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| EMBL FILE SERVER News Number 1, October 12th 1990 |
| |
| European Molecular Biology Laboratory, Data Library & Computer Group, |
| Postfach 10.2209, 6900 Heidelberg, Germany. |
| E-mail: NetHelp at EMBL.bitnet Tel: +49 6221 387258 Fax: +49 6221 387306 |
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Contents:
<1> Introduction
<2> File sizes
<3> New data collections
<4> Updates to existing data collections
<5> Updates to software collection
<6> Summary of contents of file server
<7> Getting started ?
<8> and finally...
<1> Introduction
-------------
This is the first issue of the EMBL File Server News. We intend to
use it to summarise changes to the EMBL File Server. The databases, software
and other files on the server are updated so frequently that this mode of
notification is preferable to individual announcements.
It will be available itself from the server (eg. GET DOC:EMBL_Server_News.1)
and also posted to appropriate electronic network bulletin-boards.
<2> File Sizes
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On October 9th 1990, the size limit on files sent from the EMBL File Server
was reduced from 256 to 100 Kbytes. Files larger than this limit are
split into smaller parts and labelled appropriately: the recipient should
assemble these to re-create the whole.
<3> New Data Collections
---------------------
The following new data collections have been added to the file server
recently:
* TFD *
Version 1.0 of the relational Transcription Factor Database (Nucl. Acids
Res. 18, 1990:1749-1756), maintained by David Ghosh at NCBI, is now
available as ASCII dumps of the database tables in the new file server
directory TFD.
* Drosophila Genetic Map Database *
The new directory DROSOPHILA contains the files comprising the database of
genetic information about Drosophila maintained by Michael Ashburner,
Cambridge, UK. PostScript versions of every file are available as well.
* CodonUsage *
A collection of codon frequency tables, produced by J.M. Cherry, was kindly
provided by Don Gilbert, Indiana, and is stored in the directory CODONUSAGE.
Codon usage information is available for Drosophila, human, mouse, sea
urchin, S. pombe and S. saccharomyces. All files are in the format
required by the GCG sequence analysis package.
<4> Updates to Existing Data Collections
------------------------------------
The following data collections have been updated recently:
REBase - Release 9010, October 1990, of Rich Robert's restriction
enzyme database.
Prosite - Release 5.1 of Amos Bairoch's protein pattern database.
ProteinData - Release 53, July 1990 of the Brookhaven Protein Data Bank
Enzyme - Release 2.0 of Amos Bairoch's enzyme database.
RefList - Release 12.1 of Amos Bairoch's SeqAnalRef database.
The directory NUC is continually updated with nucleotide sequence data
from EMBL/GenBank/DDBJ.
<5> Updates to Software Collection
------------------------------
To keep all files below the limit of 100K, some files in the DOS_SOFTWARE,
UNIX_SOFTWARE and VAX_SOFTWARE directory were split into smaller parts.
Therefore, the filenames of some of these files have now changed from
myfile.UUE to myfile.UAA. If you receive an error message "File not found",
this will probably be caused by a change of filename; use the DIR command to
get the most recent directory listings. Please refer to the corresponding
HELP files for information about handling split files.
Here is a list of new molecular biological programs or updates, submitted
for redistribution.
DOS:
-----
COSY.UAA - Package for calculations of enzyme kinetics
(M. Eberhard; CABIOS 6, 1990, 213-221)
CUTCOST.UUE - Program to determine the cheapest source for
restriction enzymes
(C.G. Meinhof)
ENZKIN.UAA - Enzyme kinetics calculation (req. Math co-proc)
(S.R. Maloy; CABIOS 6, 1990, 63-65)
PROSRCH.UUE - Protein pattern searching using Prosite (req. Awk)
(L.F. Kolakowski)
SEQAIDFD.UAA - New v3.8 of this sequence analysis package
(D. Roufa)
PRNTGL.UAA - Utility to print HGPL files (e.g. GCG output) on
matrix or laser printer (new v1.09).
(C. Ravitz)
Mac:
----
MACPATTERN.HQX - New v1.1.1 of this protein pattern search program
(R. Fuchs)
UNSTUFFITDELUXE.HQX - New version of ASCII->binary decoding software
(R. Lau)
UNIX:
-----
PROSEARCH.UUE - v1.1 of protein pattern searching program
(L.F. Kolakowski)
VAX/VMS:
--------
NOCUT.COM - Production of restriction enzyme database file of
non-cutters taken from MAP output for use with MAP/SIL
(T. Easton)
PROFILESCAN.BUGFIX - Bug fix for GCG ProfileScan
(M. Gribskov)
PROSEARCH.UUE - v1.1 of protein pattern searching program
(L.F. Kolakowski)
RST_OLAP.UUE - Creates sorted list of restriction enzymes giving
adhesive ends from REBASE database file
(P.A. Stockwell)
SCRUTINE.UAA - Update of SCRUTINEER protein analysis program
(P. Sibbald)
ZOO.UAA - New version of ZOO which hopefully works under most
versions of VMS
<6> Summary of Directories of the EMBL File Server
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Databases:
EMBL Nucleotide Sequence Database NUC
(Rel. 24, Aug 90 + new data from EMBL/GenBank/DDBJ)
Eukaryotic Promotor Database (Rel. 24, Aug 90) EPD
SwissProt Protein Database (Rel. 14, Aug 90) PROT
ProSite pattern database (Rel. 5.1, Aug 90) PROSITE
ENZYME database (Rel. 2, Aug 90) ENZYME
Brookhaven Protein Structure Database (Rel. 53, Jul 90) PROTEINDATA
REBASE, Restriction Enzyme Database (Rel. 9010, Oct 90) REBASE
TFD, Transcription Factor Database (Ver 1.0) TFD
The E.coli Database (Rel. 4, Aug 90) ECD
Drosophila Genetic Map Database (Rel. 3.5, Aug 90) DROSOPHILA
Listing of Molecular Biology Databases, LiMB (Rel. 2.0) LIMB
Sequence analysis bibliography (SEQANALREF Rel. 12.1, Sep 90) REFLIST
Software:
Software for MS-DOS computers DOS_SOFTWARE
Software for Apple Macintosh MAC_SOFTWARE
Software for UNIX UNIX_SOFTWARE
Software for VAX/VMS VAX_SOFTWARE
Other software, GenBank Clearinghouse, etc. MISC_SOFTWARE
Miscellaneous:
Technical documents, submission and order forms, etc. DOC
Multiple DNA sequence alignments and consensus sequences ALIGN
Codon Usage tables CODONUSAGE
<7> Getting Started ?
-----------------
The EMBL File Server is a facility available on the EMBL computing system
for external users to request files by electronic mail. The service is free.
For initial information, send standard electronic mail to the address
NETSERV at EMBL.bitnet
containing just the word HELP on a line by itself. No essays please.
For human contact, send electronic mail to NetHelp at EMBL.bitnet.
<8> and finally...a compliment ?
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"I also would like to congrtulate the EMBO/EMBL for providing such
unvaluable services to the european scientific community"
^^
