new NCBI toolkit

Tom Madden madden at CORIN.NLM.NIH.GOV
Thu Mar 26 10:17:03 EST 1998

New archives of the NCBI toolkit (for UNIX, PC, and Macintosh) are available 
from the NCBI FTP in  New binaries
for BLAST (, Entrez
( and Sequin (
are also available. 

             Special note for UNIX BLAST users.
    If you retrieved the ncbi.tar.Z file or the DEC or Solaris BLAST
binaries between March 5, 1998 and March 25, 1998, please retrieve the
newest tar file or binaries.  A bug in the distribution made on March 5
caused BLAST to core dump under DEC UNIX and another bug caused the
Solaris binaries to not multi-thread.  No erroneous results were produced 
owing to either of these bugs.

What's new in the newest BLAST version:

> The new BLAST version is 2.0.4.  The new version of BLAST has some enhancements
> compared to 2.0.3:
> 1.) multiple database searches:
> Version 2.0.4 will accept multiple database names (bracketed by quotations).
> An example would be
>               -d "nr est"
> which will search both the nr and est databases, presenting the results as if one
> 'virtual' database consisting of all the entries from both were searched.   The
> statistics are based on the 'virtual' database.
> 2.) new options:
>   -W  Word size, default if zero [Integer]
>     default = 0
>   -z  Effective length of the database (use zero for the real size) [Integer]
>     default = 0
> 3.) The number of identities, positives, and gaps are now printed out before the
> alignments for gapped blastx, tblastn, and tblastx.  Additionally this feature is
> now also enabled for ungapped BLAST.
> 4.) Formatdb now accepts ASN.1, as well as FASTA, as input.
> Two significant bugs were also fixed:
> 1.) In blastx, tblastn, and tblastx a codon was incorrectly formatted as a start codon in
> some cases.
> 2.) The last alignment of the last sequence being presented was incorrectly dropped
> in some cases.  This change could affect the statistical significance of the last database
> sequence if the dropped alignment had a lower e-value than any other alignments from the
> same database sequence.

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