------------------------------------------------------------------------------
| EMBL FILE SERVER News Number 10, July 7th 1993 |
| |
| 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 |
------------------------------------------------------------------------------
Contents:
<1> Introduction
<2> Blitz e-mail server
<3> Updates 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. The service is free.
<2> Blitz e-mail server
-------------------
BLITZ is an automatic electronic mail server for the MPsrch program of
Shane Sturrock and John Collins, Biocomputing Research Unit, University
of Edinburgh, Scotland.
MPsrch allows you to perform sensitive and extremely fast comparisons of
your protein sequences against the Swiss-Prot protein sequence database
using the Smith and Waterman best local similarity algorithm. It runs
on the MasPar family of massively parallel machines; the BLITZ server
uses a 4096-processor MasPar MP-1 system. A typical search time for a
query sequence of 400 amino acids is approximately 40 seconds to search
the entire Swiss-Prot database.
Additional time is required to reconstruct the alignments; the time for
this will depend on the number of alignments requested. MPsrch is the
fastest implementation of the SW algorithm currently available on any
machine.
How to use BLITZ
----------------
Send a properly formatted electronic mail message to
BLITZ at EMBL-Heidelberg.DE
containing required commands and parameters and the answer will be
automatically mailed to you. To obtain full documentation of the service
and algorithms used, send a message containing just the word HELP.
If you have any problems using the BLITZ service, or any questions, please
send them to:
NETHELP at EMBL-Heidelberg.DE
Example
-------
SEQ
STKKKPLTQE QLEDARRLKA IYEKKKNELG LSQESVADKM GMGQSGVGAL
FNGINALNAY NAALLAKILK VSVEEFSPSI AREIYEMYEA VSMQPSLRSE
YEYPVFSHVQ AGMFSPELRT FTKGDAERWV STTKKASDSA FWLEVEGNSM
TAPTGSKPSF PDGMLILVDP EQAVEPGDFC IARLGGDEFT FKKLIRDSGQ
VFLQPLNPQY PMIPCNESCS VVGKVIASQW PEETFG
END
The possible parameters (eg gap penalty, weight matrix) are explained in
the HELP documentation.
<3> Updates to Data Collections
------------------------------------
New databases have been added to the file server since Newsletter issue 9:
(a) RELIBRARY - Restriction Enzyme List, by E. Raschke
Raschke, E. (1993) Comprehensive restriction enzyme lists to update
any DNA sequence computer program. Genetic Analysis, Techniques and
Applications, Vol. 10, in press.
(b) REPBASE - Protoypic sequences for human repetitive DNA, by J. Jurka
Jurka, J., Walichiewicz, J. and Milosavljevic, A. (1992) J. Mol. Evol.
35:286
(c) HLA - Alignments of human class I and II HLA sequences, by S. Marsh,
J. Zemmour and P. Parham.
(d) TRANSTERM - Translational termination signal database, by C. Brown
Brown, C.M., Dalphin, M.E., Stockwell, P.A., Tate, W.P. (1993) Nucleic
Acids Res. Supplement, submitted
(e) LISTA - Compilation of nucleotide sequences encoding proteins from
the yeast saccharomyces, by P. Linder
Mosse, M.O., Linder, P., Lazowska, J. and Slonimski, P.P. (1993) Curr.
Genet. 23, 66.
