EMBL Data Library Products and Services, 1992/93

David Hazledine David.Hazledine at EMBL-HEIDELBERG.DE
Mon Jul 6 10:35:00 EST 1992


	    EMBL Data Library Products and Services, 1992/93
	    ================================================

Here is a copy of the material concerning services and subscriptions to the EMBL
Data Library for 1992/93, which was recently posted to everyone on our mailing
list. 

If you know of someone who might be interested in this, and who may not see it
on this bulletin board, then please forward it on to them.  Thank you. 

We would in particular like to draw your attention to the new data distribution
format we plan to introduce in the course of the coming 12 months (i.e. our
nucleotide sequence database in the form of a text file dump of tables from a
relational schema; if you would like more details then please contact us at
Datalib at EMBL-Heidelberg.DE with your fax number or postal address). 
 

Products and Services available from the EMBL Data Library.
----------------------------------------------------------- 

Contents

*  EMBL Databases on CD-ROM
*  EMBL Databases on Magnetic Tape
*  EMBL Network File Server
*  Summary of Available Databases
*  EMBnet: European Molecular Biology Network
*  Mail-Quicksearch and Mail-FastA
*  Sequence Data Submission
*  Database Subscription Form


Subscriptions

To RENEW YOUR SUBSCRIPTION, please fill in the form at the end of
this package and return it to us.

PLEASE NOTE that we offer to supply products by courier - costs borne by
the subscriber. Also we now provide a faciltiy for automatic subscription
renewal from year to year.

A NEW FEATURE to be provided during the course of 1992 will be the
availability of each quarterly release as a table dump from a relational
schema, suitable for loading into any RDBMS. Please contact us if you wish
to know more about this feature.


May 1992

EMBL Databases on CD-ROM
------------------------

The following are available on CD-ROM:
------------------------------------------------------------------------------
EMBL NUCLEOTIDE     Nucleotide sequence data, indices and documentation.
SEQUENCE DATABASE
------------------------------------------------------------------------------
SWISS-PROT          Protein sequence data, indices and documentation.
DATABASE
------------------------------------------------------------------------------
RELATED DATABASES   Several related databases are distributed as supplied by
                    their authors. In cooperation with Nucleic Acids Research,
                    we include databases published in their annual 'Sequence
                    Supplement'. See the accompanying document 'Summary of
                    Available Databases' for a full listing.
------------------------------------------------------------------------------
DATABASE QUERY/     MS-DOS software, CD-SEQ, is provided for query and
RETRIEVAL           retrieval of data from both the sequence databases on the
                    CD-ROM allowing access by entry name,  accession number,
                    citation, author name, taxonomy,  feature key,  free text,
                    database cross-reference and date.
                    New Macintosh software, EMBL-Search, is provided to access
                    the sequence databases via binary indices on the CD-ROM
------------------------------------------------------------------------------
SEQUENCE            Sequence databases are provided in NBRF format for use
SIMILARITY          with software such as FASTA on Macintosh or MS-DOS systems.
SEARCHING           MS-DOS software, EMBLScan, is provided for rapid searching
                    of the nucleotide database for very similar sequences.
------------------------------------------------------------------------------
INDICES             A set of binary index files is provided which can be used
                    by software to access rapidly the sequence databases on
                    CD-ROM by, for example, entryname, accession number, free
                    text, keywords, author names and taxonomy.
------------------------------------------------------------------------------

The CD-ROM is structured according to the ISO standard 9660 format.


FURTHER INFORMATION:

The EMBL Data Library            E-mail:DataLib at EMBL-Heidelberg.DE
Postfach 10.2209,
Meyerhofstrasse 1,               Fax:  +49 6221 387519
D-6900 Heidelberg, Germany.      Tel:  +49 6221 387258

May 1992

EMBL Databases on Magnetic Tape
-------------------------------

The EMBL databases are  available on magnetic tape in a choice of medium and
format making them usable on a range of computer systems. The options available
are detailed on the Subscription Form.


