the type of ID (e.g., GenBank or Refseq) from the accession alone if the –parse_seqids flag is used. The search executables now produces reports identifying matches using accession.version by default.
The new executables are available on the NCBI FTP site at ftp://ftp.ncbi.nlm.nih.gov/blast/executables/LATEST
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Introducing: Magic-BLAST
Wed, 24 Aug 2016 11:00:00 EST
Magic-BLAST is a new tool for mapping large sets of next-generation RNA or DNA sequencing runs against a whole genome or transcriptome.
Magic-BLAST optimizes a composite score for each alignment, taking into account both reads of a pair and, in the case of RNA-seq, locating the candidate introns and adding up the score of all exons. Magic-Blast implements ideas developed in the NCBI Magic pipeline using the NCBI BLAST libraries.
Sequencing reads can be provided as NCBI SRA accessions, FASTA or SRA files. A reference genome or transcriptome is a BLAST database that can be created in a matter of seconds.
Read more about Magic BLAST at
ftp://ftp.ncbi.nlm.nih.gov/blast/executables/magicblast/README
Magic BLAST executables for LINUX, MacOSX, and Windows as well as the source files are available at ftp://ftp.ncbi.nlm.nih.gov/blast/executables/magicblast/1.0.0
Magic-BLAST is under active development, and we expect the next few releases to occur on a monthly basis.
.BLAST and HTTPS
Thu, 28 Jul 2016 12:00:00 EST
The BLAST URL API is moving to HTTPS.
On September 30, 2016, the NCBI will move to HTTPS. Applications using the BLAST URL API without HTTPS may stop working. For more details, please read this NCBI News item.
.BLAST+ 2.4.0 released
Thu, 02 Jun 2016 14:00:00 EST
A new version (2.4.0) of the BLAST+ executables is now available.
The new version offers improved scoring for selenocysteine residues in the query and database sequences. It also improves performance for the BLASTP/BLASTX/TBLASTN programs by allowing multi-threaded calculation of the traceback . BLASTN has had this feature since the 2.2.29 release. The full release notes are here.
The new executables are available on the NCBI FTP site at ftp://ftp.ncbi.nlm.nih.gov/blast/executables/LATEST
.New BLAST home page preview.
Thu, 12 May 2016 08:00:00 EST
The new design provides improved navigation, a cleaner look, and easier access to new BLAST services.
Read more about the new home page here.
See the preview page here.
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Searching Whole Genome Shotgun sequences
Wed, 20 Jan 2016 10:00:00 EST
It is now much easier to search WGS (Whole Genome Shotgun) with stand-alone BLAST on your own computer.
BLAST+ 2.3.0 released
Tue, 22 Dec 2015 14:00:00 EST
A new version (2.3.0) of the stand-alone BLAST+ executables is now available.
This new version includes a beta release of SAM format as well as support for single-file mode for the BLAST XML2 and JSON formats. Single-file mode means that results are delivered as a single-file regardless of the number of queries. A number of other improvements and bug fixes are also included.
The release notes are available at https://www.ncbi.nlm.nih.gov/books/NBK131777/LINUX, Windows, and MacOSX executables are available from ftp://ftp.ncbi.nlm.nih.gov/blast/executables/LATEST The BLAST AMI at cloud providers will also be updated to 2.3.0 soon.
This release also uses a new versioning policy
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SmartBLAST
Wed, 29 Jul 2015 18:00:00 EST
Use SmartBLAST for faster BLASTp searches with a graphical view.
Read about SmartBLAST at the NCBI Insights blog or just try it at https://blast.ncbi.nlm.nih.gov/smartblast/
.BLAST XML
Fri, 10 Jul 2015 18:00:00 EST
The BLAST+ 2.2.31 executables can produce a new version of the BLAST XML (XML2). XML2 is also also available from the NCBI BLAST website and the BLAST AMI at the AWS marketplace. XML2 is an update of the current BLAST XML that has been available for more than 10 years. The NCBI is also making JSON available with the same information. The XML changes are described here. An important change is how BLAST delivers the XML2 output. For a search with many queries, BLAST does not hold the XML2 results in memory until all the searches are done, but instead writes out one file per query. This minimizes the memory consumed and is an important consideration for users searching a large batch of queries.
You may provide feedback on the new XML here. Currently, the "classic" XML is also still available.
The NCBI is moving to a standard API for the BLAST website and supported cloud instances (currently AWS). Documentation on this standard API is at https://ncbi.github.io/blast-cloud/dev/api.html
The bash shell script at ftp://ftp.ncbi.nlm.nih.gov/blast/documents/NEWXML/get_xml_json.sh
demonstrates how to download results in XML2 and JSON from the NCBI website, and the same syntax applies at a cloud instance.
User with a large number of searches should consider the cloud option. More information on BLAST on the Cloud is available here.
BLAST 2.2.31+ released
Mon, 15 Jun 2015 17:00:00 EST
A new version (2.2.31) of the stand-alone BLAST+ executables is now available. This release includes the new and improved XML and JSON. Additonally there are a number of other improvements and bug fixes. The full release notes are here.
See here for information on the new XML.
LINUX, Windows, and MacOSX executables are available from ftp://ftp.ncbi.nlm.nih.gov/blast/executables/LATEST The BLAST AMI at AWS will also be updated to 2.2.31 (see here for information).
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BLAST XML
Wed, 29 Apr 2015 18:00:00 EST
The NCBI is now making a new version of the BLAST XML available for testing. Read about the changes and how to access BLAST results using the new XML here.
