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 ftp://ncbi.nlm.nih.gov/toolbox/ncbi_tools/  New binaries
for BLAST (ftp://ncbi.nlm.nih.gov/blast/executables/), Entrez
(ftp://ncbi.nlm.nih.gov/entrez/network/) and Sequin (ftp://ncbi.nlm.nih.gov/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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