An EMBL Nucleotide Sequence subscription on magnetic tape includes:

------------------------------------------------------------------------------
EMBL NUCLEOTIDE     Nucleotide sequence data, indices and documentation.
SEQUENCE DATABASE
------------------------------------------------------------------------------
RELATED DATABASES   Eukaryotic Promotor database (EPD)
                    E. coli database (ECD)
                    Restriction Enzyme database (REBASE)
------------------------------------------------------------------------------



A  SWISS-PROT subscription on magnetic tape includes:

------------------------------------------------------------------------------
SWISS-PROT          Protein sequence data, indices and documentation.
DATABASE
------------------------------------------------------------------------------
RELATED DATABASES   Prosite pattern database
                    Enzyme nomenclature database.
------------------------------------------------------------------------------




FURTHER INFORMATION:

The EMBL Data Library            E-mail:DataLib at EMBL-Heidelberg.DE
Postfach 10.2209,
Meyerhofstrasse 1,               Fax:  +49 6221 387519
D-6900 Heidelberg, Germany.      Tel:  +49 6221 387258

May 1992

EMBL Network File Server
------------------------

The EMBL Network File Server is a facility enabling remote users to request
files from EMBL via electronic mail.

Information Accessible

------------------------------------------------------------------------------
* The EMBL Nucleotide Sequence Database  (continuously updated with data from
  EMBL and GenBank & DDBJ)
------------------------------------------------------------------------------
* The SWISS-PROT Protein Sequence Database  (including updates)
------------------------------------------------------------------------------
* The Brookhaven Protein Data Bank (and other structure data)
------------------------------------------------------------------------------
* Databases like E. coli database (ECD), eukaryotic promotor database (EPD),
  restriction enzyme database (REBASE), protein pattern database (Prosite)
------------------------------------------------------------------------------
* Free molecular biology software for MS-DOS, Apple Macintosh,VAX/VMS and UNIX.
------------------------------------------------------------------------------
* General documentation (like subscription and submission information)
------------------------------------------------------------------------------


Commands

The file server is used by sending commands within electronic mail to the
following Internet address:

NetServ at EMBL-Heidelberg.DE.

Requested files are returned automatically.
The mail you send to the file server should contain one file server command
per line. The best command to start with is:-

HELP

In response, the file server provides further documentation on how to proceed.


FURTHER INFORMATION:

The EMBL Data Library            E-mail:DataLib at EMBL-Heidelberg.DE
Postfach 10.2209,
Meyerhofstrasse 1,               Fax:  +49 6221 387519
D-6900 Heidelberg, Germany.      Tel:  +49 6221 387258

May 1992

Summary of Available Databases
------------------------------

--------------------------------------------------------------------------------
                                                   Ref. Mag.Tape  CD-ROM  Server
EMBL       Nucleotide sequence database            (1)     *        *       *
SWISS-PROT Protein sequence database               (2)     *        *       *
ENZYME     Database of EC nomenclature             (3)     *        *       *
ECD        E. coli map database                    (4)     *        *       *
EPD        Eukaryotic promoter database            (5)     *        *       *
FLYBASE    Drosophila genetic map database         (6)     *        *       *
PROSITE    Protein pattern database                (7)     *        *       *
REBASE     Restriction enzyme database             (8)     *        *       *
BERLIN     5S rRNA sequences                       (9)              *       *
CUTG       Codon usage tabulated from GenBank      (10)             *       *
HAEMB      Haemophilia B database of mutations     (11)             *       *
METHYL     Site specific methylation               (12)             *       *
RRNA       Small subunit rRNA sequences            (13)             *       *
SMALLRNA   Small RNA sequences                     (14)             *       *
TFD        Transcription factor database           (15)             *       *
TRNA       tRNA sequences                          (16)             *       *
3D_ALI     Sequence alignments based on structure
           superposition                           (17)                     *
ALU        ALU sequences and alignments            (18)                     *
DSSP       Secondary structure digests of PDB
           files                                   (19)                     *
HSSP       Homology-derived protein structures     (20)                     *
LIMB       Listing of mol. biology databases       (21)                     *
PDB        Brookhaven protein 3D structures        (22)                     *
SEQANALREF Articles dealing with sequence analysis (23)                     *
--------------------------------------------------------------------------------

