[BiO BB] [blast-announce] [ BLAST_Announce #044] BLAST 2.2.10 released

Joe Landman landman at scalableinformatics.com
Thu Oct 28 11:46:24 EDT 2004

Binaries can be obtained from:

Source code can be obtained from:

Additionally, NCBI now provides anoncvs access
lkit.section.cvs_external) to toolkit sources. A cvsweb source browser
re/) and doxygen documentation
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


	-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

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

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