---------- Forwarded message ---------- Date: Thu, 28 Oct 2004 11:46:24 -0400 (EDT) From: Joe Landman <landman at scalableinformatics.com> Reply-To: bio_bulletin_board at bioinformatics.org To: biocluster at bioinformatics.org Cc: biobb at bioinformatics.org Subject: [BiO BB] [blast-announce] [ BLAST_Announce #044] BLAST 2.2.10 released Binaries can be obtained from: ftp://ftp.ncbi.nlm.nih.gov/blast/executables/release/2.2.10/ Source code can be obtained from: ftp://ftp.ncbi.nlm.nih.gov/toolbox/ncbi_tools/old/20041020/ Additionally, NCBI now provides anoncvs access (http://www.ncbi.nlm.nih.gov/books/bv.fcgi?call=bv.View..ShowSection&rid=too lkit.section.cvs_external) to toolkit sources. A cvsweb source browser (http://www.ncbi.nlm.nih.gov/cvsweb/index.cgi/internal/c++/src/algo/blast/co re/) and doxygen documentation (http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/group__AlgoBlast.h tml) are also available. Notes for the 2.2.10 release New engine We have been rewriting and restructuring the BLAST engine in order to make BLAST more modular and extensible. bl2seq and megablast currently support the new engine; it can be enabled with the -V F option. Using the new engine may result in significant performance improvements in some cases. General changes -megablast now performs ungapped extensions in order to prevent suboptimal alignments -consolidated formatting code -removed fmerge.c -small fixes to sum statistics code -better error handling -fixed masking of translated queries -fixed several readdb threading bugs -improved protein neighbor generation -hsp sorting/inclusion fixes -many changes in HSP linking -several fixes for translated RPS blast BlastPGP -added code to spread out gap costs when extracting data from the sequence alignment to build PSSM -changed handling of all-zero columns of residue frequencies to use the underlying scoring matrix frequency ratios rather than scoring matrix's scores - disallowed an ungapped search if more than one iteration is specified scoremat.asn specification -added a new 'formatrpsdb' application; given a collection of Score-mat ASN.1 files, this application creates a database suitable for use with RPSBLAST -Simplified NCBI-ScoreMat specification to represent PSSMs instead of arbitrary scoring matrices. blastpgp and formatrpsdb can deal with this format. If you have any questions please write to blast-help at ncbi.nlm.nih.gov _______________________________________________ BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org https://bioinformatics.org/mailman/listinfo/bio_bulletin_board