1.Stoehr,P.J. and Cameron,G.N. (1991) Nucl. Acids Res., 19, 2227-2230.
2.Bairoch,A. and Boeckmann,B. (1991) Nucl. Acids Res., 19, 2247-2249.
3.Bairoch,A. (1990) University of Geneva, Geneva.
4.Krger,M., Wahl,R. and Rice,P. (1991) Nucl. Acids Res., 19, 2023-2043.
5.Bucher,P. and Trifonov,E.N. (1986) Nucl. Acids Res., 14, 10009-10026.
6.Ashburner,M. (1990) University of Cambridge, Cambridge.
7.Bairoch,A. (1991) Nucl. Acids Res. , 19, 2241-2245.
8.Roberts,R.J. (1985) Nucl. Acids Res., 13, r165-r200.
9.Specht,T., Wolters,J. and Erdmann,V.A. (1991) Nucl. Acids Res., 19, 2189-2191.
10.Wada,K., Wada,Y., Doi,H., Ishibashi,F., Gojobori,T. and Ikemura,T.
  (1991) Nucl. Acids Res.., 19, 1981-1986.
11.Giannelli,F., Green,P.M., High,K.A., Sommer,S., Lillicrap,D.P., Ludwig, M.,
   Olek,K., Reitsma,P.H., Goosens,M., Yoshioka,A. and Brownlee,G.G.
   (1991) Nucl. Acids Res., 19, 2193-2220.
12.Nelson,M. and McClelland,M. (1991) Nucl. Acids Res., 19, 2045-2071.
13.Neefs,J.-M., Van de Peer,Y., De Rijk,P. Goris,A. and De Wachter,R.
   (1991) Nucl. Acids Res., 19, 1987-2015.
14.Gupta,S. and Reddy,R. (1991) Nucl. Acids Res., 19, 2073-2075.
15.Ghosh,D. (1990) Nucl. Acids Res., 18, 1749-1756.
16.Sprinzl,M, Dank,N., Nock,S. and Schoen A. (1991) Nuc.Acids Res.,19,2127-2171.
17.Pascarella,P. and Argos,P. (1992), in press.
18.Jurka,J. and Smith,T. (1988) Proc. Natl. Acad. Sci.  U.S.A., 85, 74775-74778.
19.Kabsch,W. and Sander,C. (1983) Biopolymers 22, 2577-2637
20.Sander,C. and Schneider,R. (1991) Proteins 9, 56-68.
21.Lawton,J.R.,Martinez,F.A. and Burks,C. (1989)Nucl.Acids Res., 17, 5885-5899.
22.Bernstein,F.C., Koetzle,T.F., Williams,G.J.B., Meyer,E.F., Brice,M.D.,
   Rodgers,J.R., Kennard,O., Shimanouchi,T. and Tasumi,M.
   (1977) J. Mol. Biol., 112, 535-542.
23.Bairoch, A. (1991) University of Geneva, Geneva.

May 1992

EMBnet : European Molecular Biology Network
-------------------------------------------

Research in molecular biology and biotechnology requires computerised access
to data including genetic sequences of proteins and nucleic acids, structures
of biological macromolecules, human genome maps, genetic diseases, microbial
strains, hybridomas, restriction enzymes, cloning vectors, industrial enzymes,
taxonomic classification, toxicological data, and biomedical abstracts.

EMBnet
EMBnet is a collaborative initiative promoting access to information resources
of importance to the European molecular biology and biotechnology research
community. The computer network is based on nodes in European states providing
biocomputing services for their academic and commercial users. Other nodes are
involved as hosts of databases, specialised facilities or biocomputing research.

