Basic Local Alignment Search Tool

This release adds the Domain Enhanced Look-up Time Accelerated BLAST application, a new finite size correction (FSC) algorithm, and the Makeprofiledb application. Assorted bugfixes.

This release adds support for hard-masking of BLAST databases. It improves the performance of makeblastdb for FASTA input with large numbers of sequences, and improves error checking. Allows Best Hit options and XML formatting for Blast2Sequences mode, multiple query sequences for psiblast, and specification of any multiple sequence alignment sequence as the master. Adds support for query and subject length to tabular output. Performance of the -seqidlist argument has been improved. Assorted bugfixes.

This release 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. The Windows installer has been fixed for 64-bit installations.

This release adds support for spaces in database pathnames on Windows,
fixes an ordering bug in queries, and modifies the 2-hit blastn
algorithm so that no overlap is allowed between hits. Ungapped blastn
searches now allow arbitrary reward/penalty scores. Seedtop now has
gilist support.

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.