Difference between revisions of "EMBL File Server News, No. 8 June 25th 1992"

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From bronze!sol.ctr.columbia.edu!ucselx!bionet!EMBL-HEIDELBERG.DE!NETHELP Thu Jun 25 07:51:53 EST 1992
Article: 75 of bionet.molbio.embldatabank
Path: bronze!sol.ctr.columbia.edu!ucselx!bionet!EMBL-HEIDELBERG.DE!NETHELP
From: [email protected]
Newsgroups: bionet.molbio.embldatabank
Subject: EMBL File Server News, No. 8 June 25th 1992
Message-ID: <[email protected]>
Date: 25 Jun 92 12:10:00 GMT
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Distribution: bionet
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------------------------------------------------------------------------------
|  EMBL FILE SERVER News                        Number 8, June 25th 1992     |
|                                                                            |
|  European Molecular Biology Laboratory, Data Library & Computer Group,     |
|  Postfach 10.2209, 6900 Heidelberg, Germany.                               |
|                                             Tel: +49 6221 387258           |
|  E-mail: [email protected]         Fax: +49 6221 387519           |
------------------------------------------------------------------------------


Contents:

 <1> Introduction
 <2> Anonymous FTP server
 <3> Gopher server
 <4> Updates to data collections
 <5> Updates to software collection
 <6> Other updates
 <7> Summary of directories on the file server
 <8> Getting started ?
 <9> Network addresses at EMBL
<10> Footnotes


<1> Introduction
    -------------

    The EMBL File Server is a facility available on the EMBL computing system
    for external users to request files by electronic mail or anonymous FTP.
    The service is free.


<2> Anonymous FTP server
    --------------------

    An anonymous FTP server is now operational at the internet address

                        FTP.EMBL-Heidelberg.DE  (192.54.41.33)

    Users should log in with the username "anonymous", and for the password
    give their e-mail address.

    The FTP archive currently contains molecular biology databases, free
    molecular biology software and other files similar to the facilities
    offered by the e-mail server ([email protected]).

    Weekly batches of additions to the EMBL nucleotide sequence database (data
    from EMBL/GenBank/DDBJ) are made available as compressed tar files in the
    directory: /pub/databases/embl/new
    Individual sequence database entries are not available via FTP: we
    recommend use of the e-mail server for this purpose.


<3> Gopher server
    -------------

    A gopher server is available as part of an experimental network of
    EMBnet gopher sites, providing access to the EMBL FTP archive and
    to other "Biogophers" in Europe, Israel and the USA.

    Gopher clients should connect to FTP.EMBL-Heidelberg.DE at port 70.
    Administrators of other Gopher servers may add the following link
    information:

    Name=EMBnet BioInformation Resource EMBL
    Type=1
    Port=70
    Path=1/
    Host=ftp.embl-heidelberg.de


<4> Updates to Data Collections
    ------------------------------------

    Two new databases have been added to the file server recently:

    (a) The Reference Library Database system (RLDB) provided by
        Guenther Zehetner, Genome Analysis Laboratory, ICRF, London.
        E-mail server: directory RLDB
        Anonymous ftp: /pub/databases/rldb

    (b) A database of 3-D alignments (3D_ALI) provided by Stefan Pascarella and
        Pat Argos, EMBL.
        Pascarella S., Argos P. 
        "A data bank merging related protein structures and sequences"
        Protein Engineering 5 (1) 121-137 (1992).

        E-mail server: directory 3D_ALI
        Anonymous ftp: /pub/databases/3d_ali


<5> 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:
    ----

    DNAFRAG.UUE         (N) Measures molecule size of gel bands from standards
                            (J. Nash)
                            [/pub/software/dos/dnafrag.uue]

    GEL-JML.UAA         (N) Calculation of DNA restriction fragment sizes
                            (J.M. Lacroix)
                            [/pub/software/dos/gel-jml.uaa and gel-jml.uab]

    GMD.TXT             (N) Programs to assist in the design of genome mapping
                            experiments (contig mapping) (Y. Fu)
                            [/pub/software/dos/gmd.txt]

