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BLAST Changelog

What's new in BLAST 2.3.0

Jan 15, 2016
  • This new version includes a beta release of SAM format as well as support for single-file mode for the BLAST XML2 and JSON formats. Single-file mode means that results are delivered as a single-file regardless of the number of queries. A number of other improvements and bug fixes are also included.
  • 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.

New in BLAST 2.2.26 (Mar 6, 2012)

  • Mac executables are now Universal Binaries for 32- and 64-bit architectures, we no longer produce PPC and Intel Universal binaries. The executable archive names remain unchanged.
  • Added DELTA-BLAST - a new tool for sensitive protein searches
  • Added makeprofiledb - a tool for creating a database for RPS-BLAST
  • Improvements:
  • The blast_formatter application can now format bl2seq RIDs.
  • PSI-BLAST can produce archive format, blast_formatter can format that output.
  • PSI-BLAST has two new options that work with multiple-sequence alignments: ignore_msa_master and msa_master_idx (see BLAST+ manual).
  • mkmbindex can now create masked indices from a BLAST database and ASN.1 masking data.
  • An improved finite size correction is now used for blastp/blastx/tblastn/rpsblast. The FSC is subtracted from the query and database sequence length for the calculation of the expect value. The new FSC results in more accurate expect values, especially for alignments with a short query or target sequence. Re-enable the old size correction by setting the environment variable OLD_FSC to a non-NULL value.
  • The blastdbcmd -range parameter now accepts a blank value for the second parameter to signify the end of a sequence (e.g., -range "100-")
  • There was a performance improvement for long database sequences in results with many matches.
  • Bug fixes:
  • There was a blastn problem if subject_loc and lcase_masking were used together.
  • There was a problem with multi-threaded blastx if the query included a long (10,000+) sequence of N's.
  • The percent identity calculation was wrong if the best-hit algorithm was used.
  • There was a problem with the multiple BLAST database statistics report in XML format.
  • Makeblastdb failed to return an error when input was not available.
  • The formatting option -outfmt "7 nident" always printed zero.
  • The search strategy was not properly saving the -db_soft_mask option.
  • An error message was emitted if there was a "