Bioperl: about blastcl3

Jonathan Epstein
Mon, 27 Mar 2000 11:10:57 -0500

Many of you are familiar with "Network Entrez", which was an Internet
client/server program built upon the NCBI "Dispatcher" system, which appeared
in 1993.  All client/server communication uses the ASN.1 protocol, using
relatively stable ASN.1 specifications.  I.e., the specifications typically
only change about once per year, the specification changes are well-documented,
and corresponding server changes are made backwards compatible with older
clients when feasible.  From a software point of view, these interfaces are
much more stable than most Web interfaces or the GenBank flat file.

Network Entrez still exists, although its communication is now Web-based, but
continues to use the ASN.1 protocol as described above.  Blastcl3 is a blast
network client which is analogous to network Entrez.  It can also perform blast
HTML formatting, and the software interface is relatively stable.  The blastcl3
client software can be downloaded at:
or can be built from the NCBI toolkit:

Note that using the client software is more palatable than writing embedded
bioperl software which "speaks" ASN.1 and communicates directly with these
stable NCBI resources.  An XML solution would be even nicer, but I am not aware
of any XML resources currently available from NCBI.

- Jonathan

Jonathan Epstein                      
Unit on Biologic Computation                    (301)402-4563
Office of the Scientific Director               Bldg 31, Room 2A31
Nat. Inst. of Child Health & Human Development  31 Center Drive
National Institutes of Health                   Bethesda, MD 20892
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