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| EMBL FILE SERVER News Number 4, March 21st 1991 |
| |
| European Molecular Biology Laboratory, Data Library & Computer Group, |
| Postfach 10.2209, 6900 Heidelberg, Germany. |
| Tel: +49 6221 387258 |
| E-mail: NetHelp at EMBL-Heidelberg.DE Fax: +49 6221 387519 or 387306 |
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Contents:
<1> Introduction
<2> Updates to data collections
<3> Updates to software collection
<4> Other updates
<5> Common questions
<6> Summary of contents of file server
<7> Notice of EMBL's withdrawal from Bitnet
<8> Getting started ?
<1> Introduction
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The EMBL File Server Newsletter summarises changes to the EMBL File Server.
This newsletter and older issues are available from the server (eg. GET
DOC:EMBL_Server_News.2).
<2> Updates to Data Collections
------------------------------------
The following data collections have been updated recently:
Nuc - Release 26, February 1991, of the EMBL Nucleotide Sequence
Database.
Prot - Release 17, February 1991, of the SWISS-PROT Protein Sequence
Database.
ProteinData - A database of homology-derived protein structures (HSSP)
supplied by Chris Sander is now available along with the
existing Brookhaven PDB and the DSSP secondary structure
digest of the PDB protein files.
ProSite - Release 6.1 of Amos Bairoch's pattern database.
A version of ProSite suitable for use with Scrutineer is
now available.
Enzyme - Release 4 of Amos Bairoch's enzyme database.
ECD - Release 6 of Manfred Kroeger's E.coli database
Reflist - Release 15 of Amos Bairoch's sequence analysis bibliography.
ReBase - Release 9103 of Rich Roberts's restriction enzyme database.
Alu - Jerzy Jurka's Alu Sequence Database, October 1988
The directory NUC is continually updated with nucleotide sequence data
from EMBL/GenBank/DDBJ, and the directory PROT is updated with data
from the SWISS-PROT protein sequence database.
<3> Updates to Software Collection
------------------------------
Here is a list of new (N) molecular biological programs or updates (U):
DOS:
----
EASISTAT.UAA (N) Statistical analysis package (D. Curtis)
PEDRAW.UAA (N) Pedigree drawing (D. Curtis)
Mac:
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MATMETH.HQX (U) New version 5.0 of Material & Methods stack
J. Brown
MACREVIEW.1 (N) Two reviews of Mac software in molecular biology
MACREVIEW.2 (P. Markiewicz)
UNIX:
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SEQF.UAA (N) Package for searching genetic sequence libraries
(D. Davison and M. Kanehisa)
VAX:
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SCRUTINE.UAA (U) New version of SCRUTINEER protein database
analysis package (P. Sibbald)
CDACCESS.UAA (U) Update (v2.06) of CD-ROM access software
(P. Stockwell)
<4> Other updates
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DOC - BIOSCI.DOC March 1991 version of the BIOSCI
bulletin-board description.
- SERVER.TXT Michael Gribskov's Molecular Biology FTP and
Server List, March 7th 1991.
- BIOBIT.19 Rob Harper's newletter, BioBit No. 19: "Archie"
ALIGN - DS6748.UUE Alignment of germline VH gene sequences, submitted
by W. Mueller, 6-Mar-1991.
CODONUSAGE - A collection of codon usage tables in GCG format provided by
Mike Cherry.
<4> Common questions
----------------
Q: Can I access the EMBL File Server via FTP ?
A: Not yet. We are on Internet and await an upgrade to our connection
before starting an anonymous ftp service.
<6> Summary of Directories of the EMBL File Server
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Databases:
EMBL Nucleotide Sequence Database NUC
(Rel. 26, Feb 91 + new data from EMBL/GenBank/DDBJ)
Eukaryotic Promotor Database (Rel. 26, Feb 91) EPD
SwissProt Protein Database (Rel. 17, Feb 91) PROT
Prosite pattern database (Rel. 6.1, Feb 91) PROSITE
ENZYME database (Rel. 4, Feb 91) ENZYME
Brookhaven Protein Structure Database (Rel. 54, Nov 90) PROTEINDATA
REBASE, Restriction Enzyme Database (Rel. 9103, Mar 91) REBASE
TFD, Transcription Factor Database (Ver 2.1, Feb 91) TFD
The E.coli Database (Rel. 6, Feb 91) ECD
Drosophila Genetic Map Database (Rel. 9012, Dec 90) DROSOPHILA
Listing of Molecular Biology Databases, LiMB (Rel. 2.0) LIMB
Sequence analysis bibliography (SEQANALREF Rel. 15, Feb 91) REFLIST
Functional Analysis of Nucleotide Sequences bibliography REFLIST
(FANS_REF Rel. 1.3, Nov 90)
Alu sequence database and alignment ALU
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> Notice of EMBL's withdrawal from Bitnet
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EMBL intends to withdraw from Bitnet as from January 1st 1992. The network
address EMBL.Bitnet should function up until that date, but we recommend
that users switch to using EMBL-Heidelberg.DE (Internet) from now onwards.
<8> Getting Started ?
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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-Heidelberg.DE
containing just the word HELP on a line by itself. No essays please.
For human contact, send electronic mail to NetHelp at the address(es)
given above.
