BLAST NEWS

New checkboxes in the "Choose Search Set" section of the BLAST search pages exclude Model sequences (XM/XP) and environmental samples.    The environmental sample sequences are identified with the entrez query:   environmental samples[filter] OR metagenomes[orgn]   Accessions of model sequences start with XM or XP. .

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.

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There is a new feature to include or exclude multiple organisms from a search.   The BLAST web pages now allow you to exclude organisms from your search as well as limit you search to multiple organisms, instead of just one.  Use the "Organism" box in the "Choose Search Set" part of the web page. Use the plus sign "+" to add another organism to include/exclude. .

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

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COBALT incorporates pairwise constraints into a progressive multiple alignment.    The pairwise constraints are derived from the conserved domain database, the protein motif database, and sequence similarity searches, using RPS-BLAST, BLASTP, and PHI-BLAST
(http://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 http://www.ncbi.nlm.nih.gov/tools/cobalt/cobalt.cgi?CMD=Web        .

454 transcript sequences are now searchable through BLAST.
  The search sets are grouped by organism and include all public 454 transcript sequences in the NCBI SRA database.  Go to http://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE=MegaBlast&PROGRAM=blastn&BLAST_PROGRAMS=megaBlast&PAGE_TYPE=BlastSearch&BLAST_SPEC=SRA to run a search.

New BLAST binaries are available on the NCBI FTP site.  The list of changes are:
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.

The Align two sequences link on the BLAST home page now uses the standard BLAST submission form.   The Align two sequences link from the BLAST home page at blast.ncbi.nlm.nih.gov now uses the standard BLAST interface.  This new form can accept mutliple queries or target sequences.  The page will also issue an RID that you can see under the "Recent Results" tab so you can get back to your results for 36 hours.    .

New BLAST binaries are available on the NCBI FTP site.   List of changes:

• 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.

Bugs Fixed

• seedtop now supports searches with gi lists.
• The X3 value for blastn/megablast was corrected.

The NCBI BLAST web pages (blastn, blastp, blastx, tblastn, tblastx ) have a new option to align a query against a set of target sequences, rather than a BLAST database.This option allows you to align your query to one or more subject sequences and still use the standard BLAST web interface to optimize your search and change algorithm parameters. Each search is assigned a "Request ID" (RID) and is also listed under the "Recent Results" tab that you can access from the BLAST home page at http://blast.ncbi.nlm.nih.gov/Blast.cgi. The results are formatted as a standard BLAST report, except a "Dot Matrix view" (a "dot-plot" like graphic of the alignments) is available in the new report design if only one subject sequence was searched. Step-by-step instructions can be found at http://blast.ncbi.nlm.nih.gov/docs/align_seqs.pdf.

Primer-BLAST was developed to help users make primers specific to a PCR template. Primer-BLAST combines primer design (using Primer3) and a specificity check via a BLAST search. The specificity check against user selected databases can avoid primer pairs that amplify targets other than the input template. Primer-BLAST can also used with pre-designed primers.
To get started with Primer-BLAST go to http://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
.

Free full text for this article about the NCBI BLAST web interface is available at http://nar.oxfordjournals.org/cgi/content/full/36/suppl_2/W5.

A detailed list of improvement are:   - Two new evolutionary distance models for protein sequences developed by N. Grishin that allow construction of guide trees between sequences with more than 75% mismatched amino acids.
- 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..

To use the new report select the link "Please, try our new design!: at the top right corner of the report.   In this modified report the information at the top of the BLAST report is better organized so as to be easier to read and take up less space.  Links to other information about the BLAST results (such as tree view and taxonomy) are now grouped together and there is a new "Search summary" link.    The different sections such as Graphic summary, Descriptions, and Alignments are also now collapsible.    Formatting options can also now be opened on the report page and a new "Download" link includes a CSV format that works well with spreadsheet programs such as Excel. .

The NCBI has activated a new URL for BLAST searches at the NCBI: http://blast.ncbi.nlm.nih.gov. Searches sent to this URL can take advantage of a larger number of machines for searches and the system has a better overall fault tolerance. We recommend migration of all BLAST links and bookmarks (e.g., http://www.ncbi.nlm.nih.gov/BLAST/ and http://www.ncbi.nlm.nih.gov/blast/bl2seq/wblast2.cgi) to the new URL. Links on the NCBI and BLAST home pages will start to change in the coming weeks. At this point in time the plans are to also maintain the current BLAST URL..

After beta testing the new BLAST pages will become the default BLAST portal as of 04/16/2007. April 2, 2007: New BLAST design to be released on April 16, 2007
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The new NCBI BLAST pages will become the default interface at
http://ncbi.nlm.nih.gov/blast on April 16, 2007. The new
interface is currently available as a beta release at
http://ncbi.nlm.nih.gov/blast/beta/. For details on the new
interface, see http://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
http://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 http://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
http://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.

NCBI is holding a beta test for a new BLAST interface design. Special Announcement: Beta Test of New BLAST Interface.
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:
http://www.ncbi.nlm.nih.gov/blast/beta/
or as a link from the BLAST home page at
http://www.ncbi.nlm.nih.gov/blast/
Please send all comments suggestions or bug reports to
mcginnis@ncbi.nlm.nih.gov.

BLAST release 2.2.14 offers a universal binary for Mac OS X, and improved performance on some platforms.

BLAST 2.2.14 is now available on the BLAST download page.

Major Changes

blastall now uses the new engine by default, resulting in significant performance improvements\  and enabling query concatenation for all program types.

The Mac OS X build is now a universal binary.

Multithreaded searches now work properly under ia32-win32.

The sparc64-solaris build now requries Solaris 10.

Support for axp64-tru64 will be discontinued.

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The new release includes a new engine for blastall, changes to statistical parameters, and bug fixes. BLAST 2.2.13 is now available on the BLAST download page.  

Major changes

New engine now available in blastall

Statistical parameter change

Bug fixes

 

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:   

Large word-sizes with a BLASTN search. The new engine uses the

  "stride" idea of AGBLAST and this can lead to a considerable speedup   for large wordsizes. For a run of a typical mRNA sequence (u00001)   with a word size of 25 the new code runs about twice as fast as the   old code. Note that the AG "stride" has been available in megablast   since the 2.2.10 release. This enhancement is platform-independent.     

Searching multiple queries at once. The new engine will search

  multiple queries by scanning the database once, rather than once for   each query. The speedup will depend upon the queries being searched   and what part of the time is spent scanning the databases vs. actual   compuations (e.g., extensions etc.). Typically this feature is most   important if a number of short queries (e.g., mRNA's or EST's) are   being searched with blastn or if a tblastn search is performed. This   feature is partially supported in the old code with the -B option as   well as by megablast.     

For very large queries. The memory management (especially during

  the dynamic programming phase) has been improved and this may allow   searches with lots of matches or large queries that used to fail to   now run to completion.

 

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.

Bug Fixes

A bug has been fixed in formatdb. This bug occurred when the -o

   option was not used, meaning that the FASTA definition lines of the    input file were not parsed, and multiple database volumes were    generated. The bug normally did not become apparent to the user    until the BLAST run at which point the BLAST binary (e.g.,    blastall) would produce messages containing "ObjMgrChoicE: Pointer    [0] type [1] not found".

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