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BLAST 2.2.27+ released

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A new version of the stand-alone BLAST applications has been released.      BLAST+ applications may be downloaded here.  Installation instructions can be found here.  The BLAST 2.2.27+ release contains a number of important changes and improvements.
1.) We have implemented composition-based statistics for BLASTX.  It offers better statistical accuracy and is the default mode, but the older behavior can be recovered with the –comp_based_stats flag.   The BLASTX implementation is based upon the methods described in pmid 17156431.
2.) The deltablast application now allows searches with the –remote flag.
3.) We have reduced the memory usage of the blastn application when searching many small queries.  This involved reducing the number of queries searched during one pass through the database as well as reducing the number of database sequences retrieved for the tabular output formatting.  Section 4.3.1 and 4.3.2 of the manual present details on this change as well as information on how to control the number of queries searched during one pass through the database.  
4.) The output for reports without separate descriptions and alignments sections (all –outfmt greater than 4) should now use –max_target_seqs to control the output rather than –num_descriptions and –num_alignments.
5.) In megaBLAST mode, the blastn application now reduces the number of gaps if possible.  As described in pmid 10890397, the megaBLAST algorithm (with linear gapping) assigns an equal score to an alignment with two mismatches and to an alignment with two gaps plus an additional match.  If possible, the blastn application now presents the alignment without the gaps.
6.) We have extensively rewritten the BLAST+ manual.  Appendix C now contains tables of options for different programs.  This is an updated set of tables based on the supplementary information of pmid 20003500.
7.) We have fixed various bugs in the blast_formatter, blastdbcmd and other programs. These include one that did not render an asterisk (stop codon) properly as well as one that improperly applied compostion-based statistics to any use of the Smith-Waterman option.        

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