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| EMBL FILE SERVER News Number 11, Feb 10th 1994 |
| |
| European Molecular Biology Laboratory, Data Library & Computer Group, |
| Postfach 10.2209, 69012 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> New Data Collections
<3> Changes to Data Collections
<4> Updates to Software Collection
<5> Other Updates
<6> Summary of Directories on the File Server
<7> Getting Started ?
<8> Network Addresses at EMBL
<1> Introduction
------------
The EMBL File Server is a facility available on the EMBL computing system
for external users to request files by electronic mail, anonymous FTP or
Gopher, and to perform sequence similarity searches. The service is free.
<2> New Data Collections
--------------------
(a) New databases
o BIO_CATAL - Catalogue of mol biol software, maintained by
P. Rodriguez-Tome and D. Caterina, Rel. 2.1, Dec 93.
[/pub/databases/bio_catal]
o KABAT - Database of proteins of immunological interest,
maintained by E. Kabat et al., Rel. 5, Aug 92.
[/pub/databases/kabat] (Not available by email).
o PRINTS - Database of protein signatures, maintained by
T. Attwood and M. Beck, Rel. 4.0, Oct 93.
[/pub/databases/prints]
o SBASE - Protein domain database, maintained by S. Pongor and
v. Skerl, Rel. 2.0, Dec 93.
[/pub/databases/sbase] (Not available by email).
o SRP - Signal recognition particle database, maintained by
N. Larsen and C. Zwieb, Dec 93.
[/pub/databases/srp] (Not available by email).
(b) New directory /pub/databases/journal_toc
This new directory contains the tables of content from various molecular
biological journals. It is mirrored weekly from ncbi.nlm.nih.gov.
Data in this directory is not available by email.
<3> Changes to Data Collections
---------------------------
(a) Due to their growing size, the Transcription Factor Database (TFD) and
the Drosophila database (Flybase) are no longer available by email.
They are still available by anonymous FTP or Gopher.
(b) Some databases are now mirrored weekly from their site of origin:
RLDB - ncbi.nlm.nih.gov
Flybase - ftp.bio.indiana.edu
SRP - iris.hct.utexas.edu
<4> Updates to Software Collection
------------------------------
All DOS files are no longer stored in encoded form on the EMBL FTP server.
Make sure you use BINARY mode to transfer them to your local computer.
All files are self-extracting archives so there is no need for a un-
compression program.
Here is a list of new (N) molecular biological programs or updates (U):
The full path specifications for these files on the EMBL ftp server are
shown in square brackets.
DOS:
----
BANDLEAD.UAA (N) Image processing and analysis of data from protein
gel electrophoresis (M. Aharoni)
[/pub/software/dos/bandlead.exe]
DOLINK.UAA (N) Program to help manage genetic data and set up
analyses (D. Curtis)
[/pub/software/dos/dolink.exe]
EASISTAT.UAA (U) Package for statistical analyses (D. Curtis), v2.1
[/pub/software/dos/estat21.exe]
FASTMAP.UAA (N) Apprx. multipoint lod score calculation (D. Curtis)
[/pub/software/dos/fstmap11.exe]
FE51-A.UAA (N) FileExpress shareware database management system,
FE51-B.UAA for use with DOLINK
FE51-C.UAA [/pub/software/dos/fe51-A.zip etc.]
