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| EMBL FILE SERVER News Number 6, September 20th 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 |
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Contents:
<1> Introduction
<2> Updates to data collections
<3> Updates to software collection
<4> Other updates
<5> Summary of contents of file server
<6> 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 DROSOPHILA directory was renamed to FLYBASE to reflect the new
official name for Michael Ashburner's Drosophila genetic database.
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
------------------------------
Here is a list of new (N) molecular biological programs or updates (U):
DOS:
----
CLUSTALV.UAA (N) Multiple sequence alignments
(Higgins D. et al.)
EASYCLON.UUE (N) Simulation of DNA cloning, incl. plasmid map
drawing (Shillitoe E.)
MAPSRT.UUE (N) Reformating of GCG MapSort output file, sorting
by number-of-cuts and enzyme name (Easton T.G.)
LSTSQ.UAA (N) Toolkit for nonlinear regression in enzymology
(Carmenes R.S.)
PLASMIDG.UUE (N) Plasmid drawing program (Kleman G.)
SSCAN.UAA (N) Identification of signals in DNA sequences
(Prestridge D.)
PEDRAW31.UAA (U) Pedigree drawing program v3.1 (Curtis D.)
SQAID381.UAA (U) DNA and protein sequence analysis package v3.81
(Roufa D. et al.)
Mac:
----
AUTHORIN.HQX (N) Sequence data submission preparation tool
(Intelligenetics)
CLUSTALV.HQX (N) Multiple sequence alignments
(Higgins D. et al.)
COVARIATION.HQX (N) Identification of compensating base changes and
covariations in aligned RNA sequences
E-MAIL_INFO.HQX (N) HyperCard stack with information about e-mail,
ftp and biological databases and servers
(Markiewicz P.)
MACCOMPRESS.HQX (N) UNIX-compatible compress/uncompress (Chambers L.)
CHEMINVENTORY.HQX (U) HyperCard stack to keep track of chemical
inventory v2.1 (Swartling D.)
MACPATTERN.HQX (U) Protein pattern searching with Prosite v1.5
(Fuchs R.)
READSEQ.HQX (U) Sequence format conversion program (Gilbert D.)
UNIX:
-----
CLUSTALV.UAA (N) Multiple sequence alignments
(Higgins D. et al.)
FILTER.UAA (N) Programs for finding suboptimal alignments,
reliable regions in alignments and to multiply
align and find conserved motifs (Argos P. et al.)
GDE1_0.UAA (N) Expandable set of programs for sequence align-
GDE_DOC.UAA ments and analysis (executables, sources, and
GDE_SRC.UAA documentation) (Harvard Genome Lab.)
ISSC.UAA (N) Sensitive sequence comparison package
(Argos P. et al.)
NSEQTOOL.UAA (N) Integrated display of aligned protein sequences
and protein structures (Schnobel R.)
PIMA.UAA (N) Pattern-induced multiple sequence alignment
program (Smith R.F. et al.)
SSCAN.UAA (N) Identification of signals in DNA sequences
(Prestridge D.)
SUNUUD.C (N) Version of UUD compatible with standard Sun C
compiler
VAX:
----
ALIGN_X.UAA (N) Sensitive sequence comparison package
(DEC-Windows version) (Argos P. et al.)
CLUSTALV.UAA (N) Multiple sequence alignments
(Higgins D. et al.)
FILTER.UAA (N) Programs for finding suboptimal alignments,
reliable regions in alignments and to multiply
align and find conserved motifs (Argos P. et al.)
ISSC.UAA (N) Sensitive sequence comparison package
(UIS version) (Argos P. et al.)
MALFORM.UUE (N) Conversion of MALIGNED output to PostScript
(Clark S.)
PRETTYBOX.TXT (N) Nice plotting of multiple alignments
(Westerman R.)
SSCAN.UAA (N) Identification of signals in DNA sequences
(Prestridge D.)
SUBFORM.UAA (N) Sequence data submission tool (Spaulding M. et al.)
BOXSHADE.UUE (U) Nice plotting of multiple aligments v2.4
(Hoffmann K.)
MALIGNED.UAA (U) Multiple sequence editor (Clark S.)
OVERSEER.UUE (U) Nucleic acid sequence database analysis package
(Sibbald P.)
READSEQ.UUE (U) Sequence format conversion program (Gilbert D.)
SCRUTINE.UAA (U) Scrutineer protein sequence database analysis
package, version Jun 1991 (Sibbald P.)
ZOO.UAA (U) Compression/archieving tool, v2.1 (Dhesi R.)
<4> Other updates
-------------
ALIGN directory:
DS7582.DAT - Consensus sequences of three highly repeated
and conserved HaeIII fragments from newts of
the genus Triturus, by J. Varley.
DS8200.DAT - Alignment of entire histone gene repeat
unit sequences from Drosophila hydei and
Drosophila melanogaster, by D. Fitch.
<5> Summary of Directories of the EMBL File Server
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Databases (* = new or updated):
*EMBL Nucleotide Sequence Database NUC
(Rel. 28, Sep 91 + newest data from EMBL/GenBank/DDBJ)
*Eukaryotic Promotor Database (Rel. 28, Sep 91) EPD
*SwissProt Protein Sequence Database PROT
(Rel. 19, Aug 91 + newest data)
*Prosite pattern database (Rel. 7.10, Aug 91) PROSITE
*ENZYME database (Rel. 6.00, Aug 91) ENZYME
*Brookhaven Protein Structure Database (Rel. 57, Jul 91) PROTEINDATA
*REBASE, Restriction Enzyme Database (Rel. 9109, Sep 91) REBASE
tRNA sequence and gene sequence database (1991) TRNA
TFD, Transcription Factor Database (Ver 3.0, Jun 91) TFD
*The E.coli Database (Rel. 8, Aug 91) ECD
*Drosophila Genetic Map Database (9107, 27-Jul-1991) FLYBASE
Listing of Molecular Biology Databases, LiMB (Rel. 2.0) LIMB
*Sequence analysis bibliography (SEQANALREF Rel. 20, Sep 91) REFLIST
Functional Analysis of Nucleotide Sequences bibliography REFLIST
(FANS_REF Rel. 3.4, Apr 91)
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
<6> 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-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.