.MOLE-BLAST
Thu, 29 Jan 2015 10:00:00 EST
MOLE-BLAST is a new tool to classify multiple query sequences and discover their relationship to each other.
This tool provides a taxonomic context for the queries. It is intended to work with a specific locus from a set of organisms rather than sequences like the entire genome of an organism or unannotated contigs. Example input would be 16S sequences from different bacteria or ITS sequences from fungi. Currently, MOLE-BLAST only accepts nucleotide queries.
Read more about MOLE-BLAST here. MOLE-BLAST is available here or from the BLAST homepage.
.Webinar: The Statistics of Local Pairwise Sequence Alignment, Parts 1 and 2.
Thu, 15 Jan 2015 17:00:00 EST
On Thursday, January 22nd, Stephen Altschul of NCBI will present the first part of a discussion of the statistical theory for local sequence alignments like those produced by the BLAST database search programs. It will cover the statistical parameters for local alignment scoring systems, and the formulas for calculating bit scores and asymptotic E-values and p-values from raw alignments scores.
This presentation will continue the following Thursday, January 29th. Part 2 will be a discussion of the considerations that go into the construction and selection of amino acid and nucleic acid scoring systems for pairwise local sequence alignment. It will briefly cover the PAM and BLOSUM series of amino acid substitution matrices, and also the concepts of relative entropy and efficiency for substitution matrices.
To sign up, click here:
* Part 1 - https://attendee.gotowebinar.com/register/5157554322839318274
* Part 2 - https://attendee.gotowebinar.com/register/1397330108961689090
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PDB and Swiss-Prot on the FTP site
Tue, 25 Nov 2014 16:00:00 EST
The NCBI is now distributing the BLAST databases for protein PDB (pdbaa) and Swiss-Prot (swissprot) as stand-alone BLAST databases, rather than as subsets of the non-redundant (nr) database. This change means that the pdbaa and swissprot databases can now be used independently of the nr database. This change does require users to first remove all existing swissprot and pdbaa alias files and mask files. On a UNIX/LINUX system this can be accomplished by executing the command below.
rm –f swissprot.*.pal swissprot.*.msk pdbaa.*.pal pdbaa.*.msk
.BLAST 2.2.30+ released
Wed, 29 Oct 2014 15:00:00 EST
A new version (2.2.30) of the stand-alone BLAST executables is now available.
Find Genomic BLAST pages
Thu, 02 Oct 2014 11:00:00 EST
You can now find Genomic BLAST pages using the search box from the BLAST homepage. Simply start typing your organism into the box and suggestions will appear. Once you select a suggestion, you will be taken to a BLAST page with the best genomic database preselected. This suggest box also works with metagenomic and microbial sequences.
.New gap costs available for PAM30 and PAM70
Tue, 29 Jul 2014 13:00:00 EST
The BLAST webpage now offers additional, more stringent, gap costs for PAM30 and PAM70. These gap costs may produce better alignments for closely related sequences. Try out more stringent costs with PAM30 here.
.BLAST in the Cloud Webinar, July 30th, 3:00 PM
Mon, 07 Jul 2014 17:00:00 EST
The NCBI now provides an experimental BLAST installation hosted at Amazon Web Services. This presentation shows you how to use the experimental NCBI-BLAST Amazon Machine Image(AMI) to configure hardware for BLAST searches using the Amazon Elastic Compute Cloud (EC2). The BLAST AMI includes the BLAST+ applications, a client that can download databases from the NCBI, a web application that implements a subset of the NCBI URL API, and a simplified BLAST search webpage. This talk assumes that you already know how to run standalone and web BLAST on your own computer.
To register, please go to:
https://attendee.gotowebinar.com/register/8126572163773355778
.BLAST in the Cloud
Fri, 20 Jun 2014 18:00:00 EST
The NCBI now provides an experimental BLAST installation hosted at Amazon Web Services. BLAST is provided as an Amazon Machine Image that allows users to run stand-alone searches with the BLAST+ applications, submit searches through a subset of the NCBI-BLAST URL API, and perform searches with a simplified webpage. For additional details see the BLAST Searches at the Cloud Provider help document.
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Custom BLAST databases
Mon, 14 Apr 2014 08:00:00 EST
BLAST XML
Wed, 12 Mar 2014 15:00:00 EST
BLAST 2.2.29+ released
Mon, 06 Jan 2014 12:00:00 EST
This release includes a number of improvements as well as a large number of bug fixes. The BLAST+ applications may be downloaded here.
The improvements are:
1.) Improved the criteria for segging subject sequences used in composition based statistics with protein and translated searches.
2.) Improved blastn batch query performance
3.) Improved blastdbcmd performance when retrieving taxonomic data from the BLAST databases.
4.) blastdb_aliastool supports reading a list of BLASTDBs from a file.
5.) Source releases build optimized multi-threaded binaries by default.
6.) Multi-threaded traceback: provides performance improvement for nucleotide-nucleotide BLAST with large (>25k) queries.
7.) Made makeprofiledb error messages more user friendly.
8.) Ungapped BLAST no longer uses sum statistics by default. Recover old behavior with -sum_statistics flag.
9.) Improved multithreading by better dividing the BLAST database among threads.
A full list of BLAST+ 2.2.29 changes is at https://www.ncbi.nlm.nih.gov/books/NBK131777/ .
