Blast News

A new Bl2seq functionality has been added to the standard BLAST pages that allows you to align a query against a set of subject sequences.

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 combines primer design (using Primer3) and a specificity check with BLAST.

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

A new article  about the BLAST web pages describes the new interface features, explains design decisions, and outline plans for future improvement.

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

The new version of the blast tree view features new distance measures, tree downloading, re-rooting, simplification and sequence grouping.

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.

 

Click here for an example.

A new version of the BLAST report features better organization, download links and collapsible sections.

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.

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.

The binaries for BLAST 2.2.18 are now available at our FTP site

Bugs fixed:
- fastacmd coredump with -a T under certain circumstances
- fastacmd -t produced incorrect output
- -D option caused coredump for tblastx
- With blastn or megablast, if soft-masking and -W 10 or lower is used, lower-case masking ignored.
- megablast missed hits on one strand on rare occasions
- blastpgp echoing query to blastpgp with -a 4, gave different K value
- blastpgp ignored -v -b values with -m7
- seedtop error " double free or corruption" due to too small buffer size to hold hits
- blastclust produces bogus results when BLOSUM62 cannot be found
- megablast error "realloc() error caused segfault" with alias file
- Problem with sorting of matches when composition-based statistics is enabled has been fixed
List of major changes:
-t 2 is now the default for composition-based statistics. Using -t2 rather than -t1 will produce a more intuitive ordering of the results so that exact matches always appear a the top. Users may recover the old behavior by using -t 1.
New feature: "tr" token now accepted for FASTA IDs by formatdb (with -o option). Example is "tr|Q4QBU6|Q4QBU6_LEIMA". This allows for support of the Trembl database defline (http://www.ebi.ac.uk/trembl/).

BLAST results now contain information from the NCBI gene database.

BLAST results now contain information from the NCBI gene database. These can be found under the definition lines of the alignments where applicable. The information includes gene database IDs, gene name and the gene entry title as well as the organism associated with the matching gene entry. A link will take you to the main record for the gene. Also represented is an indication of how many PubMed records are directly associated with the gene entry as a measure of how much literature is available.

Human and mouse genomic + transcript megablast searches now use a faster, indexed algorithm that typically reduces run time by two thirds, as compared with standard megablast.

The database is pre-filtered to eliminate matches to low-complexity and repeat sequences.
The faster search is available from the "nucleotide blast" link on the home page if the megablast "Program Selection" is used.

As previously announced access to the old pages will be removed on June 11, 2007.

The redesigned NCBI BLAST pages became the default interface on April 16, 2007. To ease the transition for user the old pages were kept available for around two months. As previously announced access to the old pages will be removed on June 11, 2007. Bookmarks and script which access the old pages will no longer function.

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
----------------------------------------------------------------

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.

 

 

 

 and enabling query concatenation for all program types.

 

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.

 

 

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.

 

 

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

with any questions, bug reports, or requests for different parameter

sets.

 

Below are listed the supported combinations. Note that above a certain gap existence and extension penalty any value is permitted, as the statistics for ungapped searches can be used. These are marked as "ungapped threshold" below.

 

The supported combinations are:

(*) - ungapped threshold

 

   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".