    MACAW103.UAA        (N) Multiple sequence editor (G. Schuler)
                            [/pub/software/dos/macaw103.uaa to macaw103.uac]

    MARKER.UUE          (U) Creation of restriction fragments banding patterns
                            and DNA length standards v1.1 (S. Rensing)
                            [/pub/software/dos/marker.uue]

    MISMATCH.TXT        (N) Selection of PCR designed mismatch primers
                            (L.S. Davidow)
                            [/pub/software/dos/mismatch.txt]

    NUMCLONE.UUE        (N) Estimates the number of clones one has to screen
                            from a genomic library in order to find a desired
                            clone (J. Nash)
                            [/pub/software/dos/numclone.uue]

    PRIMGEN.UUE         (N) Oligonucleotide primer design by
                            reverse-translation of amino acid sequences
                            (J. Nash)
                            [/pub/software/dos/primgen.uue]

    PRNTGL.UAA          (U) Prints HGPL files on matrix of laser printer v1.18
                            (C. Ravitz)
                            [/pub/software/dos/prntgl.uaa and prntgl.uab]

    SIM.UUE             (U) Local similarity searching (G. Huang)
                            [/pub/software/dos/sim.uue]

    SSCAN.UAA           (U) Identification of eukaryotic signals in DNA
                            sequences, v3.0 (D. Prestridge)
                            [/pub/software/dos/sscan.uaa to scan.uad]

    Mac:
    ----

    ALIGNER.HQX         (N) Multiple sequence editor (D. Eernisse)
                            [/pub/software/mac/aligner.hqx]

    AMPLIFY.HQX         (N) Tools for PCR primer checks (B. Engels)
                            [/pub/software/mac/amplify.hqx]

    DNAID.HQX           (U) DNA sequence editor and analysis program v1.6
                            (F. Dardel)
                            [/pub/software/mac/dnaid.hqx]

    EMBL-SEARCH.HQX     (N) Database retrieval software for EMBL CD-ROM
                            (R. Fuchs)
                            [/pub/software/mac/embl-search.hqx]

    EMBL-SEARCH_SRC.HQX (N) Source code for EMBL-Search v2.0
                            [/pub/software/mac/embl-search_src.hqx]

    GBSEARCH.HQX        (U) Tool to assist access to GenBank server
                            (D. Gilbert)
                            [/pub/software/mac/gbsearch.hqx]

    GENEWORKS_DEMO.HQX  (N) Demo version of IG's sequence analysis package
                            [/pub/software/mac/geneworks_demo.hqx]

    GENE_JOCKEY_DEMO.HQX (N) Demo version of Biosoft's sequence analysis
                            package
                            [/pub/software/mac/gene_jockey_demo.hqx]

    GMD.TXT             (N) Programs to assist in the design of genome mapping
                            experiments (contig mapping) (Y. Fu)
                            [/pub/software/mac/gmd.txt]

    MACMIMIC_DEMO.HQX   (N) Demo version of Instar's molecular modelling
                            package
                            [/pub/software/mac/macmimic_demo.hqx]

    MACMOLECULE.HQX     (U) 3d models of biomolecules v1.7 (E. Myers)
                            [/pub/software/mac/macmolecule.hqx]

    MACPATTERN.HQX      (U) Protein pattern searching with Prosite, v1.6.2
                            (R. Fuchs)
                            [/pub/software/mac/macpattern.hqx]

    MACSIGNALSCAN.HQX   (N) Identification of eukaryotic signals in DNA
                            sequences, v3.0 (D. Prestridge)
                            [/pub/software/mac/macsignalscan.hqx]

    MACVECTOR_DEMO.HQX  (N) Demo of IBI's sequence analysis package
                            [/pub/software/mac/macvector_demo.hqx]

    SIGNALASE.HQX       (N) Analysis of mammalian signal peptide sequences
                            (N. Matei)
                            [/pub/software/mac/signalase.hqx]


