March 15, 2011 * 2.2.25 release * Enhanced documentation, includes simplified setup instructions, available at http://www.ncbi.nlm.nih.gov/books/NBK1762 Improvements: * 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. * Possbile failure to run in multi-threaded mode with multiple queries or large database sequences. * Tblastn runs with database masking might miss matches. October 30, 2010 * 2.2.24 bug fix release * Improved makeblastdb performance and taxid_map option * Fixed segmentation faults on blastn and megablast * Fixed truncated output for sequence input with extra spaces in the defline * Fixed problem with MacOSX binaries on MacOSX 10.5 August 2, 2010 * 2.2.24 release * Added support for BLAST Archive format (see BLAST+ user manual) * Added the blast_formatter application (see BLAST+ user manual) * Added support for translated subject soft masking in the BLAST databases * Added support for the BLAST Trace-back operations (btop) output format * Added command line options to blastdbcmd for listing available BLAST databases * Improved performance of formatting of remote BLAST searches * Use a consistent exit code for out of memory conditions * Fixed bug in indexed megablast with multiple space-separated BLAST databases * Fixed bugs in legacy_blast.pl, blastdbcmd, rpsblast, and makeblastdb * Fixed Windows installer for 64-bit installations Feb 03, 2010 * 2.2.23 release * Bug fix for tabular output formatting involving BLAST databases that do not have parseable deflines. * Fixed problem displaying accessions in XML output format. * Prevent collisions between queries and subject sequences with local identifiers. * Fixed megablast performance regression when used with query masking. * Fixed seg filtering failure for blastx and genomic sequences. * Implemented saving search strategies in bl2seq mode. * Fixed bug in tabular output format with qseq, sseq, pident and ppos keywords. * Fixed bug with blastp-short task. * Fixed blastdbcmd retrieval of taxids for BLAST databases without GIs. * Added makeblastdb support for adding masking information to existing BLAST databases. Nov 02, 2009 * Internal bug fix release for 2.2.22 * Fix issue dealing with opening BLAST databases which contain references to a BLAST database specified with a relative path. * Prevent collisions between queries and subject sequences with local identifiers Sep 27, 2009 * 2.2.22 release * Added entrez_query command line option for restricting BLAST databases. * Added support for psi-tblastn to the tblastn command line application via the -in_pssm option. * Improved documentation for subject masking feature in user manual. * User interface improvements to windowmasker. * Made the specification of BLAST databases to resolve GIs/accessions configurable. * update_blastdb.pl downloads and checks BLAST database MD5 checksum files. * Allowing long words with blastp. * Added support for overriding megablast index when importing search strategy files. * Added support for best-hit algorithm parameters in strategy files. * Bug fixes in blastx and tblastn with genomic sequences, subject masking, blastdbcheck, and the SEG filtering algorithm. May 27, 2009 * First 2.2.21 release * Added support for Best-Hit algorithm. * Added support for -in_msa psiblast option. * Performance improvements and bug fixes to subject soft masking feature (note: the file format for the files containing the masking information has changed in a non-backwards compatible way). * Changed command line option to specify single soft masking algorithm to mask BLAST databases from -mask_subjects to -db_soft_mask. * Masked FASTA and subject masks can be obtained via blastdbcmd. * Improved error messages when makeblastdb processes masking information. * Bug fixes in tabular output for translated searches. * Bug fixes to makeblastdb. * Bug fixes to search strategies and megablast. * Bug fixes to XML output. * Bug fixes and performance improvements to multi-threaded execution. * Bug fixes to lower case masking in blastx. * Bug fixes to ungapped searches. * Added support for smaller lookup tables for small queries. * Added support for partial sequence fetching during traceback. * Fixed the 2-hit algorithm so that no overlap between two hits is allowed. * Implemented a new method to compute effective observations and new entropy-based method to compute column-specific pseudocounts in PSI-BLAST. * Remote BLAST database data loader is used as a fallback if local BLAST databases cannot be found. * Bug fixes, improved error messages, and support for ASN.1 input in makeblastdb. * Bug fixes and performance improvements to subject masking feature. * Added the update_blastdb.pl script * Updated BLAST+ user manual with documentation about configuring BLAST, automatic resolution of sequence identifiers, and a description of how the BLAST databases are searched. November 3, 2008 * First 2.2.19 release * Made sequence ID/title display uniform in sequence filtering applications. * Fixed incorrect display of filtering options in XML output. * Fixed handling of empty sequences in BLAST input. * Fixed negative strand handling for tblastn/tblastx. October 14, 2008 * Added update_blastdb.pl script to distribution of BLAST+ command line applications. * Changed a few PSI-BLAST constants for pseudo-counts. * Bug fix in blastdbcmd to distinguish non-redundant sequence titles. * Bug fix to display BLAST database information remotely from outside NCBI for XML output. September 24, 2008 * Fix to prevent initial seed extension from going beyond context boundary. * Improvements to reduce memory usage when query splitting is applied. * Print the accession and version for blastdbcmd's %a output format. * gilists/negative gilists are not saved in search strategies or supported in remote blast searches. * legacy_blast.pl fixed for MacOSX, as well as extended support for megablast formatting options (-D, -f). * Enhancements to Mac installer to add installation path to user's PATH. * ASN.1 output is now of type Seq-annot. * -lcase_masking option now applies to subject sequences as well as queries. * Bug fix for creation of masked databases with non-redundant sequences that use a BLAST database as its data source. * Bug fix for merging masking locations. August 21, 2008 * First internal release