Update to organism BLAST databases
Thu, 17 Oct 2013 14:00:00 EST
Organism BLAST pages are available from:
* The Map Viewer home page: https://www.ncbi.nlm.nih.gov/mapview/
* The Genome page for the species, under Tools: https://www.ncbi.nlm.nih.gov/genome/?term=mus+musculus
* A subset are available from the BLAST home page: https://blast.ncbi.nlm.nih.gov/Blast.cgi
The new databases are named 'Genome * top-level' in the popup menu, for example "Genome (Annotation Release 105 all assemblies top-level)", with more details about their contents available from the "?" link.
For eutils users, the ref_contig and all_contig BLAST databases are replaced by the ref_top_level and all_top_level databases. The ref_contig and all_contig databases will be phased out starting in October. .
Update to SRA-BLAST
Thu, 20 Jun 2013 11:00:00 EST
SRA-BLAST now includes:
* Targeted searching within one or more SRA Experiment sets (i.e., "SRX accessions"). Users may now search combined datasets of up to 2 billion individual reads.
* An "autocomplete" feature that will allow users to specify SRX accession, SRX title, organism scientific name, or tax id to help build the search set.
* Data obtained from Roche 454 and newer Illumina instruments (HiSeq and MiSeq) are now included in the SRA-BLAST database, owing to longer read lengths from these technologies.
These updates to SRA-BLAST make it an even more useful tool for searching through more than 700 trillion open-access bases currently housed within the SRA..
NAR article describes IgBLAST
Mon, 20 May 2013 10:00:00 EST
The article is available through https://www.ncbi.nlm.nih.gov/pubmed/23671333 and discusses the IgBLAST algorithm, retrieval performance, and website.
IgBLAST is available here.
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New NAR article on the BLAST report
Mon, 29 Apr 2013 16:00:00 EST
The article is available through https://www.ncbi.nlm.nih.gov/pubmed/23609542 and discusses the redesigned BLAST report as well as other improvements to the BLAST website.
BLAST can be accessed here. .
BLAST 2.2.28+ released
Tue, 02 Apr 2013 09:00:00 EST
1.) The custom tabular report now has support for query coverage, subject sequence title, and taxonomic information.
2.) Blastdbcmd has support for batch subsequence retrieval.
3.) The blastn application now uses a new "adaptive chunk size" for batch searches. This feature is important if the query file for the blastn application contains many FASTA entries. In that case, the BLAST application reads in many of the queries to search at once, and this improvement allows it to optimize the number of entries read at once. This features can speed up the search and reduce memory usage. See the BLAST+ user manual for details.
4.) Previous BLAST releases did not produce XML until the entire search was done. This behavior could cause the application to use too much memory if the query file contained many FASTA entries. BLAST+ 2.2.28 produces XML as soon as the search of each query is finished.
5.) RPSBLAST has software modifications to enable better composition-based statistics. Use of these statistics require changes to the conserved domain databases (CDD). Watch for an announcement from the NCBI.
A full list of BLAST+ 2.2.28 changes is at https://www.ncbi.nlm.nih.gov/books/NBK131777.
Microbial BLAST improved
Thu, 21 Mar 2013 16:00:00 EST
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Improved BLAST statistics described in BMC Research Notes.
Fri, 11 Jan 2013 10:00:00 EST
nt will become default BLAST db
Fri, 16 Nov 2012 14:00:00 EST
Starting November 26, 2012, the nucleotide collection (nt) will be the default nucleotide search database. The nucleotide collection consists of GenBank+EMBL+DDBJ+PDB+RefSeq sequences, but excludes EST, STS, GSS, WGS, TSA, patent sequences as well as phase 0, 1, and 2 HTGS sequences.
The nt database recently joined a list of other fast, indexed database searches offered by the NCBI that include the human G+T (genome plus transcript) and mouse G+T databases, as well as the human and mouse reference genome databases. The indexed databases are available when using megaBLAST. Indexed megaBLAST, at the NCBI BLAST web page, can search queries of a couple thousand bases against the 43 billion base nt database in a few seconds.
Indexed searches at the NCBI use an in-memory index described by Morgulis et al. and the megaBLAST algorithm.
.New BLAST report
Wed, 31 Oct 2012 16:00:00 EST
BLAST 2.2.27+ released
Mon, 10 Sep 2012 14:00:00 EST
1.) We have implemented composition-based statistics for BLASTX. It offers better statistical accuracy and is the default mode, but the older behavior can be recovered with the –comp_based_stats flag. The BLASTX implementation is based upon the methods described in pmid 17156431.
2.) The deltablast application now allows searches with the –remote flag.
3.) We have reduced the memory usage of the blastn application when searching many small queries. This involved reducing the number of queries searched during one pass through the database as well as reducing the number of database sequences retrieved for the tabular output formatting. Section 4.3.1 and 4.3.2 of the manual present details on this change as well as information on how to control the number of queries searched during one pass through the database.
4.) The output for reports without separate descriptions and alignments sections (all –outfmt greater than 4) should now use –max_target_seqs to control the output rather than –num_descriptions and –num_alignments.
5.) In megaBLAST mode, the blastn application now reduces the number of gaps if possible. As described in pmid 10890397, the megaBLAST algorithm (with linear gapping) assigns an equal score to an alignment with two mismatches and to an alignment with two gaps plus an additional match. If possible, the blastn application now presents the alignment without the gaps.
6.) We have extensively rewritten the BLAST+ manual. Appendix C now contains tables of options for different programs. This is an updated set of tables based on the supplementary information of pmid 20003500.