Activities currently include:

*  daily distribution of new sequence data from EMBL Data Library to EMBnet
   national nodes, and then on to end-users.
*  on-line services with access to databases and analysis software
*  training

On-line Access to the EMBL Nucleotide Sequence Database:

The following EMBnet national nodes maintain daily-updated copies of the EMBL
nucleotide sequence database for on-line access within their country.

--------------------------------------------------------------------------------
Denmark:        France:          Germany:         Greece:
BIOBASE,        CITI2, Paris.    DKFZ,            IMBB,
Aarhus.                          Heidelberg.      Heraklion.
--------------------------------------------------------------------------------
Israel:         Italy:           Netherlands:     Norway:
Weizmann        CNR Bari.        CAOS/CAMM        Biotechnology
Institute,                       Centre,          Centre of Oslo.
Rehovot.                         Nijmegen.
--------------------------------------------------------------------------------
Spain:          Sweden:          Switzerland:     UK:
CNB, Madrid.    Biomedical       Biozentrum,      Daresbury Lab.
                Centre,          Basel.           Warrington.
                Uppsala.
--------------------------------------------------------------------------------

EMBnet has received financial support from the Commission of the European
Communities (CEC) under the BRIDGE programme.



FURTHER INFORMATION:

The EMBL Data Library            E-mail:DataLib at EMBL-Heidelberg.DE
Postfach 10.2209,
Meyerhofstrasse 1,               Fax:  +49 6221 387519
D-6900 Heidelberg, Germany.      Tel:  +49 6221 387258

May 1992

Mail-Quicksearch and Mail-FastA
-------------------------------

Mail-Quicksearch and Mail-FastA are two services available on the EMBL
computing system that allow external users to search the DNA and protein
sequence databases, including the most recent entries, via electronic mail.

--------------------------------------------------------------------------------
MAIL-QUICKSEARCH  Mail-Quicksearch is based on the NewQuicksearch and Quickmatch
                  programs written by Peter Rice at EMBL, which are extensions
                  of the Quicksearch programs contained in the GCG software
                  package. You can very quickly search the EMBL database for
                  sequences very similar to your query sequence. In addition to
                  all entries contained in the latest EMBL release, all new
                  EMBL and GenBank entries created since then are also
                  accessible.
--------------------------------------------------------------------------------
MAIL-FASTA        Mail-FastA is based on Bill Pearson's FastA program. It allows
                  you to perform rapid but sensitive comparisons of protein or
                  DNA sequences against the databases. The databases available
                  for searching include EMBL, GenBank, SwissProt and PIR. All
                  new EMBL and GenBank entries are also accessible as soon as
                  created.
--------------------------------------------------------------------------------

Access
These services are provided free of charge, though users may have to meet some
of the communication costs depending on the accounting system at their site.

To use Mail-Quicksearch, send mail to  QUICK at EMBL-Heidelberg.DE.

To use Mail-FastA, send mail to    FASTA at EMBL-Heidelberg.DE.

The mail you send should contain your query sequence and commands to specify
search parameters. By typing HELP on a line by itself you can have returned to
you further documentation on how to proceed.

You should find out locally how to send electronic mail on your own computer to
the Internet addresses above, but the EMBL Data Library will help in case of
difficulty.



FURTHER INFORMATION:

The EMBL Data Library            E-mail:DataLib at EMBL-Heidelberg.DE
Postfach 10.2209,
Meyerhofstrasse 1,               Fax:  +49 6221 387519
D-6900 Heidelberg, Germany.      Tel:  +49 6221 387258

May 1992

Sequence data Submission
------------------------

The EMBL Data Library accepts sequence data submissions in the
following ways:

--------------------------------------------------------------------------------
AUTHORIN SOFTWARE  The latest versions of Macintosh and MS-DOS Authorin software
Package            are available from the file server by mailing the appropriate
                   command to NETSERV at EMBL-HEIDELBERG.DE
                   Use any of the following commands:
                   HELP software
                   GET Mac_software:authorin.hqx
                   GET DOS_software:authorin.uaa
--------------------------------------------------------------------------------
SUBMISSION FORM    One submission form should be used for each nucleotide and
                   protein sequence.
                   * A computer-readable copy of the submission form is
                     included with each release of the sequence databases.
                   * It is also available from the file server by sending the
                     following command to NETSERV at EMBL-HEIDELBERG.DE

