EMBL File Server News, Number 11

embnet at embl-heidelberg.de embnet at embl-heidelberg.de
Fri Feb 11 08:17:49 EST 1994


------------------------------------------------------------------------------
|  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           |
------------------------------------------------------------------------------


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



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