7.) We have fixed various bugs in the blast_formatter, blastdbcmd and other programs. These include one that did not render an asterisk (stop codon) properly as well as one that improperly applied compostion-based statistics to any use of the Smith-Waterman option. .
Improved BLASTX statistics
Wed, 01 Aug 2012 17:00:00 EST
BLASTX searches translate a nucleotide query and compare it to a protein database. BLASTX searches with CBS produce more reliable results. The increased accuracy is especially noticeable for query and subject sequences with biased compositions (i.e., low-complexity sequences). CBS has been available for some time with BLASTP, PSI-BLAST, and TBLASTN.
CBS is enabled by default for BLASTX searches at the NCBI BLAST website. CBS may be disabled by using the "Composition adjustment menu" in the Algorithm parameters part of the page. CBS will be available in the 2.2.27+ release of stand-alone BLASTX.
The CBS implementation for BLASTX is similar to that of TBLASTN, described at https://www.ncbi.nlm.nih.gov/pubmed/17156431.
OLD_BLAST URL to be discontinued. Alternative NCBI BLAST parsable formats are available
Thu, 12 Jul 2012 16:00:00 EST
For information on parsable formats, please see https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=DeveloperInfo and the links on that page.
The standard BLAST report is a human readable format that is subject to change with little or no notice. In order to facilitate coming enhancements to the BLAST report, it is necessary to discontinue support for the OLD_BLAST URL parameter. The OLD_BLAST parameter is currently used by a very small fraction of interactive users and results in an older version of the BLAST report (in HTML). The BLAST web pages will simply ignore the OLD_BLAST parameter starting September 10, 2012.
Please address any concerns or questions to blast-help@ncbi.nlm.nih.gov..
Primer-BLAST article in BMC Bioinformatics
Thu, 05 Jul 2012 16:00:00 EST
The article is available through https://www.ncbi.nlm.nih.gov/pubmed/22708584 and discusses the design and implementation of Primer-BLAST.
The Primer-BLAST web page is at https://www.ncbi.nlm.nih.gov/tools/primer-blast/index.cgi.
Microbial BLAST
Mon, 04 Jun 2012 12:00:00 EST
The microbial BLAST page has been redesigned for ease of use and better integration with other BLAST pages. The page now allows selection of taxonomic catgegories through an auto-complete mechanism (start typing in "Organism" box and select a suggestion). Multiple taxonomic categories can be included or excluded. For nucleotide databases, the search sets have also been divided into Complete and Draft genomes. Other standard features of the BLAST pages such as "Edit and Resubmit" (start a new search from a BLAST report with current settings) and the ability to optimize for a specific search (under "Program Selection") are available.
The old microbial page will be available at https://www.ncbi.nlm.nih.gov/sutils/genom_table.cgi at least until the end of June, 2012..
DELTA-BLAST
Mon, 23 Apr 2012 12:00:00 EST
Since 1997, the BLAST web site has offered searches with a “Position Specific Scoring Matrix” (PSSM) through the PSI-BLAST program. This normally required the user to launch a few searches. Domain Enhanced Lookup Time Accelerated BLAST (DELTA-BLAST) is a new addition to the web site that performs a PSSM search. It runs a fast RPSBLAST search in order to construct the PSSM and then searches the PSSM against a BLAST database. Tests using the SCOP based benchmark set demonstrate that DELTA-BLAST yields retrieval accuracy greater than BLASTP and similar to a few PSI-BLAST iterations. The DELTA-BLAST results can also be used to initiate a PSI-BLAST search.
You may start a DELTA-BLAST search from the protein-protein page.
An article in Biology Direct describes the DELTA-BLAST algorithm and benchmark results..
BLAST 2.2.26+ release.
Thu, 01 Mar 2012 14:00:00 EST
BLAST+ applications may be downloaded here. Instructions on the installation of BLAST+ applications are available here.
The BLAST+ 2.2.26 release contains a number of important changes and improvements:
1.) DELTA-BLAST. A new application called deltablast is included in this release. Deltablast stands for Domain Enhanced Look-up Time Accelerated BLAST. It first uses RPS-BLAST to align a protein query to conserved domains in CDD, then performs a sequence database search using a position specific score matrix (PSSM) derived from the aligned domains. The PSSM construction method is similar to that of PSI-BLAST, but begins by aligning the query to CD's rather than to individual sequences. DELTA-BLAST can be much more sensitive than standard BLASTP. DELTA-BLAST is also available from the "protein blast" link at blast.ncbi.nlm.nih.gov. DELTA-BLAST needs a special version of CDD database that contains some extra files. Instructions for downloading and installing this specialized copy of the CDD database can be found in section 5.18 of the BLAST Command Line Application Manual at https://www.ncbi.nlm.nih.gov/books/NBK1763/
2.) New finite size correction (FSC). The FSC is subtracted from the query and database sequence length for the calculation of the BLAST statistics used to rank the results. The older FSC did not properly handle short query or database sequences, as the estimated FSC might be longer than a short sequence, and it was necessary to simply set the resulting length to an ad hoc value (typically one). The new approach elides this issue by looking at the expected values of both the query and database length together, rather than separately. In general, it ranks matches involving a short query or database sequence as more significant. The new FSC increases the ROC score (at 4853 FP) found with a SCOP test set by about 2%. For short queries or database sequences, it may change the expect value reported by orders of magnitude. Currently, the new FSC is only implemented for protein-protein programs (e.g., blastp, psiblast, blastx, rpsblast, etc.), but not the blastn application. The old behavior may be recovered by setting the environment variable OLD_FSC to a non NULL value.