    UNIX:
    -----

    BLAST.UAA           (U) Fast sequence database searching
                            [/pub/software/unix/blast.tar.Z]
    
    DFA.UAA             (U) Required by BLAST.UAA
                            [/pub/software/unix/dfa.tar.Z]

    FILTER.UAA          (N) Set of programs for suboptimal alignments ans
                            recognition of reliably aligned sequences
                            (P. Argos)
                            [/pub/software/unix/filter.tar.Z]

    GCI.UAA             (N) A network server for interactive 3D graphics
                            (G. Tuparev)
                            [/pub/software/unix/gci.tar.Z]

    GISH.UUE            (U) Required by BLAST.UAA
                            [/pub/software/unix/gish.tar.Z]

    GMD.TXT             (N) Programs to assist in the design of genome mapping
                            experiments (contig mapping) (Y. Fu)
                            [/pub/software/unix/gmd.txt]

    MAILFASTA.UUE       (U) Script for using EMBL/GenBank Mail-FASTA servers
                            v2.1 (T. deBoer)
                            [/pub/software/unix/mailfasta.tar.Z]

    NCBI.UAA            (U) Required by BLAST.UAA
                            [/pub/software/unix/ncbi.tar.Z]

    PIMA.UAA            (U) Pattern-induced multi-sequence alignments v1.22
                            (R.F. Smith)
                            [/pub/software/unix/pima.tar.Z]

    PLSEARCH.UAA        (U) Pattern detection in proteins v4.2 (R.F. Smith)
                            [/pub/software/unix/plsearch.tar.Z]

    READSEQ.UUE         (U) Sequence format conversion program, Apr 1992
                            (D. Gilbert)
                            [/pub/software/unix/readseq.tar.Z]

    SIGSCAN.UAA         (U) Identification of eukaryotic signals in DNA
                            sequences, v3.0 (D. Prestridge)
                            [/pub/software/unix/sigscan.tar.Z]

    SIM.UUE             (U) Local similarity searching (G. Huang)
                            [/pub/software/unix/sim.tar.Z]

    
    VAX:
    ----

    BLASTMAIL.COM       (N) DCL script for using GenBank's BLAST server
                            (E.L. Sonnhammer)
                            [/pub/software/vax/blastmail.com]

    FASTEMBL.COM        (U) Script for using the EMBL Mail-Fasta server
                            (for GCG 7), v 1.w (E. Sonnhammer)
                            [/pub/software/vax/fastembl.com]

    FILTER.UAA          (N) Set of programs for suboptimal alignments ans
                            recognition of reliably aligned sequences
                            (P. Argos)
                            [/pub/software/vax/filter.uaa to filter.uac]

    GMD.TXT             (N) Programs to assist in the design of genome mapping
                            experiments (contig mapping) (Y. Fu)
                            [/pub/software/vax/gmd.txt]

    INTERFACE.UUE       (N) Pascal programming interface for GCG package
                            (J. Prilusky)
                            [/pub/software/vax/interface.uue]

    MALIGNED.UAA        (U) Multiple sequence editor, v1.65b (S. Clark)
                            [/pub/software/vax/maligned.uaa to maligned.uad]

    READSEQ.UAA         (U) Sequence format conversion program, Apr 1992
                            (D. Gilbert)
                            [/pub/software/vax/readseq.uaa and readseq.uab]

    SCRUTINE.UAA        (U) Scrutineer, sequence database analysis, Jun 1992
                            (P. Sibbald)
                            [/pub/softare/vax/scrutine.uaa]

    SIM.UUE             (U) Local similarity searching (G. Huang)
                            [/pub/software/vax/sim.uue]

    SSCAN.UAA           (U) Identification of eukaryotic signals in DNA
                            sequences, v3.0 (D. Prestridge)
                            [/pub/software/vax/sscan.uaa to sscan.uac]



<6> Other updates
    -------------
    ALIGN directory:

        o DS10014.DAT            - Alignment of exon 1 of the interphoto-
                                   receptor binding protein (IRBP) gene.
                                   Submitted by J. Stanhope, 4-Feb-1992.

