IUBio GIL .. BIOSCI/Bionet News .. Biosequences .. Software .. FTP

Re. EMBL File Server

JONG, SONG-MUH J SJJ at ICBR.IFAS.UFL.EDU
Sat Apr 3 10:01:00 EST 1993


From: tonko at hprd26a.cern.ch (Tonko Ljubicic)
Subject: Free EMBL-database query/search software ?
Date: 3 Apr 93 13:08:13 GMT


tonko at hprd26a.cern.ch (Tonko Ljubicic) wrote:
>Does anybody know of a free (or cheap) EMBL database searching
>software ? In the manner of CD-SEQ from the EMBL CD for instance.
>Preferably for DOS (Windows?) and Unix (X11?).

Here is a newsletter from EMBL:

From: NETHELP at EMBL-Heidelberg.DE
Subject: EMBL File Server Newsletter No. 9, Dec. 4th 1992
Date: 4 Dec 92 11:03:17 GMT

------------------------------------------------------------------------------
|  EMBL FILE SERVER News                         Number 9, December 4th 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           |
------------------------------------------------------------------------------


Contents:

 <1> Introduction
 <2> Improvement of EMBL's Internet connectivity
 <3> Anonymous FTP services - alternative sites
 <4> New mail server command
 <5> Updates to data collections
 <6> Updates to software collection
 <7> Other updates
 <8> Summary of directories on the file server
 <9> Getting started ?
 <10> 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> Improvement of EMBL's Internet connectivity
    -------------------------------------------

    Recently there has been a improvement in EMBL's Internet connection which
    results in considerably faster access to our anonymous FTP server and to
    our Gopher server, and also a quicker response to e-mail file server
    requests.

    Please note that the FTP and Gopher servers both run on 
                   FTP.EMBL-Heidelberg.DE  (192.54.41.33)
    Do not use the host name EMBL-Heidelberg.DE

<3> Anonymous FTP services - alternative sites

    (a) The anonymous FTP archives at EMBL are mirrored by an FTP server
        managed by the Israeli EMBnet national node (INN) at the Weizmann
        Institute.
        Internet address: sunbcd.weizmann.ac.il

    (b) Complete copies of the EMBL quarterly releases are also available
        by anonymous FTP from:
        - Swiss EMBnet Node, Biozentrum der Universitaet Basel (Switzerland) 
          Internet address: bioftp.unibas.ch [131.152.8.1]
          Maintained by Reinhard Doelz  (doelz at comp.bioz.unibas.ch)
          Plain ASCII flat files. See the file DESCRIPTION in the top level
          directory for more information, also on other formats of data.

        - Department of Molecular Biology Massachusetts General Hospital
          Internet address: amber.mgh.harvard.edu [132.183.190.26]
          Maintained by Mike Cherry (CHERRY at Frodo.MGH.Harvard.EDU)
          Compressed EMBL flat files. See the 000readme.txt file in the EMBL
          directory for more information, also on other formats of data. 


<4> New mail server command
    -----------------------

    The SIZE command was added to the set of commands recognised by the EMBL
    e-mail server. Because some mailer systems have a maximum file size
    limitation the EMBL mail server splits large files into parts. The default
    size of these packets is 95K but can be changed with the SIZE command.
    E.g. SIZE 30 would change the packet size to 30K, whereas SIZE 500 would
    set it to 500K. Note, however, that uuencoded files are stored in
    individual parts of 90K each on our server, so changing the packet size to
    larger values will have no effect on them.


<5> Updates to Data Collections
    ------------------------------------

    New databases have been added to the file server recently:

    (a) Steven Henikoff's BLOCKS database
        Henikoff, S. and Henikoff, J. G. (1991) Automated assembly of protein
        blocks for database searching. Nucleic Acids Res. 19, 6565-6572.
        E-mail server: directory BLOCKS
        Anonymous ftp: /pub/databases/blocks

    (b) A database of CpG islands in the human genome (CPGISLE)
        Larsen, F., Gundersen, G., Lopez, L. and Prydz, H. (1992) CpG island as
        Gene Markers in the Human Genome. Genomics 13, 1095-1107.
        E-mail server: directory CPGISLE
        Anonymous ftp: /pub/databases/cpgisle

    (c) A database of protein kinase catalytic domains (PKCDD)
        provided by S.K. Hanks, A.M. Quinn and T. Hunter, Salk Institute.
        E-mail server: directory PKCDD
        Anonymous ftp: /pub/databases/pkcdd

    (d) Pre-release data from the Brookhaven Protein Data Bank (PDB) are now
        available in addition to the full releases.
        E-mail server: directory PROTEINDATA


<6> 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:
    ----

    AUTHORIN.UAA        (N) Sequence data submission tool
                            (Intelligenetics/DDBJ/EMBL/GenBank)
                            [/pub/software/dos/authorin.uaa to authorin.uaf]

    CODONS.UUE          (N) Codon usage analysis (A. Lloyd and P. Sharp)
                            [/pub/software/dos/codons.uue]

    CREGEX.C            (U) Conversion of PROSITE to Prosearch format v1.2
                            (J. Leunissen)
                            [/pub/software/dos/cregex.c]

    DOTPLOT.UUE         (N) Dot plot analysis (R> Nakisa)
                            [/pub/software/dos/dotplot.uue]

    ESEE.UAA            (U) Multiple sequence alignment editor v1.09e
                            (E. Cabot)
                            [/pub/software/dos/esee.uaa to esee.uac]

    FASTMAP.UAA         (N) Approx. multipoint lod score calculation
                            (D. Curtis)
                            [/pub/software/dos/fastmap.uaa to fastmap.uac]

    GEPASI.UAA          (N) Modelling of metabolic pathways (P. Mendes)
                            [/pub/software/dos/gepasi.uaa to gepasi.uai]

    MACAW105.UAA        (U) Multiple sequence editor v1.05 (G. Schuler)
                            [/pub/software/dos/macaw105.uaa and macaw105.uab]

    PEDRAW14.UAA        (U) Pedigree drawing program v1.4 (D. Curtis)
                            [/pub/software/dos/pedraw14.uaa to pedraw14.uae]

    RAMHA.UAA           (N) Monte Carlo simulation of random mutagenesis
                            synthetic cDNA (D. Siderovski)
                            [/pub/software/dos/ramha.uaa and ramha.uab]

    SAR2PCIT.UUE        (N) Conversion of SeqAnalRef to ProCite format
                            (E. Sonnhammer)
                            [/pub/software/dos/sar2pcit.uue]

    SORFIND.UAA         (N) Prediction of exons in vertebrate genomic DNA
                            (G. Hutchinson)
                            [/pub/software/dos/sorfind.uaa and sorfind.uab]

    TRBBS.UAA           (N) File exchange program for automated fluorescent DNA
                            sequencer data (I. Consani)
                            [/pub/software/dos/trbbs.uaa and trbbs.uab]
                            
    Mac:
    ----

    AUTHORIN.HQX        (N) Sequence data submission tool
                            (Intelligenetics/DDBJ/EMBL/GenBank)
                            [/pub/software/mac/authorin.hqx]

    DATAMINDER.HQX      (N) Data management tools for molecular biologists
                            (K. Usdin)
                          



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