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BLAST+ executables

Edit Package ncbi-blast+
https://www.ncbi.nlm.nih.gov/books/NBK1762/

BLAST+ is a new suite of BLAST tools that utilizes the NCBI C++ Toolkit. The BLAST+ applications have a number of performance and feature improvements over the legacy BLAST applications. For details, please see the BLAST+ user manual and the article in BMC Bioinformatics.
http://www.ncbi.nlm.nih.gov/pubmed/20003500?dopt=Citation

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Source Files
Filename Size Changed
ncbi-blast-2.7.1-src.tar.gz 0023254824 22.2 MB
ncbi-blast.changes 0000006673 6.52 KB
ncbi-blast.spec 0000002835 2.77 KB
Revision 5 (latest revision is 9)
Matthias Mailänder's avatar Matthias Mailänder (Mailaender) accepted request 633575 from Pierre Bonamy's avatar Pierre Bonamy (flyos) (revision 5)
- Change the name of the package to nbci-blast+ to be avoid conflicts
with ncbi-blast packaged in "ncbi" and to be aligned with other systems
(e.g. Debian world)
- Update to version 2.7.1
	* BLAST+ 2.7.1: October 23, 2017
	- Improvements::
	    Provided an upper limit on the number of threads for BLAST+ 
	search applications.
	    Improved performance of taxonomic name lookups.
	    Fixed Mac installers so they are interoperable with other NCBI 
	applications.
	    Reduced the amount of locking in BLASTDB reading library (CSeqDB).
	- Bug fixes::
	    Fixed race condition when using gilist parameter.
	    Fixed culling_limit bug with HSPs from different strands
	    Fixed dustmasker bug with long region of Ns
	    Fixed bl2seq problem with HTML output
	
	* BLAST+ 2.6.0: January 09, 2017
	- New features::
	    Handle bare accessions on blastdb_aliastool.
	    Change defaults for output formats 6, 7, and 10 to incorporate 
	version in accessions.
	- Improvements::
	    Add support for NCBI_DONT_USE_LOCAL_CONFIG and 
	NCBI_DONT_USE_NCBIRC environment variables.
	    Better runtime performance in blastdbcmd when the entry_batch 
	parameter is used.
	    SAM output improvements.
	    Changed gapped alignment starting point to minimize the chance to 
	produce sub-optimal alignments.
	    For custom matrices absent from the util/tables source file, use 
	BLOSUM62 for reporting number of positives.
	    Added long_seqids flag to blastdbcmd to use long (legacy) NCBI 
	Seq-id format.
	- Bug fixes::
	    Fixed issue with missing alignments in blastx.
	    Fixed problem processing accession.version in makeblastdb.
	    Fixed blastdbcmd problem with local IDs.
	    Removed memory leak for multi-threaded runs.
	    Fixed blastdbcmd crash when listing all entries and a sequence has 
	no title.
	    
	* BLAST+ 2.5.0: September 12, 2016
	- New features::
	    Composition based statistics for rpstblastn.
	    Added output format for taxonomic organism report.
	    Support for bare accessions in FASTA and BLAST reports.
	- Improvements::
	    -remote option connects to NCBI via HTTPS. This adds a dependency 
	on GNUTLS (see https://www.ncbi.nlm.nih.gov/books/NBK279690/)
	    Pre-fetch sequences for formatting.
	- Bug fixes::
	    Fixed improper functioning of output format 6 tokens ssciname, 
	staxid, sscinames and staxids.
	    tblastn core-dumps in multi-threaded mode.
	    Ensure stable sorting of results in multi-threaded mode.
	    Fixed incorrect percent identity in tabular format for sequences 
	containing selenocysteine.
	
	* BLAST+ 2.4.0: June 02, 2016
	- New features:
	    Introduced multi-threaded traceback for blastp, blastx, tblastn 
	and tblastx.
	    Added new tabular format specifiers for taxonomic information 
	(staxid, ssciname, scomname, sblastname, skingdom) that correspond to 
	the first subject ID.
	- Improvements:
	    Speed up makeblastdb runtime performance with input consisting of 
	many ambiguities.
	    Better support for 'bare' IDs in taxid_map option to makeblastdb.
	    Score U (selenocysteine) as C (not X) in protein-protein and 
	translated searches.
	- Bug fixes:
	    Corrected E-value computation in finite-size correction.
	    Removed memory leak from rpsblast.
	    Made handling of ambiguities in subjects identical when using 
	FASTA and BLAST database inputs.
	    makeblastdb no longer replaces tabs in definition line by '#'.
	    Corrected problem with spaces in database names on windows.
	    Corrected handling of subject_loc.
	
	* BLAST+ 2.3.0: December 21, 2015
	- New features:
	    Added new PSIBLAST command line options to support saving PSSM 
	and checkpoint files for each iteration and calculate checkpoint and 
	PSSM for the last iteration.
	    Added unique subject sequence query coverage to tabular output.
	    Added support single file JSON and XML2 Blast output format.
	    Beta release of SAM output format.
	    Treat N subject sequences, entered with the -subject argument 
	(bl2seq mode), as one search set rather than N sets.
	- Improvements:
	    makeblastdb ignores and warns users about empty sequences in 
	input.
	    BLAST+ only accepts "obinary" windowmasker files for performance 
	reasons.
	- Bug fixes:
	    Best hits processing multi-threaded context.
	    Fixed memory leak when invoking composition based statistics with 
	an argument of 2.
	    Return non-zero exit code when failing to write output file.
	    Use relative paths in XInclude file for multi-file XML2 output 
	format.
	    Fixed memory leak in blastx.
	    Fixed inconsistent XML2 output to standard output vs. file.
	    Fixed psiblast incorrectly processing large input MSA.
	    Fixed bug when running BLAST+ on windows with multiple threads.
	
	* BLAST+ 2.2.31: May 18, 2015
	- New features:
	    Added support for BLAST-XML2 specification.
	    Added support for JSON Blast output format.
	- Improvements:
	    Improved adaptive batch size algorithm to better handle small 
	databases.
	    Preface error/warning message(s) with name of the application.
	    Allow multiple deflines even without GIs.
	    Download more concise database information for -remote searches.
	- Bug fixes:
	    Fixed problem with makeblastdb's -max_file_sz.
	    Reenabled support for word size 5 in tblastn.
	    Fixed memory initialization problems.
	    Use score for sorting search results if evalue less than 1.0e-180.
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