Release Notes: 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.
Release Notes: 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.
Release Notes: 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.
Release Notes: 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.
Release Notes: 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.
Release Notes: Numerous minor bugs were fixed. Assorted minor feature enhancements were done.
Release Notes: Assorted minor bugfixes and code cleanups.
Release Notes: Performance improvements were made for nucleotide searches. XML output for the masking of ungapped translating searches has been fixed. Assorted object manager and memory leaks were fixed along with filtering of low-complexity regions at the ends of a sequence.
Release Notes: BLAST now uses a 28-letter protein alphabet supporting the J (leucine or isoleucine) and O (pyrrolysine) residues. Support has been added for incremental ASN.1 output. Searches larger than 10kbp have been accelerated. Support has been added for BLOSUM50 and BLOSUM90 score matrices. Headers are now correctly printed for concatenated queries.
Release Notes: The previously experimental improved search algorithms are now used by default. The Mac OS X build is now a universal binary. Multithreaded searches now work properly under ia32-win32. The sparc64-solaris build now requries Solaris 10. Support for axp64-tru64 is deprecated.