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Basic Local Alignment Search Tool Changelog

What's new in Basic Local Alignment Search Tool 2.2.25

Apr 4, 2011
  • 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

New in Basic Local Alignment Search Tool 2.2.24 (Aug 25, 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.

New in Basic Local Alignment Search Tool 2.2.19 (Dec 18, 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.