EMBL File Server Newsletter 10

fuchs at embl-heidelberg.de fuchs at embl-heidelberg.de
Wed Jul 7 09:05:39 EST 1993


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



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