                     GET DOC:datasub.txt

                   * Printed copies of the submission form are published in the
                     first issue each year of Nucleic Acids Resarch. They are
                     also available on request from the Data Library.
--------------------------------------------------------------------------------
DATA SUBMISSION    by E-mail    Send the completed form and appended sequence
                                to : DATASUBS at EMBL-HEIDELBERG.DE ensuring data
                                lines are no longer than 80 characters.

                   by Post      Send the sequence on MACINTOSH or IBM-PC
                                COMPATIBLE DISKETTES together with the
                                completed form either on the disk or as paper
                                copy.
                                Use the 'Save as text only' feature of your
                                editor, to produce ASCII formatted data
--------------------------------------------------------------------------------



FURTHER INFORMATION:

The EMBL Data Library            E-mail:DataLib at EMBL-Heidelberg.DE
Postfach 10.2209,
Meyerhofstrasse 1,               Fax:  +49 6221 387519
D-6900 Heidelberg, Germany.      Tel:  +49 6221 387258

May 1992

             EMBL DATA LIBRARY SUBSCRIPTION FORM 1992/93

Subscription No: [      ] Please quote this, if given, in any correspondence.
------------------------------------------------------------------------------
Name:
------------------------------------------------------------------------------
Institute/Company:
------------------------------------------------------------------------------
Postal Address:                  | Invoice Address  ( If not Postal Address
                                 |
                                 |
                                 |
                                 |
                                 |
                                 |
                                 |
------------------------------------------------------------------------------
Telephone:                         Telefax:
------------------------------------------------------------------------------
Email address:
------------------------------------------------------------------------------
CD-ROM RELEASES

[  ] copies containing       Release 32 & SWISSPROT Release 23  September 1992
[  ]                         Release 33 & SWISSPROT Release 24  December  1992
[  ]                         Release 34 & SWISSPROT Release 25  March     1993
[  ]                         Release 35 & SWISSPROT Release 26  June      1993

------------------------------------------------------------------------------
MAGNETIC TAPE RELEASES

EMBL NUCLEOTIDE SEQUENCE DATABASE          SWISSPROT PROTEIN SEQUENCE DATABASE

[  ] Release 32,  September  1992          [  ] Release 24,  November  1992
[  ] Release 33,  December   1992          [  ] Release 25,  February  1993
[  ] Release 34,  March      1993          [  ] Release 26,  May       1993
[  ] Release 35,  June       1993          [  ] Release 27,  August    1993

------------------------------------------------------------------------------
TAPE FORMAT: Tape density will be 6250 bpi.
             Options * will be used for items left blank.

Tape Medium:                  Tape blocksize:           Tape Character Set:
[* ] Unlabelled tape          [* ] 8000 bytes           [* ] ASCII
[  ] ANSI labels              [  ] 4000 bytes           [  ] EBCDIC
[  ] IBM labels               [  ]      bytes
[  ] VMS Backup
[  ] TK70 cartridge

--------------------------------------------------------------------------------
SUBSCRIPTION CATEGORY               [ ] Academic      [ ] Commercial
--------------------------------------------------------------------------------
COURIER  DELIVERY                   [ ] Yes           [ ] No
--------------------------------------------------------------------------------
AUTOMATIC SUBSCRIPTION RENEWAL      [ ] Yes           [ ] No
--------------------------------------------------------------------------------




Prices in DM per quarterly release:
--------------------------------------------------------------------------------
SUBSCRIPTION CATEGORY            |       CDROM       |       Mag Tape
---------------------------------+-------------------+--------------------------
Academic - EMBL/ EC member state |       75.00       |        75.00
Academic - non-member state      |      150.00       |       150.00
Commercial                       |      300.00       |       300.00
--------------------------------------------------------------------------------



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