FIRST.UAA (N) Finds a "good" order for markers based on the
two-point lod scores between them (D. Curtis)
[/pub/software/dos/first11.exe]
FRAME.UUE (N) Identification of ORFs based on codon usage and GC
content (G. Kleman)
[/pub/software/dos/frame$.exe]
GEPASI.UAA (U) Modelling of metabolic pathways (P. Mendes)
[/pub/software/dos/gepasi.exe]
GMAP.UUE (N) Search translationally silent restriction sites
that have allowable mismatches (for gene synthesis)
(G. Raghava)
[/pub/software/dos/gmap$.exe]
HTH.C (U) Prediction of helix-turn-helix regions (C. Halling)
v1.0.5
[/pub/software/dos/hth.c]
INTANA.UAA (N) Intron analyzer (M. Liss)
[/pub/software/dos/intana$.exe]
MACAWNTA.UAA (N) Multiple sequence editor for Alpha/NT (G. Schuler)
[/pub/software/dos/macawNTa.exe]
MACAWNTI.UAA (N) Multiple sequence editor for Intel/NT (G. Schuler)
[/pub/software/dos/macawNTi.exe]
MACAWWIN.UAA (N) Multiple sequence editor for MS Windows
(G. Schuler)
[/pub/software/dos/macawWin.exe]
MCTETRD6.UUE (N) Excel spreadsheet for yeast tetrad analysis
(J. Greene)
[/pub/software/dos/mctetrd6.exe]
PEDHLP14.UUE (U) Popup help for PEDRAW (D. Curtis)
[/pub/software/dos/pedhlp14.exe]
PEDRAW16.UAA (U) Pedigree drawing program (D. Curtis)
[/pub/software/dos/pedraw16.exe]
PROANAL.UAA (N) Analysis of relationship between protein structure
and activity (Eroshkin and Zhilkin)
[/pub/software/dos/proanal.exe]
RASMOL.UAA (U) Visualisation of macromolecules using PDB files
(R. Sayle), v2.2
[/pub/software/dos/rasmol.exe]
SAR2PCIT.UUE (U) Converts SeqAnalRef to ProCite format
(E. Sonnhammer), v1.1
[/pub/software/dos/s2p.exe]
SAR2RIS.UUE (N) Converts SeqAnalRef to Reference Manager format
(G. Hutchinson)
[/pub/software/dos/sar2ris$.exe]
SSCAN.UAA (U) Identification of known eukaryotic signals in
DNA sequences (D. Prestridge), v3.3
[/pub/software/dos/sscan.exe]
Only on FTP server:
wingenie.exe (N) MS Windows interfaces to Internet mol biol servers
(demo version) (A. Sivaprasad)
[/pub/software/dos/wingenie.exe]
Mac:
----
DBCONV.HQX (U) Transformation of line-oriented databases into tab-
delimited format v3.2 (J. Valverde)
[/pub/software/mac/dbconb.hqx]
EMBL-EMAIL-SEARCH.HQX (N) HyperCard frontend to EMBL email servers
(H. Lehvaslaiho)
[/pub/software/mac/embl-email-search.hqx]
EMBL-SEARCH.HQX (U) Database retrieval software for EMBL CD-ROM v2.4
(EMBL Data Library)
[/pub/software/mac/embl-search.hqx]
EMBL-SEARCH_SRC.HQX (U) Source code for EMBL-Search v2.4
[/pub/software/mac/embl-search_src.hqx]
GDBACCESSOR.HQX (N) GDB front-end and database search client (C. Reed
and T. Marr)
[/pub/software/mac/gdbaccessor.hqx]
HTH.HQX (U) Prediction of helix-turn-helix regions (C. Halling)
(v1.0.5)
[/pub/software/mac/hth.hqx]
INFOTRAC_DEMO.HQX (N) Demo of FileMaker version of Transcription Factor
Database (TFD) (W. Hoeck)
[/pub/software/mac/infotrac_demo.hqx]
LABHELPER.HQX (U) General laboratory tools for buffer preps etc.