3.) Makeprofiledb. Makeprofiledb can be used to make search sets for RPS-BLAST, including the specialized data needed by DELTA-BLAST. Makeprofiledb is a replacement for the C toolkit application formatrspdb.
4.) Blastcl3 users should switch to BLAST+. Blastcl3 is deprecated and the service will need to be retired in the not too distant future. This client and service have served the community well since 1997, but changes in the way BLAST searches are done at the NCBI (e.g., a Request ID can be issued for a search) mean that a better and more robust client can be offered. The BLAST+ applications can send off remote searches if the argument -remote is added. More details are available at https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastNews
5.) Last C toolkit binary release. This is the last release of the C toolkit BLAST binaries (e.g., blastall, blastpgp, etc.). The source code for these application is not being updated anymore, but will continue to be available. Users of these legacy binaries are encouraged to move to the BLAST+ applications that are being actively developed. Help on transitioning to the BLAST+ applications can be found at https://www.ncbi.nlm.nih.gov/books/NBK1763/
ChangeLog:
-----------------------------
* 2.2.26 release.
* Mac executables are now Universal Binaries for 32- and 64-bit architectures, we no longer produce PPC and Intel Universal binaries. The executable archive names remain unchanged.
* Added DELTA-BLAST - a new tool for sensitive protein searches
* Added makeprofiledb - a tool for creating a database for RPS-BLAST
Improvements:
* The blast_formatter application can now format bl2seq RIDs.
* PSI-BLAST can produce archive format, blast_formatter can format that output.
* PSI-BLAST has two new options that work with multiple-sequence alignments: ignore_msa_master and msa_master_idx (see BLAST+ manual).
* mkmbindex can now create masked indices from a BLAST database and ASN.1 masking data.
* An improved finite size correction is now used for blastp/blastx/tblastn/rpsblast. The FSC is subtracted from the query and database sequence length for the calculation of the expect value. The new FSC results in more accurate expect values, especially for alignments with a short query or target sequence. Re-enable the old size correction by setting the environment variable OLD_FSC to a non-NULL value.
* The blastdbcmd -range parameter now accepts a blank value for the second parameter to signify the end of a sequence (e.g., -range "100-")
* There was a performance improvement for long database sequences in results with many matches.
Bug fixes:
* There was a blastn problem if subject_loc and lcase_masking were used together.
* There was a problem with multi-threaded blastx if the query included a long (10,000+) sequence of N's.
* The percent identity calculation was wrong if the best-hit algorithm was used.
* There was a problem with the multiple BLAST database statistics report in XML format.
* Makeblastdb failed to return an error when input was not available.
* The formatting option -outfmt "7 nident" always printed zero.
* The search strategy was not properly saving the -db_soft_mask option.
* An error message was emitted if there was a "<" in the query title.
* A problem reading lower-case masking from the query could cause a search to fail.
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BLAST+ remote searches.
Fri, 24 Feb 2012 09:00:00 EST
The BLAST+ applications can perform remote searches.
The BLAST+ applications can not only run searches on local machines, but also perform searches on the NCBI servers. Sending searches to the NCBI servers can be advantageous if you have not downloaded the BLAST databases or do not have sufficient resources for a set of searches. Please run only one remote instance of the BLAST+ application at a time.
Information on downloading, installing and using the BLAST+ applications is available at https://www.ncbi.nlm.nih.gov/books/NBK1762/ To enable remote searches, simply add -remote to any BLAST+ command-line.
The BLAST+ remote service replaces the older blastcl3 application. This new service has a number of advantages over the blastcl3 application. Blastcl3 requires a persistent connection during the entire search, can only submit one query at a time, and is unable to return the BLAST Request ID (RID) used in the search. The BLAST+ remote service can submit multiple queries (from FASTA input) at once, poll for the results using the BLAST RID, and also print the RID in the BLAST report. Using the BLAST RID, it is possible to reformat the search with the blast_formatter application, reformat the search at the NCBI web site, or use analysis tools such as the BLAST treeview or the taxonomy report.
On March 5, 2012, the blastcl3 client will start printing a reminder to standard error that the service is deprecated and that users should change to the BLAST+ applications. The reminder will not interfere with the search or the formatting of results.
.BLAST database list
Wed, 01 Feb 2012 09:00:00 EST
1.) The WGS database on the nucleotide blast, tblastn and tblastx pages now allows taxonomic limits with an auto-complete menu (start typing and look at the suggestions).
2.) The est_others database has been removed. Instead, use the taxonomic auto-complete menu to search a subset of the est database.
3.) The env_nt database has been removed. These sequences are actually WGS metagenomic sequences. They can now be searched by selecting the WGS database and limiting the search (with the taxonomic auto-complete menu) to "metagenome".
4.) A new 16S database is now available through the main nucleotide BLAST page. See the NCBI News for details.
5.) The env_nr database has been renamed "Metagenomic proteins".
Note that the new WGS functionality makes the WGS link under specialized BLAST redundant and it has been removed. .
SOAP BLAST
Mon, 18 Jul 2011 08:00:00 EST
Genomic BLAST page update
Thu, 19 May 2011 11:00:00 EST
Transcriptome Shotgun Assembly database
Tue, 10 May 2011 13:00:00 EST
BLAST 2.2.25 release
Thu, 24 Mar 2011 09:00:00 EST
Users are encouraged to use the BLAST+ applications available at ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/ This release includes a substantial number of bug fixes and new features for the BLAST+ applications.
