Sequence Retrieval System

Christoph Gartmann christophg at no.uio.biomed
Mon May 4 09:22:49 EST 1992


An experimental telnet gopher hole has been set up at the
Norwegian EMBnet node where you are invited to test Thure
Etzold's SRS (Sequence Retrieval System). Thure belongs to
EMBL's Biocomputing Programme, P. Argos group were he has
developed most of the current version of the system.

SRS is a comprehensive program that searches the EMBL, EMBL_New,
SwissProt, and PIR International databases installed on this EMBnet node.
The searches are made primarily on the documentation of the sequences 
and permits the retrival of FEATURES (as subsequences) from the feature 

In SRS the databases are cross-linked; meaning that EMBL entries 
referenced in a SwissProt query (or entries) may be retrieved or

A simple example would be:

1. Search for all entries in EMBL with the word 'RAS*'(all words starting
   with 'RAS' in the definition field).
2. Find from this list all relevant SwissProt entries and extract all
   RAS oncogene sequences of mammalian origin.

This file may be simply an file of sequence names (FOSN) or a 
file(s) containing both or only one of the documentation and sequence
in GCG (one file per entry) or NBRF format (one file for all entries).

A secondary set of databases is provided which comprises SeqAnalRef, 
Prosite, PrositeDoc, ENZYME (A. Bairoch), EPD (Bucher and Trifonov),
ECD (Kroger & Rice), TFD (Ghosh) and REBASE (Roberts) which can 
be searched either on their own or in conjunction with the
primary databases. 


Start your gopher and try to find 'Other gophers/' in 'Europe/'.
Try to find the 'University of Oslo/'. Alternatively you might try:

% gopher gopher.uio.no 70

Once you are here, go to item 8 (Faggruper/) of the main list (it's all in
Norwegian at the moment, sorry about that!). Then chooce item 2 
(Informasjonstjenere for faggrupper/), then item 2 (genteknologi/) and
finally, item 5 (Norsk EMBnet node (BIOMED) <TEL>).

Start the telnet session and log into the node as user SRS.
The system will ask you for you e-mail address. It will be used to 
forward any search results you produced using SRS. Read the 2 
instruction pages carefully. The basic use of the package including how
to invoke the interactive help facility are explained here. When SRS 
starts press <return> and <o> for options. You are already on your way.... 

The setup currently supports only 5 interactive users on the SRS account and
permits each user to work for a maximum period of 30 minutes. If you
produce extremely large (>50K) files, these will NOT be mailed to you 
in order to prevent an e-mail bottle neck on our system.

All comments are welcome. Please send any to the current node

 Christoph Gartmann (christophg at biomed.uio.no) 

or to:

 Rodrigo Lopez (rodrigol at ulrik.uio.no, lopez at embl-heidelberg.de).

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