(T. Tzeng), v3.1
[/pub/software/mac/labhelper.hqx]
MACCLADE304_DEMO.HQX (U) Demo of phylogenetic analysis program
(W. Maddison) v3.04
[/pub/software/mac/macclade304_demo.hqx]
MACCLADE304_UPDATE.HQX (U) MacClade updater to v3.04 (W. Maddison)
[/pub/software/mac/macclade304_update.hqx]
MACPATTERN.HQX (U) Protein pattern searching with PROSITE and
BLOCKS database v3.2 (R. Fuchs)
[/pub/software/mac/macpattern.hqx]
MACSTAN.HQX (U) Random nucleotide sequence generator and analyzer
(F. Gast), v1.8.5
[/pub/software/mac/macstan.hqx]
MACTETRAD6.HQX (N) Excel spreadsheet for yeast tetrad analysis
(J. Greene)
[/pub/software/mac/mactetrad6.hqx]
OLIGO.HQX (N) Calculation and storage of oligonucleotide data
(H. Zabin)
[/pub/software/mac/oligo.hqx]
SEQSIMPRESENTER.HQX (N) Graphic display of similarities of long sequences
(K. Froehlich)
[/pub/software/mac/seqsimpresenter.hqx]
STRAIGHTLINES.HQX (N) Curve-fitting of experimental data (M. Diaz)
[/pub/software/mac/straightlines.hqx]
STUFFITLITE.HQX (U) Compression/decompression/binhex program v3.0.7
(R. Lau)
[/pub/software/mac/stuffitlite.hqx or
stuffitlite.sea]
TOPPPRED.HQX (U) Prediction of transmembrane segments and their
topology (G. v. Heijne, M.G. Claros), v3.2
[/pub/software/mac/toppred.hqx]
UU.HQX (N) UUdecoder/encoder with Mac interface (R. Valverde)
[/pub/software/mac/uu.hqx]
UNIX:
-----
BLKSRCH.UUE (U) Block search analysis of protein sequences with
the BLOCKS database (R. Fuchs), v.2.1
[/pub/software/unix/blocksearch.tar.Z]
DBGET.UUE (N) Utility for downloading database entries from mail
servers (R. Fuchs)
[/pub/software/unix/dbget.tar.Z]
HTH.C (U) Prediction of helix-turn-helix regions (C. Halling)
v1.0.5
[/pub/software/unix/hth.c]
MAILFASTA.SHAR (U) Script for using EMBL/GenBank Mail-FASTA servers
v3.2 (T. deBoer)
[/pub/software/unix/mailfasta.shar]
MENUGCG.UUE (N) Menu interface to GCG package (M. Colet)
[/pub/software/unix/menugcg.tar.Z]
MSU.UUE (N) Configurable utility for accessing electronic mail
servers (R. Fuchs)
[/pub/software/unix/msu.tar.Z]
PROFILE.UUE (N) Creation of sequence profiles for use with GCG
ProfileSearch (J. Thompson)
[/pub/software/unix/profile.tar.Z]
RASMOL.UAA (U) Visualisation of macromolecules using PDB files
(R. Sayle), v2.2
[/pub/software/unix/rasmol.tar.Z]
SIGNAL.UAA (N) Prediction of signal sequence cleavage site
(R. Colgrove)
[/pub/software/unix/signal.tar.Z]
SIGSCAN.UAA (U) Identification of known eukaryotic signals in
DNA sequences (D. Prestridge), v3.3
[/pub/software/unix/sigscan.tar.Z]
Only on FTP server:
sigma (N) System for integrated genome map assembly (LANL)
[/pub/software/unix/sigma.tar.Z]
VAX:
----
ALPHAZOO.UAA (N) ZOO compression utility for Alpha systems
[/pub/software/vax/alphazoo.uaa to .uac]
BLKSRCH.UUE (U) Block search analysis of protein sequences with
the BLOCKS database (R. Fuchs), v2.1
[/pub/software/vax/blksrch.uue]
DBGET.UUE (N) Utility for downloading database entries from mail
servers (R. Fuchs)
[/pub/software/vax/dbget.uue]
EGCG.UAA (U) EMBL extensions to GCG interface (P. Rice, R. Lopez
et al.)
[/pub/software/vax/egcg/]
GCGMENU.UAA (U) Menu interface to GCG package (C. Gartmann)
[/pub/software/vax/gcgmenu.uaa and gcgmenu.uab]
GMAP.UUE (N) Search translationally silent restriction sites
that have allowable mismatches (for gene synthesis)
(G. Raghava)
[/pub/software/vax/gmap.uue]
HTH.C (U) Prediction of helix-turn-helix regions (C. Halling)
v1.0.5
[/pub/software/vax/hth.c]
MSU.UUE (N) Configurable utility for accessing electronic mail
servers (R. Fuchs)
[/pub/software/vax/msu.uue]
PROFILE.UAA (N) Creation of sequence profiles for use with GCG
ProfileSearch (J. Thompson)
[/pub/software/vax/profile.uaa to .uab]
SSCAN.UAA (U) Identification of known eukaryotic signals in
DNA sequences (D. Prestridge), v3.3
[/pub/software/vax/sscan.uaa to .uad]
<5> Other Updates
-------------
(a) New sequence alignments in the ALIGN directory:
DS13953.DAT - Somatic hypermutation in the immunoglobulin
heavy chain VDJ DNA of germinal center B
cells.