Improvements:
* Enhanced documentation, includes simplified setup instructions, available at https://www.ncbi.nlm.nih.gov/books/NBK1762
* Added support for hard-masking of BLAST databases.
* Improve performance of makeblastdb for FASTA input with large numbers of sequences, improve error checking.
* Allow Best Hit options and XML formatting for Blast2Sequences mode
* Allow multiple query sequences for psiblast.
* Allow specification of any multiple sequence alignment sequence as the master with the -in_msa psiblast argument.
* Add an optional -input_type argument to makeblastdb.
* Added support for query and subject length to tabular output.
* Performance of -seqidlist argument improved.
* The minimum of the number of descriptions and alignments is now used for tabular and XML output (consistent with the behavior of the older blastall applications).
Bug fixes:
* Makeblastdb and blastdbcmd problems with parsing, storing, and retrieving sequence identifiers.
* Missing subject identifiers in tabular output.
* Blast_formatter ignoring -num_alignments and -num_descriptions
* Blast archive format could be saved incorrectly with multiple queries.
* Blast_formatter established an unneeded network connection.
* Blast_formatter did not save masking information correctly.
* Rpstblastn might crash if searching many sequences.
* Indexed megablast would not run in multi-threaded mode.
* Query title in the PSSM saved by psiblast was not being stored.
* Possible failure to run in multi-threaded mode with multiple queries or large database sequences.
* Tblastn runs with database masking might miss matches.
* Truncated output for sequence input with extra spaces in the defline
* Problem with MacOSX binaries on MacOSX 10.5
BLAST+ applications, as well as the legacy C applications (e.g. blastall), may be downloaded from https://www.ncbi.nlm.nih.gov/blast/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=Download .
New SNP BLAST page
Wed, 12 Jan 2011 14:00:00 EST
The SNP blast databases are built from RefSNP(rs) flanking sequences as their sequence source. The RefSNP set includes not only polymorphisms but also rare clinical variants from human. In addition to single nucleotide variants, SNP blast databases also include flanks from insertions/deletions, short tandem repeats and multi-base nucleotide variations. Typical use cases for dbSNP BLAST page includes:
1.) Confirming that a novel SNP has not been reported in dbSNP using your flanking sequences.
2.) Determining if a sequence you have overlaps flanks from or includes variations stored in dbSNP.
.New WGS BLAST page
Mon, 22 Nov 2010 09:00:00 EST
The main menu on the new page lists search sets by genus, or by species if only one species in a genus is available. A sub-menu allows selection of one or more of the species from a given genus. The example below shows the genus Mycobaterium selected/ There are five species available for this genus.
makeblastdb update available
Mon, 13 Sep 2010 11:00:00 EST
The makeblastdb application distributed with the BLAST+ 2.2.24 release has a very significant performance problem when the -parse_seqids option is used. Patched binaries for common platforms are available at ftp://ftp.ncbi.nlm.nih.gov/blast/executables/snapshot/2010-09-13/.
BLAST 2.2.24 release
Mon, 23 Aug 2010 13:00:00 EST
This release includes a number of bug fixes as well as new features for the BLAST+ applications:
* Introduced the BLAST Archive format to permit reformatting of stand-alone BLAST searches with the blast_formatter (see BLAST+ user manual)
* Added the blast_formatter application (see BLAST+ user manual)
* Added support for translated subject soft masking in the BLAST databases
* Added support for the BLAST Trace-back operations (btop) output format
* Added command line options to blastdbcmd for listing available BLAST databases
* Improved performance of formatting of remote BLAST searches
* Used a consistent exit code for out of memory conditions
* Fixed bug in indexed megablast with multiple space-separated BLAST databases
* Fixed bugs in legacy_blast.pl, blastdbcmd, rpsblast, and makeblastdb
* Fixed Windows installer for 64-bit installations
BLAST+ applications, as well as the legacy C applications (e.g. blastall), may be downloaded from https://www.ncbi.nlm.nih.gov/blast/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=Download .
BLAST 2.2.23 release
Mon, 22 Mar 2010 15:00:00 EST
This release includes a number of bug fixes for the BLAST+ applications:
1.) BLASTN runs with word-size four were missing hits in the 2.2.22 release, this has been fixed.
2.) Query/subject offsets for tabular formatting (query on minus strand) was fixed.
3.) A MEGABLAST performance regression (with query masking) was fixed.
4.) Seg filtering for long blastx queries was failing. This has been fixed and optimized.
5.) A bug that caused tabular output to contain tokens like "gnl|BL_ORD_ID|1 " was fixed.
6.) Search strategies can now be used in bl2seq mode.
7.) Problems with displaying accessions in XML output have been fixed.
8.) Problems with percent identity and percent positive matches in the the tabular output have been fixed.
BLAST+ applications, as well as the legacy C applications (e.g. blastall), may be downloaded from https://www.ncbi.nlm.nih.gov/blast/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=Download .
COBALT improvements
Thu, 21 Jan 2010 17:00:00 EST
The following popular formats, used by alignment viewers as well as sequence and phylogeny analysis tools, are supported: FASTA plus gaps, ClustalW, Phylip, and Nexus. The alignment can also be downloaded as a Seq-align in ASN.1 format.
In order to download your alignment click the 'Download' link on the top of the results page and then select desired format in the 'Download alignment' box.
