EMBL Newsletter 10

Rainer Fuchs EMBL Data Library Rainer.Fuchs at EMBL-Heidelberg.DE
Wed Jul 7 08:55:04 EST 1993


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|  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           |
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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_dem


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