ANNOUCEMENT FROM THE NORWEGIAN EMBnet NODE
The Norwegian EMBnet node has set up anonymous ftp services in order
to make available to the community the SRS (Sequence Retrival Package) of
Thure Etzold, from the EMBL.
The SRS package is made available as a backup save set containing all
sources, help files and user documentation, as provided to us by the
author.
All sources and documentation are copyright of Thure Etzold, EMBL.
DESCRIPTION
The SRS system was designed to ease, expand and exploit all the information
we have available in the documentation part of the major nucleic and
protein sequence databases: EMBL, GENBANK, PIR and SwissProt.
It also exploits support databases such as EPD, Prosite, etc...
The system is capable of retrieving groups of entries depending on
a user specification and indeed is capable of extracting sequence features
into individual entries according to the annotation rules for the feature
table agreed by EMBL, GenBank and DDBJ. Extraction format may be defined
to be GCG or PIR (NBRF).
In this release, the system uses the GCG formated databases which it uses
to create the search indexes. Other databases in their original distribution
format are supported (ie: prosite,enzyme, rebase, epd, ecd, etc...).
The databases are linked together in SRS making use of the cross-linking
information provided by the database curators. This feature results in a
the fast and accurate retrival of say, all DNA's related to a particular
protein sequence.
AVAILABILITY:
The Norwegian EMBNet node may be reached by:
ftp biomed.uio.no
or
ftp 129.240.2.38
Login as user 'anonymous'
Password: Please type your e-mail address
An INSTALL_SRS.COM has been provided by us in order to ease the work load.
Compilation of the programs requires a VAX C compiler. After ftping the
backup save set make sure the record length is OK (users of UCX will probably
have to modify this). If it is not, you will find FIXREC.C (by Stockwell,P)
(also available by ftp in the same directory) useful for fixing up this
problem. Just compile and link FIXREC.C and give it the SRS backup save set
as input file:
$ fixrec srs21.bck
If everything is OK you may proceed to run INSTALL_SRS.COM.
IMPORTANT NOTES FOR INSTALLATION:
INSTALL_SRS.COM checks that the user has SYSPRV privs in order to prevent
common mortal users installing the package on their login directories (nothing
wrong with this). Should such a user proceed to complile and link some disk
space will be gone (ca.6000 block) which may be precious at sites were
CPU and disk space accounting are used (nothing wrong with this either). But,
should this user begin to compile indexes (now she/he is in trouble!) he
will require AT LEAST 84000 blocks to accomodate the EMBL database indexes.
An installation of the following databases requires ca. 140000 blocks:
EMBL (Including EMBL daily updates)
PIR (including NRL_3D)
SWISSPROT
Prosite
Enzyme
EPD
ECD
SEQANALREF
TOC's (from The University of Indiana's fly.bio.indiana.edu ftp server)
Instructions descibing the compile and linking of the programs and also
instructions for making the different indexes may be found in the file
INSTRUCTIONS.TXT. Please read this file carefully!
Please contact anyone of us if you have problems, but don't expect an
immediate response as we are also dealing with other matters.
Thure Etzold etzold at embl-heidelberg.de
Rodrigo Lopez rodrigol at biomed.uio.no
Jack Leunissen jackl at caos.caos.kun.nl
Christoph Gartmann gartmann at vms.mpiib-freiburg.mpg.dbp.de
