New NCBI toolkit release

Tom Madden madden at CORIN.NLM.NIH.GOV
Mon Jun 15 14:49:44 EST 1998

A new version of the NCBI toolkit has been placed on the NCBI FTP site
at ftp://ncbi.nlm.nih.gov/toolbox/ncbi_tools/   This release includes:

1.) New client/server libraries. These are designed to run through HTTP 
instead of our custom dispatcher to connect the client to the service. 
This gives more reliable support.  The WWW normally operates in a
stateless mode, meaning that the connection is not preserved between
transactions.  However, there are performance issues 
related to the stateless mode the WWW operates under and the state based
connections of our current clients.   Right now these libraries work fine if 
there is no firewall. However, we have to address the state issues (there 
are a couple of solutions) to work behind firewalls.  

If you are not behind a firewall, then you are advised to use the new 
client/server functionality, which is the default.  In other words, simply 
by using the new clients (or linking with these new libraries)
you will automatically use these new libraries and the HTTPD server at NCBI.

If you are behind a firewall, then you should still take the new clients
(or link to the new libaries).  However, to use the old connection 
functionality you need to add the line "SRV_CONN_MODE=DISPATCHER" to the
"[NET_SERV]" entries of your NCBI configuration file (e.g., .ncbirc):


2.) Client software for gapped BLAST (version 2.0).  Precompiled clients for 
platforms can be found at ftp://ncbi.nlm.nih.gov/blast/network/  These clients
use the client library mentioned above.  The source code for these clients is in 
the NCBI toolkit under network/blast3/client.  

3.) Updates to the Sequin software.

4.) Updates to the BLAST software (2.0.5).  Changes to BLAST in this release are
detailed below.

BLAST 2.0.5.


1.) The BLAST version is printed by formatdb in it's log file.

2.) Multi-database searches no longer require that the -o option be used when
preparing the databases (i.e., with formatdb).

Bugs fixed:

1.) A serious bug with multi-database iterative searches was fixed (thanks to
Steve Brenner for providing an example).

2.) 'lcl' is no longer formatted in the BLAST report when the sequence
identifier is a local identifier or does not contain a bar ("|").

3.) A large memory leak in formatdb was fixed.

4.) An unnecessary cast that caused formatdb to fail on Solaris 2.5 machines
if the binary was made under 2.6 was fixed.

5.) Better error checking was added to protect against core-dumps.

6.) Some problems with the sum statistics treatment of the blastx and tblastn
programs reported by D. Rozenbaum were fixed.  The number of alignments
involved in a sum group was misrepresented.  Also the incorrect length for
the database sequence was used, sometimes casuing a slight change in the
value reported.

7.) A problem with blastpgp was fixed that reported incorrect values for
matrices other than BLOSUM62 during iterative searches.

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