        o DS10763.DAT            - Alignment of duplicated gamme globin gene
                                   sequences from mammals.
                                   Submitted by W. Bailey, 24-Apr-1992.

        o DS10819.DAT            - Alignment of potassium channel gene family.
                                   Submitted by M. Strong, 13-May-1992

        o DS10830.DAT            - Alignment of potassium channel genes,
                                   Shaw related gene family.
                                   Submitted by M. Strong, 14-May-1992

        o DS10831.DAT            - Alignment of S4 segment of Na+,Ca++, and
                                   K+ ion channel genes.
                                   Submitted by M. Strong, 14-May-1992

        o DS10832.DAT            - Alignment of potassium channel genes,
                                   Shaker related gene family.
                                   Submitted by M. Strong, 13-May-1992

        o DS10833.DAT            - Alignment of sodium channel gene family.
                                   Submitted by M. Strong, 13-May-1992



<7> Summary of directories on the file server
    ---------------------------------------
                                           Anonymous ftp          NetServ
                                          --------------         ---------
    EMBL Nucleotide Sequence Database    /pub/databases/embl       NUC
      (Rel. 31, Jun 92 + updates)
    Eukaryotic Promotor Database         /pub/databases/epd        EPD
      (Rel. 31, May 92)
    SwissProt Protein Sequence Database  /pub/databases/swissprot  PROT
       (Rel. 22, May 92 + updates)
    Prosite pattern database             /pub/databases/prosite    PROSITE
       (Rel. 9.00, Jun 92)
    ENZYME database                      /pub/databases/enzyme     ENZYME
       (Rel. 9.00, May 92)
    Brookhaven Protein Databank          not available             PROTEINDATA
       (Rel. 58, Oct 91)
    REBASE, Restriction Enzyme Database  /pub/databases/rebase     REBASE
       (Rel. 9206, Jun 92)
    tRNA sequence and gene sequence db   /pub/databases/trna       TRNA
       (1991)
    TFD, Transcription Factor Database   /pub/databases/tfd        TFD
       (Ver 4.3, Mar 92)
    ECD, E.coli Database                 /pub/databases/ecd        ECD
       (Rel. 11, Jun 92)
    FLYBASE, Drosophila Genetic Map db   /pub/databases/flybase    FLYBASE
       (9206, 1-Jun-1992)
    LiMB, Listing of Mol. Biol. db's     /pub/databases/limb       LIMB
       (Rel. 2.0)
    SEQANALREF, Seq. analysis refs       /pub/databases/reflist    REFLIST
       (Rel. 28, Jun 92)
    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
      (Dec 1991)
    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 (1991)
    CUTG, codon usage                    /pub/databases/cutg       CUTG
      tabulated from GenBank rel. 69
    3D_Ali, 3D alignment database        /pub/databases/3d_ali     3D_ALI
      (March 1992)
    RLDB, Reference Library Database     /pub/databases/rldb       RLDB
      (April 1992)

    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


<8> Getting Started ?
    -----------------
    
    For initial information, send standard electronic mail to the address:
      [email protected]
    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.


<9> Network addresses at EMBL
    -------------------------

    EMBL File Server (e-mail requests)        [email protected]
    FASTA e-mail server                       [email protected]
    Quicksearch e-mail server                 [email protected]
    Anonymous FTP                             FTP.EMBL-Heidelberg.DE

    Problems, feedback (human contact)        [email protected]
    EMBL Data Library enquiries               [email protected]
    EMBL Data Library sequence submissions    [email protected]
    Software submissions and problems         [email protected]

<10> Footnotes
     ---------

    REMINDER: EMBL has withdrawn from the BITNET/EARN computer network.
    Use only the Internet address, eg [email protected]
    The old address, eg [email protected], is terminated.

    The EMBL File Server Newsletter summarises changes to the EMBL File Server.
    This newsletter and older issues are available from the mail server (eg. GET
    DOC:EMBL_Server_News.7), or via anonymous ftp in the directory /pub/doc