April 4th, 2011Improvements:
· 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).
· 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
August 25th, 2010
· 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.
December 18th, 2008
· 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.