Submitted by Dr Joshy Jacob, 1-Apr-1993
DS15369.DAT - Alignment of amino acid sequences of the
G protein alpha units.
Submitted by S. Yokoyama, 19-Aug-1993
DS16117.DAT - Comparative Analysis of Multiple
Protein-Sequence Alignment Methods.
Submitted by M. McClure, 17-Nov-1993
DS16863.DAT - Alignment of 5' UTS of mouse, human, bovine
and rat homologues of the voltage-gated
potassium channel gene, Kv1.4.
Submitted by G. Gutman, 24-Jan-1994
DS16864.DAT - Alignment of 3' UTS of mouse, human, bovine
and rat homologues of the voltage-gated
potassium channel gene, Kv1.4.
Submitted by G. Gutman, 24-Jan-1994
DS16865.DAT - Human and higher primates genomic sequences
corresponding to M15530 cDNA. Phylogenetic
evidence against the authenticity of a
reported 12 kDa B-cellgrowth factor (BCGF) cDNA.
Submitted by D. Labuda, 25-Jan-1994
<6> Summary of Directories on the File Server
-----------------------------------------
directories with updated information are marked by an asterisk.
Anonymous ftp NetServ
-------------- ---------
* EMBL Nucleotide Sequence Database /pub/databases/embl NUC
(Rel. 37, Dec 93 + updates)
* Eukaryotic Promotor Database /pub/databases/epd EPD
(Rel. 37, Dec 93)
* SwissProt Protein Sequence Database /pub/databases/swissprot PROT
(Rel. 27, Oct 93 + updates)
* Prosite pattern database /pub/databases/prosite PROSITE
(Rel. 11, Oct 93)
* PRINTS protein signature database /pub/databases/prints PRINTS
(Rel. 4.0, Oct 93)
* SBASE protein domain database /pub/databases/sbase SBASE
(Rel. 2.0, Dec 93)
* ENZYME database /pub/databases/enzyme ENZYME
(Rel. 14, Oct 93)
* Brookhaven Protein Databank not available PROTEINDATA
(Rel. 65, Oct 93 + pre-release)
* REBASE, Restriction Enzyme Database /pub/databases/rebase REBASE
(Rel. 402, Feb 94)
* RELIBRARY, Restriction Enzyme List /pub/databases/relibrary RELIBRARY
(Feb 1994)
METHYL, Effects of site-specific /pub/databases/methyl METHYL
methylation on methylases and
restriction enzymes (1991)
tRNA sequence and gene sequence db /pub/databases/trna TRNA
(1993)
REPBASE - Prototypic sequences for /pub/databases/repbase REPBASE
human repetitive DNA (Rel. 1.01 1992)
* TFD, Transcription Factor Database /pub/databases/tfd unavailable
(Ver 7.3, Sep 93)
* ECD, E.coli Database /pub/databases/ecd ECD
(Rel. 17, Dec 93)
* FLYBASE, Drosophila Genetic Map db /pub/databases/flybase unavailable
(Feb 94)
LiMB, Listing of Mol. Biol. db's /pub/databases/limb LIMB
(Rel. 3.0)
* SEQANALREF, Seq. analysis refs /pub/databases/reflist REFLIST
(Rel. 45, Nov 93)
FANS_REF, Functional analysis refs /pub/databases/reflist REFLIST
(Rel. 3.4, Apr 91)
* Catalogue of molecular biological /pub/databases/bio_catal BIO_CATAL
software (Rel. 2.1, Dec 93)
Alu sequence database and alignment /pub/databases/alu ALU
* Signal Recognition Particle database /pub/databases/srp SRP
(Dec 1993)
Haemophilia B database /pub/databases/haemb HAEMB
(Rel. 2, Oct 1992)
* Kabat Database of proteins of /pub/databases/kabat unavailable
immunol. interest (Rel 5, Aug 92)
Compilation of small RNA sequences /pub/databases/smallrna SMALLRNA
(Oct 91)
