Basic Local Alignment Search Tool

Basic Local Alignment Search Tool is in short BLAST is a set of similarity search programs designed to explore all of the available sequence databases regardless of whether the query is protein or DNA.

It uses a heuristic algorithm which seeks local as opposed to global alignments, and is therefore able to detect relationships among sequences which share only isolated regions of similarity.

It can be run locally as a full executable, and can be used to run BLAST searches against private, local databases, or downloaded copies of the NCBI databases. It runs on Mac OS, Win32, LINUX, Solaris, IBM AIX, SGI, Compaq OSF, and HP- UX systems.

What is new in this release:

• Improvements:
• Enhanced documentation, includes simplified setup instructions, available at http://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

What is new in version 2.2.24:

• Introduces BLAST Archive format to permit reformatting of stand-alone BLAST searches with the blast_formatter.
• It adds support for translated subject soft masking in the BLAST databases.
• It adds support for the BLAST Trace-back operations (btop) output format.
• It adds command line options to blastdbcmd for listing available BLAST databases.
• Improved performance of formatting of remote BLAST searches. Uses a consistent exit code for out of memory conditions.
• A fix for a bug in indexed megablast with multiple space-separated BLAST databases.

What is new in version 2.2.19:

• 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.