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| EMBL FILE SERVER News Number 7, January 1st 1992 |
| |
| 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 |
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Contents:
<1> Introduction
<2> Updates to data collections
<3> Updates to software collection
<4> Other updates
<5> Summary of directories on the file server
<6> Getting started ?
<1> Introduction
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REMINDER: EMBL has withdrawn from the BITNET/EARN computer network as from
today. Use only the Internet address, NetServ at EMBL-Heidelberg.DE
The old address, Netserv at EMBL.bitnet, is terminated.
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.5).
<2> Updates to Data Collections
------------------------------------
Two new databases have been added to the file server recently:
(a) The Haemophilia B database, provided by Professor Gordon Brownlee,
University of Oxford, is available in the file server directory:
HAEMB
Giannelli F., Green P.M., High K.A. et.al.
"Haemophilia B: database of point mutations and short additions and
deletions - second edition"
Nucleic Acids Res. 19:2193-2219 (1991).
For more information send the command HELP HAEMB.
(b) A compilation of small RNA sequences, provided by Ram Reddy,
Baylor College of Medicine, Houston, is available in the file
server directory: SMALLRNA
Gupta S., Reddy R.
"Compilation of Small RNA Sequences"
Nucleic Acids Res. 19:2073-2075 (1991).
For more information send the command HELP SMALLRNA.
Just about every existing collection has been updated since the last
newsletter so we will not detail them here. The current versions of all
collections are detailed below.
<3> Updates to Software Collection
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Here is a list of new (N) molecular biological programs or updates (U):
DOS:
----
CM.UAA (N) Graphically oriented restriction map construction
from multiple digestion data (K. Hoffmann)
MARKER.UUE (N) Creation of restriction fragments banding patterns
and DNA length standards (S. Rensing)
PROGRAPH.UAA (U) Graphically oriented protein sequence analysis
package (K. Hoffmann)
Mac:
----
ALIGN.HQX (N) Feng and Doolittle's sequence alignment and
phylogeny programs (ported by P. Markiewicz)
STRAINCOLLECTION.HQX (N) HyperCard stack for bacterial strain management
(D. Moore)
MACPATTERN.HQX (U) Protein pattern searching with Prosite, v1.5
(R. Fuchs)
READSEQ.HQX (U) Sequence format conversion program, Nov 1991
(D. Gilbert)
UNIX:
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READSEQ.UUE (U) Sequence format conversion program, Nov 1991
(D. Gilbert)
VAX:
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ACCESS.UUE (N) GCG tool for extracting entries from the database
(J. Prilusky)
BLAST.UAA (N) NCBI's fast database searching programs
BLASTINC.UUE (VMS version by P. Stockwell)
BLASTLIB.UAA
BLASTVMS.UAA
BLASTSEARCH.TXT (N) DCL script for using GenBank's BLAST server
(S. Clark)
EASYMENU.UUE (N) Menu interface to the GCG package (J. Prilusky)
SEQCOMP.TXT (N) Analysis of peptide composition in a protein
sequence (P. Dessen)
FASTEMBL.COM (U) Script for using the EMBL Mail-Fasta server
(for GCG 7) (E. Sonnhammer)
MALIGNED.UAA (U) Multiple sequence editor, v1.64 (S. Clark)
PRETTYBOX.TXT (U) Pretty formatting of multiple sequence alignments,
v1.1 (R. Westerman)
READSEQ.UAA (U) Sequence format conversion program, Nov 1991
(D. Gilbert)
SCRUTINE.UAA (U) Protein database analysis program, Nov 1991
(P. Sibbald)
<4> Other updates
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ALIGN directory:
DS8841 - alignment of epsilon globin gene sequences from 17 eutherian
mammals, provided by Wendy Bailey and Morris Goodman, Wayne
State University.
<5> Summary of directories on the file server
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Databases (* = new or updated since 25-Sep-91)
*EMBL Nucleotide Sequence Database NUC
(Rel. 29, Dec 91 + newest data from EMBL/GenBank/DDBJ)
*Eukaryotic Promotor Database (Rel. 29, Nov 91) EPD
*SwissProt Protein Sequence Database PROT
(Rel. 20, Nov 91 + newest data)
*Prosite pattern database (Rel. 8.0, Dec 91) PROSITE
*ENZYME database (Rel. 7.00, Nov 91) ENZYME
*Brookhaven Protein Structure Database (Rel. 58, Oct 91) PROTEINDATA
*REBASE, Restriction Enzyme Database (Rel. 9112, Dec 91) REBASE
tRNA sequence and gene sequence database (1991) TRNA
*TFD, Transcription Factor Database (Ver 4.0, Dec 91) TFD
*The E.coli Database (Rel. 9, Nov 91) ECD
*Drosophila Genetic Map Database (9111, 10-Nov-91) FLYBASE
Listing of Molecular Biology Databases, LiMB (Rel. 2.0) LIMB
*Sequence analysis bibliography (SEQANALREF Rel. 22, Dec 91) REFLIST
Functional Analysis of Nucleotide Sequences bibliography REFLIST
(FANS_REF Rel. 3.4, Apr 91)
Alu sequence database and alignment ALU
*Haemophilia B database (Dec 91) HAEMB
*Compilation of small RNA sequences (Oct 91) SMALLRNA
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
<6> 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
given above.