Berlin Databank of 5S rRNA and /pub/databases/berlin BERLIN
5S rRNA gene sequences (1991)
Compilation of small ribosomal /pub/databases/rrna RRNA
subunit RNA sequences (Jun 1993)
CUTG, codon usage /pub/databases/cutg CUTG
tabulated from GenBank rel. 69
3D_Ali, 3D alignment database /pub/databases/3d_ali 3D_ALI
(Jun 1993)
* RLDB, Reference Library Database /pub/databases/rldb unavailable
(Feb 1994)
* PKCDD, Protein Kinase Catalytic /pub/databases/pkcdd PKCDD
Domain Database (December 1993)
* CpG Islands Database /pub/databases/cpgisle CPGISLE
(Release 2.0, Jan 1994)
* Blocks database /pub/databases/blocks BLOCKS
(Rel. 7.01, Dec 1993)
HLA, Alignments of human HLA /pub/databases/hla HLA
sequences (Jul 1993)
TRANSTERM, Translational /pub/databases/transterm TRANSTERM
Termination Signal Database (Apr 1993)
* LISTA, Yeast coding sequences /pub/databases/lista LISTA
(Rel. 3.1, Dec 1993)
* HSSP, sequence-aligned protein /pub/databases/protein_extras/hssp
families (Oct 1993) PROTEINDATA
* FSSP, structure-aligned protein /pub/databases/protein_extras/fssp
families (Oct 1993) unavailable
DSSP, protein secondary structures /pub/databases/protein_extras/dssp
(Feb 1993) PROTEINDATA
* pdb_select, representative sets of /pub/databases/protein_extras/
3D proteins (Dec 93) pdb_select
Misfolded, database of deliberately /pub/database/protein_extras/misfolded
misfolded protein models (Nov 92) unavailable
Software:
Software for MS-DOS computers /pub/software/dos DOS_SOFTWARE
Software for Apple Macintosh /pub/software/mac MAC_SOFTWARE
Software for UNIX /pub/software/unix UNIX_SOFTWARE
Software for VAX/VMS /pub/software/vax VAX_SOFTWARE
Other software /pub/software/misc MISC_SOFTWARE
Miscellaneous:
* Technical documents, submission and /pub/doc DOC
order forms, etc.
* Multiple DNA sequence alignments /pub/databases/embl/align ALIGN
and consensus sequences
Codon Usage tables /pub/databases/codonusage CODONUSAGE
* Crystallographers' information /pub/databases/xray XRAY
* Journals Tables of Content /pub/databases/journals_toc
unavailable
<7> Getting Started ?
-----------------
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.
To use the anonymous ftp server, connect to the internet address
FTP.EMBL-Heidelberg.DE
using the username "anonymous" (without the quotes !) and giving your
e-mail address as the password. Look in the directory /pub/help for
various help files.
To use the Gopher server, open a connection to Gopher.EMBL-Heidelberg.DE
at the standard Gopher port 70.
<8> Network Addresses at EMBL
-------------------------
EMBL File Server (e-mail requests) NetServ at EMBL-Heidelberg.DE
Anonymous FTP FTP.EMBL-Heidelberg.DE
Gopher Server Gopher.EMBL-Heidelberg.DE
BLITZ e-mail server Blitz at EMBL-Heidelberg.DE
FASTA e-mail server FASTA at EMBL-Heidelberg.DE
Quicksearch e-mail server Quick at EMBL-Heidelberg.DE
Problems, feedback (human contact) NetHelp at EMBL-Heidelberg.DE
EMBL Data Library enquiries DataLib at EMBL-Heidelberg.DE
EMBL Data Library sequence submissions DataSubs at EMBL-Heidelberg.DE
Software submissions and problems Software at EMBL-Heidelberg.DE