<4> Updates to Software Collection
------------------------------
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:
----
BED.UAA (N) Sequence editor with speaker feeback (R. Hwan-Seok)
[/pub/software/dos/bed.uaa and .uab]
BOXSHADE.UUE (N) Plots of multiple alignments with boxes and shades
(K. Hofmann)
[/pub/software/dos/boxshade.uue]
CM.UAA (U) Restriction map construction from multiple digestion
data v1.0a (K. Hofmann)
[/pub/software/dos/cm.uaa to cm.uai]
CONSENSE.UUE (N) Calculation of consensus sequence from alignment
(S. Rensing)
[/pub/software/dos/consense.uue]
DIGEST.UAA (N) Restriction enzyme mapping (R. Nakisa)
[/pub/software/dos/digest.uaa and digest.uab]
DOTPLOT.UAA (U) Dot plot analysis v3.0 (R. Nakisa)
[/pub/software/dos/dotplot.uaa and dotplot.uaa]
EXPLORE.UAA (N) Analysis of multiple alignments (G. Golding)
[/pub/software/dos/explore.uaa and explore.uab]
HTH.C (N) Prediction of helix-turn-helix regions (C. Halling)
[/pub/software/dos/hth.c]
RASMOL.UAA (N) Visualisation of macromolecules using PDB files
(R. Sayle)
[/pub/software/dos/rasmol.uaa to rasmol.uac]
SILMUT.UUE (N) Identification of regions suitable for silent
mutagenesis (B. Shankarappa)
[/pub/software/dos/silmut.uue]
SORFIND.UUE (U) Prediction of exons in vertebrate genomic DNA v1.7
(G. Hutchinson)
[/pub/software/dos/sorfind.uue]
WINBLAST.UAA (N) Windows 3.1 interface for NCBI BLAST server
(A. Sivaprasad)
[/pub/software/dos/winblast.uaa to winblast.uae]
WINDOT.UAA (N) Dot plot analyis under Windows 3.1 (R. Nakisa)
[/pub/software/dos/windot.uaa and windot.uab]
WINIRX.UAA (N) Windows 3.1 interface for NCBI IRX server
[/pub/software/dos/winirx.uaa to winirx.uae]
WINSEQ.UUE (N) Windows version of D. Gilbert's READSEQ (R. Nakisa)
[/pub/software/dos/winseq.uue]
Mac:
----
ALIGN.HQX (U) Sequence alignments and phylogeny (replacement of
corrupt archive) (D. Feng)
[/pub/software/mac/align.hqx]
AMPLIFY.HQX (U) PCR primer checks v1.2 (B. Engels)
[/pub/software/mac/amplify.hqx]
BKGCUCLC_FONTS.HQX (N) Color fonts for use with sequence editors (M. Sogin)
[/pub/software/mac/bkgcuclc_fonts.hqx]
DBCONV.HQX (U) Transformation of line-oriented databases into tab-
delimited format v2.0 (J. Valverde)
[/pub/software/mac/dbconb.hqx]
DIGISPEAK.HQX (N) Sequence reading with sonic digitizer (N. Mantei)
[/pub/software/mac/digispeak.hqx]
DNAID.HQX (U) DNA sequence editor with grep-like search routine
v1.8 (F. Dardel)
[/pub/software/mac/dnaid.hqx]
EMBL-SEARCH.HQX (U) Database retrieval software for EMBL CD-ROM v2.3.2
(EMBL Data Library)
[/pub/software/mac/embl-search.hqx]
EMBL-SEARCH_SRC.HQX (U) Source code for EMBL-Search v2.3.2
[/pub/software/mac/embl-search_src.hqx]
HTH.C (N) Prediction of helix-turn-helix regions (C. Halling)
[/pub/software/mac/hth.c]
LABHELPER.HQX (N) General laboratory tools for buffer preps etc.
