EMBL File Server Newsletter No. 9, Dec. 4th 1992

NETHELP at EMBL-Heidelberg.DE NETHELP at EMBL-Heidelberg.DE
Fri Dec 4 06:03:17 EST 1992

|  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           |


 <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

    Please note that the FTP and Gopher servers both run on 
                   FTP.EMBL-Heidelberg.DE  (
    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
        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 []
          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 []
          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.


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

    CODONS.UUE          (N) Codon usage analysis (A. Lloyd and P. Sharp)

    CREGEX.C            (U) Conversion of PROSITE to Prosearch format v1.2
                            (J. Leunissen)

    DOTPLOT.UUE         (N) Dot plot analysis (R> Nakisa)

    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)

    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]

    AUTHORIN.HQX        (N) Sequence data submission tool

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

    EMBL-SEARCH.HQX     (U) Database retrieval software for EMBL CD-ROM v2.1.1
                            (EMBL Data Library)

    EMBL-SEARCH_SRC.HQX (N) Source code for EMBL-Search v2.1.1

    GBSEARCH-NCBI.HQX   (U) Tool to assist access to GenBank servers at NCBI
                            v2.0.2 (D. Gilbert)

    GELREADER_FPU.HQX   (N) NCSA's GelReader software for Macs with FPU

    GELREADER_NO_FPU.HQX (N) NCSA's GelReader software for Macs w/o FPU
    GELREADER_SAMPLES.HQX (N) Example files for NCSA's GelReader

    HYPERPCR.HQX        (N) Calculation of PCR conditions (B. Osborne)

    LOOPDLOOP.HQX       (N) Tool for drawing RNA structures (D. Gilbert)
    MACPATTERN.HQX      (U) Protein pattern searching with PROSITE and
                            BLOCKS database v.2.0.1 (R. Fuchs)

    MACT_GENERAL.HQX    (N) MacT package for phylogenetic tree calculation
                            (general programs and documentation) (Luettke)

    MACT_TREE26.HQX     (N) MacT package for phylogenetic tree calculation
                            (TREE26 programs for up to 26 sequences) (Luettke)

    MACT_TREE4.HQX      (N) MacT package for phylogenetic tree calculation
                            (TREE4 programs for four sequences) (Luettke)

    MACT_TREE5.HQX      (N) MacT package for phylogenetic tree calculation
                            (TREE5 programs for five sequences) (Luettke)

    PUPKIT.HQX          (N) TrueType and Postscript fonts for displaying
                            sequences in Puppy and Kitty representation
                            (U. Melcher)

    PUPPY.HQX           (U) Special display of nucleic acid and protein
                            sequences v2.0 (U. Melcher)
    STUFFITLITE.HQX     (U) Compression/decompression/binhex program v3.0.3
                            (R. Lau)                            
                            [/pub/software/mac/stuffitlite.hqx or

    YEASTSTRAINS.HQX    (U) Strain management, in particular yeast
                            (K. Froehlich)


    CREGEX.C            (U) Conversion of PROSITE to Prosearch format v1.2
                            (J. Leunissen)

    ICATOOLS.UAA        (N) Clustering and statistical analysis of large
                            cDNA collections (J. Parsons)

    ICRF_CTG.UAA        (N) Tools for ordering clone libraries based on
                            hybridisation data (R. Mott and A. Grigoriev)

    ISSC.UAA            (U) Sensitive sequence alignment package (Oct 92)
                            (P. Argos et al.)

    MAILFASTA.UUE       (U) Script for using EMBL/GenBank Mail-FASTA servers
                            v3.0 (T. deBoer)

    OVERSEER.UAA        (U) Package for searching nucleic acid databases
                            (Oct 92) (P. Sibbald)

    STATUS.UAA          (N) Tools for managing large DNA-sequencing projects
                            (M. Dubnik)

    ProtQuiz            (N) Xwindows protein 3D/1D display 
    (only available         (M.Scharf, C.Sander)
     from FTP server)       [/pub/software/unix/protquiz/ProtQuiz-0.9.tar.Z]


    CDACCESS.UAA        (U) Driver software for reading ISO CD-ROMs v2.05
                            (P. Stockwell)
                            [/pub/software/vax/cdaccess.uaa and cdaccess.uab]

    CREGEX.C            (U) Conversion of PROSITE to Prosearch format v1.2
                            (J. Leunissen)

    GENEIDSHELLS.SHARE  (N) DCL shells for using GENEID server (F. Macrides)

    GRAILSHELLS.SHARE   (N) DCL shells for using GRAIL server (F. Macrides)

    ICATOOLS.UAA        (N) Clustering and statistical analysis of large
                            cDNA collections (J. Parsons)
                            [/pub/software/vax/icatools.uaa to icatools.uai]

    ISSC.UAA            (U) Sensitive sequence alignment package (Oct 92)
                            (P. Argos et al.)
                            [/pub/software/unix/issc.uaa to issc.uak]

    NCBISHELLS.SHARE    (N) DCL shells for using GenBank servers (F. Macrides)

    OVERSEER.UAA        (U) Package for searching nucleic acid databases
                            (Oct 92) (P. Sibbald)

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

<7> 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:

        DS11144.DAT            - Alignment of insect mtDNA and ND1 gene
                                 products. Submitted by D. Pashley, 12-Jun-1992

        DS12100.DAT            - Alignment of small subunit rRNAs from
                                 higher fungi. Submitted by J. Suguyama,

<8> 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. 33, Dec 92 + updates)
*   Eukaryotic Promotor Database         /pub/databases/epd        EPD
      (Rel. 33, Nov 92)
*   SwissProt Protein Sequence Database  /pub/databases/swissprot  PROT
       (Rel. 23, Aug 92 + updates)
*   Prosite pattern database             /pub/databases/prosite    PROSITE
       (Rel. 9.10, Aug 92)
*   ENZYME database                      /pub/databases/enzyme     ENZYME
       (Rel. 10.00, Aug 92)
*   Brookhaven Protein Databank          not available             PROTEINDATA
       (Rel. 61, Jul 92 + pre-release)
*   REBASE, Restriction Enzyme Database  /pub/databases/rebase     REBASE
       (Rel. 9212, Dec 92)
    tRNA sequence and gene sequence db   /pub/databases/trna       TRNA
*   TFD, Transcription Factor Database   /pub/databases/tfd        TFD
       (Ver 5.5, Nov 92)
*   ECD, E.coli Database                 /pub/databases/ecd        ECD
       (Rel. 13, Nov 92)
*   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. 32, Oct 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
      (Rel. 2, Dec 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 (May 1992)
    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)
*   CpG Islands Database                 /pub/databases/cpgisle    CPGISLE
      (Pre-release 1.0, Oct 92)
*   Blocks database                      /pub/databases/blocks     BLOCKS
      (Rel. 5.0, Jun 92)
*   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
*   pdb_select, representative sets of   /pub/databases/protein_extras/
                3D proteins (ftp only)                              pdb_select


    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


    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
*   Crystallographer's information       /pub/databases/xray       XRAY

<9> 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
    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.

<10> Network addresses at EMBL

    EMBL File Server (e-mail requests)        NetServ at EMBL-Heidelberg.DE
    FASTA e-mail server                       FASTA at EMBL-Heidelberg.DE
    Quicksearch e-mail server                 Quick at EMBL-Heidelberg.DE
    Anonymous FTP                             FTP.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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