Announcement of the availability of the ASN.1 version of SWISS-PROT.
BAIROCH at cmu.unige.ch
Thu Feb 18 01:55:25 EST 1993
Thanks to the staff of the NCBI and more specifically to Mark Cavanaugh, a
version of SWISS-PROT in the ASN.1 notation is now publicly available from
the following anonymous FTP servers:
Organiz. : National Center for Biotechnology Information (NCBI)
Address : ncbi.nlm.nih.gov (or 220.127.116.11)
Organiz. : European MolecularBiology Laboratory (EMBL).
Address : ftp.embl-heidelberg.de (or 18.104.22.168)
Organiz. : Basel Biozentrum Biocomputing server (EMBnet SWISS node)
Address : bioftp.unibas.ch (or 22.214.171.124)
The following files are available:
A compressed, ASN.1 value in "print-form" (ie, ASCII), generated by parsing
release 24 of SWISS-PROT. Uncompressed, this file is approximately 150 Mb in
We have chosen to supply the ASN.1 version of SWISS-PROT in "print-form"
primarily for human-readability. Converted to a binary ASN.1 value, these
data require roughly 60 Mb. Public domain tools developed at the NCBI are
available for such conversions. Software libraries are also available for
processing ASN.1 values (binary or "print-form") at a fairly high level. To
obtain information about the NCBI toolbox, ftp to the address `ncbi.nlm.nih.
gov', login as `anonymous', change to the `toolbox' directory, and copy
the README file you will find there. Or, send a request for more information
via email to `info at ncbi.nlm.nih.gov'.
This file contains the ASN.1 specifications for various biomolecular data
bases (including GenBank, EMBL, PDB, etc.). A subset of the data elements
defined in the specification file were used to map SWISS-PROT to ASN.1. As
of Feb. 3, 1993, there are some known limitations in this mapping:
a) Taxonomy data are available only indirectly, via swissprot-taxon pointers
in Org-ref elements, referring to node identifiers of the SWISS-PROT
taxonomy (see the SWISS-PROT document file `speclist.txt').
b) Reference position (RP) data are not yet captured.
c) Generation of Prot-ref elements is very simplistic; an improved algorithm
would use the contents of the feature table to generate Prot-refs that
point to specific portions of the sequence.
- As improvements are made to the parser new versions of `sp24.prt.Z' may
be posted on the servers listed above.
- The Department of Medical Biochemistry of the University of Geneva and the
EMBL Data Library are not responsible for any problems arising from the
use of the ASN.1 version of SWISS-PROT. What this cryptic legal sentence
means is that the "official" version of SWISS-PROT is the one distributed
jointly by the University of Geneva and the EMBL Data Library; the ASN.1
version is not yet officialy supported.
Two demo programs compiled on a SPARC2 (gcc, SunOS 4.1.1) and a supporting
index file are available from the NCBI server, for use with the ASN.1
version of SWISS-PROT. They are being supplied strictly "as-is", for
demonstration purposes only. See the README file in the `/repository/swiss-
prot/asn/demo' directory for more information.
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