(T. Tzeng)
[/pub/software/mac/labhelper.hqx]
MACCLADE30_DEMO.HQX (N) Demo of phylogenetic analysis program (W. Maddison)
[/pub/software/mac/macclade30_demo.hqx]
MACP12.HQX (N) Protein property profile plots (A. Luettke)
[/pub/software/mac/macp12.hqx]
MACPATTERN.HQX (U) Protein pattern searching with PROSITE and
BLOCKS database v3.0 (R. Fuchs)
[/pub/software/mac/macpattern.hqx]
MACSTAN.HQX (N) Random nucleotide sequence generator and analyzer
(F. Gast)
[/pub/software/mac/macstan.hqx]
PROTEINSTRUCTURE.HQX (N) Tutorial on protein structures (C. Burchill)
[/pub/software/mac/proteinstructure.hqx]
READSEQ.HQX (U) Sequence format conversion program (D. Gilbert)
[/pub/software/mac/readseq.hqx]
RRNA-STACK.HQX (U) Phylogeny of 16/18S rRNA (J. Brown)
[/pub/software/mac/rrna-stack.hqx]
STUFFITLITE.HQX (U) Compression/decompression/binhex program v3.0.5
(R. Lau)
[/pub/software/mac/stuffitlite.hqx or
stuffitlite.sea]
TOPPPRED.HQX (N) Prediction of transmembrane segments and their
topology (G. v. Heijne, M.G. Claros)
YEASTSTRAINS.HQX (U) Strain management, in particular yeast v1.2
(K. Froehlich)
[/pub/software/mac/yeaststrains.hqx]
UNIX:
-----
BLKSRCH.UUE (N) Block search analysis of protein sequences with
the BLOCKS database (R. Fuchs)
[/pub/software/unix/blocksearch.tar.Z]
BTAB.UAA (N) BLAST output parser (M. Dubnick)
[/pub/software/unix/btab.tar.Z]
double-digester.tar.Z (N) Graphical analysis of double digest restriction
(only on FTP server) data (L. Wright).
DTASK11S.UAA (N) Smith-Waterman database searches on parallel work-
stations (G. Hauge)
[/pub/software/unix/dtask11s.tar.Z]
FILTER.UAA (U) Suboptimal alignments and motif recognition
(P. Argos)
[/pub/software/unix/filter.tar.Z]
GENAL.UUE (N) Alignments of genomic sequences with coding regions
(J. Stoevlbaek)
[/pub/software/unix/genal.tar.Z]
GM.UAA (U) Analysis of unknown DNA sequences v2.0 (C. Fields)
[/pub/software/unix/gm.tar.Z]
HTH.C (N) Prediction of helix-turn-helix regions (C. Halling)
[/pub/software/unix/hth.c]
MAILFASTA.UUE (U) Script for using EMBL/GenBank Mail-FASTA servers
v3.1 (T. deBoer)
[/pub/software/unix/mailfasta.tar.Z]
MOLBIO.UAA (N) C++ clas library for molecular biology (K. Robison)
[/pub/software/unix/molbio.tar.Z]
RASMOL.UAA (N) Visualisation of macromolecules using PDB files
(R. Sayle)
[/pub/software/unix/rasmol.tar.Z]
READSEQ.UAA (U) Sequence format conversion program (D. Gilbert)
[/pub/software/unix/readseq.tar.Z]
SUPER.UAA (N) Tool for electronic user polls (R. Doelz)
[/pub/software/unix/super.tar.Z]
VAX:
----
BLKSRCH.UUE (N) Block search analysis of protein sequences with
the BLOCKS database (R. Fuchs)
[/pub/software/vax/blksrch.uue]
FILTER.UAA (U) Suboptimal alignments and motif recognition
(P. Argos)
[/pub/software/vax/filter.uaa to filter.uad]
GCGMENU.UAA (N) Menu interface to GCG package (C. Gartmann)
[/pub/software/vax/gcgmenu.uaa and gcgmenu.uab]
HTH.C (N) Prediction of helix-turn-helix regions (C. Halling)
[/pub/software/vax/hth.c]
PDBTOGCG.FOR (N) Extracts protein sequences from PDB files (M. Mezei)
[/pub/software/vax/pdbtogcg.for]
READSEQ.UAA (U) Sequence format conversion program (D. Gilbert)
[/pub/software/vax/readseq.uaa to readseq.uac]
SUPER.UUE (N) Tool for electronic user polls (R. Doelz)
[/pub/software/unix/super.uue]
TFD2GCG.FOR (N) Converts TFD SITES table to GCG Prosite format
(D. Mathog)
[/pub/software/vax/tfd2gcg.for]
UNZIP.UUE (N) Decompresses ZIP encoded files (H. Smith)
[/pub/software/vax/unzip.uue]
<5> Other updates
-------------
(a) A new directory that will hold information for crystallographers,
XRAY. The only file currently present is the list of e-mail addresses
of crystallographers and related scientists maintained by M. Teeter,
Boston College.