COBALT is a multiple alignment program for proteins that can be accessed from https://www.ncbi.nlm.nih.gov/tools/cobalt/cobalt.cgi or BLASTP search results at the NCBI.
The COBALT algorithm is described in this paper.
.BLAST+ article in BMC Bioinformatics
Fri, 18 Dec 2009 08:00:00 EST
The BMC Bioinformatics article is available from https://www.biomedcentral.com/1471-2105/10/421/abstract and discusses changes to search chromsome length database sequences and long queries faster. The article also describes database masking, a more modular design, and new command-line applications.
The new command-line applications are available at https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=Download.
Exclude Models and environmental samples
Fri, 06 Nov 2009 10:00:00 EST
BLAST 2.2.22 now available
Mon, 19 Oct 2009 11:00:00 EST
This release includes new BLAST+ command-line applications.
The BLAST+ applications have a number of advantages over the older applications and users are encouraged to migrate to the new applications. The new applications can be downloaded from ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST These applications have been built with the NCBI C++ toolkit. Changes from the last release are listed below.
The older C toolkit applications (e.g., blastall) are still available at ftp://ftp.ncbi.nlm.nih.gov/blast/executables/release/2.2.22/
Changes from the last release are listed below.
Please send questions or comments to blast-help@ncbi.nlm.nih.gov
Changes for the BLAST+ applications:
* Added entrez_query command line option for restricting remote BLAST databases.
* Added support for psi-tblastn to the tblastn command line application via
the -in_pssm option.
* Improved documentation for subject masking feature in user manual.
* User interface improvements to windowmasker.
* Made the specification of BLAST databases to resolve GIs/accessions
configurable.
* update_blastdb.pl downloads and checks BLAST database MD5 checksum files.
* Allow long words with blastp.
* Added support for overriding megablast index when importing search strategy
files.
* Added support for best-hit algorithm parameters in strategy files.
* Bug fixes in blastx and tblastn with genomic sequences, subject masking,
blastdbcheck, and the SEG filtering algorithm.
Changes for C applications:
* Blastall was not able to use BLAST databases with only accessions to format results, this has been fixed.
.Limit by organism improved
Mon, 14 Sep 2009 09:00:00 EST
.
BLAST 2.2.21 now available
Tue, 28 Jul 2009 11:00:00 EST
This release includes new BLAST+ command-line applications.
The BLAST+ applications have a number of advantages over the older applications that include working more robustly with long sequences and a new type of masking (database masking). For details see ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/user_manual.pdf. The new applications can be downloaded from ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST These applications have been built with the NCBI C++ toolkit. Changes from the last release are listed below.
The older C toolkit applications (e.g., blastall) are still available at ftp://ftp.ncbi.nlm.nih.gov/blast/executables/release/2.2.21/
Changes from the last release are listed below.
Please send questions or comments to blast-help@ncbi.nlm.nih.gov
c toolkit binary changes:
* corrected a bug in xml output (SB-217)
* corrected a bug with query concatenation in ungapped searches (SB-263)
* tabular output header for "-m 8" now printed even if there are no results. (sb-290)
C++ toolkit binary improvements:
* best hit algorithm, see section 4.5.12 in ftp://ftp.ncbi.nih.gov/blast/executables/blast+/LATEST/user_manual.pdf
* improve culling option performance
* fix mutex problems in BLAST database reader.
* improve performance of database masking option.
C++ binary changes:
* database masking enabled, see details in ftp://ftp.ncbi.nih.gov/blast/executables/blast+/LATEST/user_manual.pdf
* makeblastdb user-interface improvements
* blastdbcmd can now emit masked fasta for a masked database
.Multiple Alignments with COBALT
Mon, 06 Jul 2009 13:30:00 EST
(https://www.ncbi.nlm.nih.gov/pubmed/17332019).
COBALT can be started from BLAST results (use the "Multiple Alignment" link) or from the COBALT web site at https://www.ncbi.nlm.nih.gov/tools/cobalt/cobalt.cgi?CMD=Web .
SRA transcript BLAST
Mon, 27 Apr 2009 11:00:00 EST
The search sets are grouped by organism and include all public 454 transcript sequences in the NCBI SRA database. Go to https://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE=MegaBlast&PROGRAM=blastn&BLAST_PROGRAMS=megaBlast&PAGE_TYPE=BlastSearch&BLAST_SPEC=SRA to run a search.
BLAST 2.2.20 now available
Fri, 03 Apr 2009 16:00:00 EST
1.) Ungapped blastn searches allow arbitrary reward/penalty scores.
2.) Spaces are allowed in database pathnames on windows
3.) Seedtop now has gilist support.
4.) Fix a bug that caused the number and order of queries to affect blastx results.
5.) Modified the 2-hit blastn algorithm so that no overlap is allowed between hits.
Align two sequences form.
Tue, 03 Feb 2009 16:00:00 EST
BLAST 2.2.19 now available
Wed, 17 Dec 2008 11:00:00 EST
- The BLASTDB environment variable now supports multiple database search paths.
- When possible, a smaller protein lookup table is used to improve performance.
- formatrpsdb now supports creating databases larger than 2G.
- seedtop now supports searches with gi lists.
- The X3 value for blastn/megablast was corrected.
