SRS VERSION 3.0 NOW AVAILABLE!
A new version of the SRS (Sequence Retrival System) is available
via anonymous ftp from the Norwegian EMBnet node biomed.uio.no,
129.240.2.38.
This new version replaces completely all previous version of the program
package.
The SRS package currently runs only on VAX/VMS systems. For
a standard installation you will need aproximately 150K blocks
of free disk space.
The package currently uses the GCG7.x formated EMBL, GenBank,
SwissProt and PIR databases (NBRF or GCG format). The reason
for this is to avoid the duplication of databases at sites
with limited storage. All other databases are used in their
original distribution format.
The following databases are currently supported by the system:
o EMBL, GenBank, PIR, Swiss-Prot and NRL_3D as Sequence libs.
o PDB, PDBNEW, HSSP, DSSP and ALI as Protein Structure libs.
o Prosite, ECD, EPD, TFD, Enzyme and ReBase as SeqRelates libs.
o SeqAnalRef, LIMB and Journals TOC as Litterature libs.
o FastA, Blast and Profile output files as SearchLists.
The following features have been added to the system:
1. The menu interface has been re-written to make it CUA
compliant, meaning that access to menus is now done via
a menu bar at the top of the SRS screen. Drop down menus
appear under each of the menu bar choices and in the whole
the package has a more intuitive and easy to use look.
2. An option to browse through all the linked libraries has
be added to the system which provides detailed information
on all available databases.
3. A 'Navigation Mode' has been added which makes it possible
to mode from any entry to the corresponding link in other
libraries without having to perform a linking via expression
operation.
4. All searches are now performed using wilcard (*) at the end
of an expression. This significantly enhances the chances
of finding hits and makes begginers feel more at home with
the concepts of the package.
5. A user profile can be generated which stores user specified
values and parameters. The package reads in this file during
startup.
6. Queries no longer lead to a query report but directly into
a query list. Report can be seen by using a query menu
option.
7. For management, a program called SRSUPDATE has been added
which checks the state of all libraries and advices on
the necessity of rebuilding indexes. It writes out DCL
files with the required commands to update the pertinent
libraries.
8. Homology searches (blast and fasta output files) can now
be linked to SRS with the program READHITS.
9. A new user manual is available.
10. The indexing routines have been re-written to make them
less memory hungry and faster.
Here follows a list of the files available via FTP:
SRS30.BCK This is the main distribution VMS backup
saveset.
SRS30.LST Saveset list
SRS30.DOC MS-WORD version of the user manual.
SRS30.PS PostScript(C) version of the manual.
INSTALL_SRS.COM DCL procedure that assists installing the
package from the SRS30.BCK saveset file.
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A reminder to everyone interested in trying out SRS:
SRS CAN BE TESTED BY LOGIN INTO THE NORWEGIAN EMBNET NODE
USING 'SRS' AS USERNAME. YOU WILL BE ALLOWED TO USE THE
PROGRAM FOR 30 MINUTTES AT THE TIME. ANY QUERY RESULTS YOU SAVE
WILL BE MAILED TO YOU WHEN YOU EXIT. PLEASE REMEMBER TO PROVIDE
YOUR CORRECT INTERNET E-MAIL ADDRESS DURING LOGIN WHICH WILL
BE REQUIRED LATER FOR MAILING PURPOSES!
%telnet biomed.uio.no
Connected to biomed.uio.no...
Welcome to VAX/VMS V5.5
Username:SRS
Or via gopher. Gopher into one of many EMBnet gopher servers
and look for the Norwegian EMBnet node telnet hole.
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Rodrigo Lopez
****************************************************
* Work: The Norwegian EMBnet node *
* The Biotechnology Centre of Oslo *
* Address: Gaustadalleen 21, N-0371 Oslo Norway *
* Telephone: +47-2-958756 *
* Fax: +47-2-694130 *
* Electronic mail addresses (Internet) *
* rodrigol at ulrik.uio.no UNIX *
* rodrigol at biomed.uio.no VMS *
****************************************************