E-mail server: directory XRAY
Anonymous ftp: /pub/databases/xray
(b) ALIGN directory:
o DS13648.DAT - Alignment of plasmodial small subunit
rRNAs.
Submitted by V.Enea, 26-Feb-1993
o DS13893.DAT - Alignment of amino acid sequences derived
from conceptual reading frames of Tc1-like
elements from fish, nematodes, fruit flies
an agnathan, and a spider.
Submitted by D.H.A. Fitch, 18-Mar-1993
o DS13894.DAT - Alignment of Tc1-like elements from salmon,
trout, zebrafish, and catfish.
Submitted by D.H.A. Fitch, 18-Mar-1993
o DS14642.DAT - Alignment of amino acid sequences of the
zinc-containing long-chain alcohol
dehydrogenases.
Submitted by S. Yokoyama, 17-Jun-1993
<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. 35, Jun 93 + updates)
* Eukaryotic Promotor Database /pub/databases/epd EPD
(Rel. 35, May 93)
* SwissProt Protein Sequence Database /pub/databases/swissprot PROT
(Rel. 25, Apr 92 + updates)
* Prosite pattern database /pub/databases/prosite PROSITE
(Rel. 10.1, Apr 93)
* ENZYME database /pub/databases/enzyme ENZYME
(Rel. 12.00, Aug 93)
* Brookhaven Protein Databank not available PROTEINDATA
(Rel. 61, Jul 92 + pre-release)
* REBASE, Restriction Enzyme Database /pub/databases/rebase REBASE
(Rel. 9307, Jul 93)
* RELIBRARY, Restriction Enzyme List /pub/databases/relibrary RELIBRARY
(Apr 1993)
* 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 TFD
(Ver 5.5, Nov 92)
* ECD, E.coli Database /pub/databases/ecd ECD
(Rel. 14, Feb 93)
FLYBASE, Drosophila Genetic Map db /pub/databases/flybase FLYBASE
(9209, 8-Sep-1992)
LiMB, Listing of Mol. Biol. db's /pub/databases/limb LIMB
(Rel. 3.0)
* SEQANALREF, Seq. analysis refs /pub/databases/reflist REFLIST
(Rel. 38, Apr 93)
FANS_REF, Functional analysis refs /pub/databases/reflist REFLIST
(Rel. 3.4, Apr 91)
Alu sequence database and alignment /pub/databases/alu ALU
Haemophilia B database /pub/databases/haemb HAEMB
(Rel. 2, Oct 1992)
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
(Jun 1993) (ftp only)
* PKCDD, Protein Kinase Catalytic /pub/databases/pkcdd PKCDD
Domain Database (April 1993)
* CpG Islands Database /pub/databases/cpgisle CPGISLE
(Release 2.0, Apr 1992)
* Blocks database /pub/databases/blocks BLOCKS
(Rel. 6.0, Jan 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. 2.0, Apr 1993)
* HSSP, sequence-aligned protein /pub/databases/protein_extras/hssp
families PROTEINDATA
* FSSP, structure-aligned protein /pub/databases/protein_extras/fssp
families (ftp only)
* DSSP, protein secondary structures /pub/databases/protein_extras/dssp
PROTEINDATA
pdb_select, representative sets of /pub/databases/protein_extras/
3D proteins (Sep 1992) (ftp only) pdb_select
Misfolded, database of deliberately /pub/database/protein_extras/misfolded
misfolded protein models (Nov 92) (ftp only)
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
<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 FTP.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
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