Align Sequences with BLAST
Thu, 04 Sep 2008 11:00:00 EST
Find specific primers with Primer-BLAST
Tue, 22 Jul 2008 11:00:00 EST
To get started with Primer-BLAST go to https://www.ncbi.nlm.nih.gov/tools/primer-blast/index.cgi?LINK_LOC=BlastNews and enter FASTA, an accession or a GI into the PCR Template box. Or alternately fill in the forward and reverse primers in the "Primer Parameters" area. By default human sequences are searched in the specificity check, but that may be changed to other organisms in the " Primer Pair Specificity Checking Parameters". Use the "Get Primers" button at the bottom of the page to submit your search.
Please send question and comments about Primer-BLAST to blast-help@ncbi.nlm.nih.gov
.
BLAST interface described in NAR web server issue
Fri, 27 Jun 2008 11:00:00 EST
New tree view available
Thu, 12 Jun 2008 11:00:00 EST
- The tree can be downloaded in Newick or Nexus format recognized by popular phylogenetic software packages.
- The tree can be rooted at any user-selected node. This option is available from the node pop-up menu.
- Any user-selected subtree can be collapsed into a single node.
- Sub-trees with sequences from only one Blast Name are automatically collapsed (a Blast Name is a high level taxonomic grouping). This behavior can be controlled by the "Collapse Mode" menu on the right side of the tree view page..
BLAST report improvements
Mon, 12 May 2008 11:00:00 EST
New BLAST URL available
Fri, 25 Apr 2008 11:00:00 EST
New BLAST Redesign in Production
Fri, 13 Apr 2007 14:00:00 EST
----------------------------------------------------------------
The new NCBI BLAST pages will become the default interface at
https://ncbi.nlm.nih.gov/blast on April 16, 2007. The new
interface is currently available as a beta release at
https://ncbi.nlm.nih.gov/blast/beta/. For details on the new
interface, see https://www.ncbi.nlm.nih.gov/BLAST/beta/about/.
After the new interface is released, the previous interface will
remain available from a link on the new front page until May 14,
2007.
A Note About URLAPI
The new BLAST pages support URLAPI, a protocol that scripts and
programs use to run BLAST searches and retrieve results over
HTTP. (For more on URLAPI, see
https://www.ncbi.nlm.nih.gov/blast/Doc/urlapi.html). The following
information only applies to you if you develop or are responsible
for software that uses URLAPI.
The new pages have been tested and produce correct results with
the following URLAPI client programs:
* the BioPERL RemoteBlast module
* the NCBI demo script https://ncbi.nlm.nih.gov/blast/docs/web_blast.pl
* various scripts used in-house at NCBI
Users of URLAPI should be aware of the following minor
changes. In the new interface:
1. The Request ID (RID) format will be shorter. The new format
is 11 alphanumeric characters (e.g. RDEFEA5012) and will have no
internal structure. The previous RID format was 36 or more
characters long, including punctuation (e.g.,
1175172712-21345-42512597310.BLASTQ3).
2. BLAST reports will show masked regions as lower-case letters
by default (see
https://nar.oxfordjournals.org/cgi/content/full/34/suppl_2/W6,
figure 2. The current default behavior is to show masked
regions as N's or X's. Users may recover the current behavior
by adding &MASK_CHAR=0 to the query string for a URLAPI
request.
3. BLAST reports will show alignments for 100 database sequences
by default. The current reports show only 50 alignments by
default.
If you have any questions please send them to mcginnis at ncbi.nlm.nih.gov.
Special Announcement: Beta Test of New BLAST Interface
Mon, 05 Mar 2007 14:00:00 EST
NCBI is holding a beta test for a new BLAST interface design. We invite you to try these pages and send us your comments and suggestions.
One major improvement is a new "Recent Results" feature that provides links to all of your recent BLAST search results. Another is "Saved Strategies", which allows you to save BLAST forms with their parameters and use them later. Saved Strategies requires a free MyNCBI account, and is compatible with existing accounts. Signing in to MyNCBI also makes your Recent Results available from any browser.
Other improvements include:
- Easier navigation
- Simplified BLAST program selection
- Easy access to genome searches
- Improved Organism selection with species name auto-complete
- Automatic parameter adjustment to optimize for short queries
- A user-specifiable title for each BLAST job
The Beta test is available at:
https://www.ncbi.nlm.nih.gov/blast/beta/
or as a link from the BLAST home page at
https://www.ncbi.nlm.nih.gov/blast/
Please send all comments suggestions or bug reports to
mcginnis@ncbi.nlm.nih.gov.
BLAST 2.2.14 now available
Wed, 07 Jun 2006 00:05:00 EST
Major Changes
blastall now uses the new engine by default, resulting in significant performance improvements\ and enabling query concatenation for all program types.BLAST 2.2.13 now available
Sun, 12 Jun 2005 12:00:00 EST
Major changes
New engine available in blastall
Blastall now has support for a new version of the BLAST engine that can be enabled by adding"-V F" to the blastall command-line. This option will probably be the default in future versions. There are a few situations where it is very advantageous to use the new engine:Statistical parameter change
Megablast, blastall and bl2seq have until now allowed users to select arbitrary gap existence and extension penalties for a blastn type search. This has been convenient for users but has led to the unfortunate situation that searches with some parameter sets were significantly overestimating the statistical significance of matches. To address this problem the proper statistical parameters for a number of reward/penalty/gap existence/gap extension values have been calculated. The parameters that might cause an issue here are-r
(match reward), -q (mismatch penalty), -G
(gap existence cost), and -E (gap extension cost). If you
do not change these, then nothing will change for you. Please email
blast-help@ncbi.nlm.nih.gov
with any questions, bug reports, or requests for different parameter
sets.