EMBL File Server News: Number 7, January 1st 1992

Wed Jan 1 18:23:00 EST 1992

|  EMBL FILE SERVER News                        Number 7, January 1st 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> Updates to data collections
<3> Updates to software collection
<4> Other updates
<5> Summary of directories on the file server
<6> Getting started ?

<1> Introduction

    REMINDER: EMBL has withdrawn from the BITNET/EARN computer network as from
    today. Use only the Internet address, NetServ at EMBL-Heidelberg.DE
    The old address, Netserv at EMBL.bitnet, is terminated.

    The EMBL File Server Newsletter summarises changes to the EMBL File Server.
    This newsletter and older issues are available from the server (eg. GET

<2> Updates to Data Collections

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

    (a) The Haemophilia B database, provided by Professor Gordon Brownlee,
        University of Oxford, is available in the file server directory:
        Giannelli F., Green P.M., High K.A. et.al.
        "Haemophilia B: database of point mutations and short additions and
         deletions - second edition"
        Nucleic Acids Res. 19:2193-2219 (1991).

        For more information send the command HELP HAEMB.

    (b) A compilation of small RNA sequences, provided by Ram Reddy,
        Baylor College of Medicine, Houston, is available in the file
        server directory: SMALLRNA

        Gupta S., Reddy R.
        "Compilation of Small RNA Sequences"
        Nucleic Acids Res. 19:2073-2075 (1991).

        For more information send the command HELP SMALLRNA.

    Just about every existing collection has been updated since the last
    newsletter so we will not detail them here. The current versions of all
    collections are detailed below.

<3> Updates to Software Collection
    Here is a list of new (N) molecular biological programs or updates (U):


    CM.UAA              (N) Graphically oriented restriction map construction
                            from multiple digestion data (K. Hoffmann)

    MARKER.UUE          (N) Creation of restriction fragments banding patterns
                            and DNA length standards (S. Rensing)

    PROGRAPH.UAA        (U) Graphically oriented protein sequence analysis
                            package (K. Hoffmann)


    ALIGN.HQX           (N) Feng and Doolittle's sequence alignment and
                            phylogeny programs (ported by P. Markiewicz)

    STRAINCOLLECTION.HQX (N) HyperCard stack for bacterial strain management
                            (D. Moore)

    MACPATTERN.HQX      (U) Protein pattern searching with Prosite, v1.5
                            (R. Fuchs)

    READSEQ.HQX         (U) Sequence format conversion program, Nov 1991
                            (D. Gilbert)


    READSEQ.UUE         (U) Sequence format conversion program, Nov 1991
                            (D. Gilbert)


    ACCESS.UUE          (N) GCG tool for extracting entries from the database
                            (J. Prilusky)

    BLAST.UAA           (N) NCBI's fast database searching programs
    BLASTINC.UUE            (VMS version by P. Stockwell)

    BLASTSEARCH.TXT     (N) DCL script for using GenBank's BLAST server
                            (S. Clark)

    EASYMENU.UUE        (N) Menu interface to the GCG package (J. Prilusky)

    SEQCOMP.TXT         (N) Analysis of peptide composition in a protein
                            sequence (P. Dessen)

    FASTEMBL.COM        (U) Script for using the EMBL Mail-Fasta server
                            (for GCG 7) (E. Sonnhammer)

    MALIGNED.UAA        (U) Multiple sequence editor, v1.64 (S. Clark)

    PRETTYBOX.TXT       (U) Pretty formatting of multiple sequence alignments,
                            v1.1 (R. Westerman)

    READSEQ.UAA         (U) Sequence format conversion program, Nov 1991
                            (D. Gilbert)

    SCRUTINE.UAA        (U) Protein database analysis program, Nov 1991
                            (P. Sibbald)

<4> Other updates
    ALIGN directory:

    DS8841 - alignment of epsilon globin gene sequences from 17 eutherian
             mammals, provided by Wendy Bailey and Morris Goodman, Wayne
             State University.

<5> Summary of directories on the file server

    Databases (* = new or updated since 25-Sep-91)

   *EMBL Nucleotide Sequence Database                              NUC
      (Rel. 29, Dec 91 + newest data from EMBL/GenBank/DDBJ)
   *Eukaryotic Promotor Database (Rel. 29, Nov 91)                 EPD
   *SwissProt Protein Sequence Database                            PROT
       (Rel. 20, Nov 91 + newest data)
   *Prosite pattern database (Rel. 8.0, Dec 91)                    PROSITE
   *ENZYME database (Rel. 7.00, Nov 91)                            ENZYME
   *Brookhaven Protein Structure Database (Rel. 58, Oct 91)        PROTEINDATA
   *REBASE, Restriction Enzyme Database (Rel. 9112, Dec 91)        REBASE
    tRNA sequence and gene sequence database (1991)                TRNA
   *TFD, Transcription Factor Database (Ver 4.0, Dec 91)           TFD
   *The E.coli Database (Rel. 9, Nov 91)                           ECD
   *Drosophila Genetic Map Database (9111, 10-Nov-91)              FLYBASE
    Listing of Molecular Biology Databases, LiMB (Rel. 2.0)        LIMB
   *Sequence analysis bibliography (SEQANALREF Rel. 22, Dec 91)    REFLIST
    Functional Analysis of Nucleotide Sequences bibliography       REFLIST
      (FANS_REF Rel. 3.4, Apr 91)
    Alu sequence database and alignment                            ALU
   *Haemophilia B database (Dec 91)                                HAEMB
   *Compilation of small RNA sequences (Oct 91)                    SMALLRNA


    Software for MS-DOS computers                                  DOS_SOFTWARE
    Software for Apple Macintosh                                   MAC_SOFTWARE
    Software for UNIX                                              UNIX_SOFTWARE
    Software for VAX/VMS                                           VAX_SOFTWARE
    Other software, GenBank Clearinghouse, etc.                    MISC_SOFTWARE


    Technical documents, submission and order forms, etc.          DOC
    Multiple DNA sequence alignments and consensus sequences       ALIGN
    Codon Usage tables                                             CODONUSAGE

<6> Getting Started ?
    The EMBL File Server is a facility available on the EMBL computing system
    for external users to request files by electronic mail. The service is free.
    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. No essays please.
    For human contact, send electronic mail to NetHelp at the address
    given above.

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