EMBL File Server News, No. 5, June 26th 1991

Wed Jun 26 11:57:00 EST 1991

|  EMBL FILE SERVER News                            Number 5, June 26th 1991 |
|                                                                            |
|  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 contents of file server
<6> Getting started ?

<1> Introduction
    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

    tRNA -    We have added a compilation of tRNA sequences from Mathias
              Sprinzl at the University of Bayreuth, Germany. The database
              files are located in the file server directory TRNA.

              Sprinzl M., Dank N., Nock S., Schon A. (1991)
              Nucl. Acids Res. 19, Supplement, 2127-.

    PROTEINDATA - A database of homology-derived protein secondary structures
                  (HSSP) has been added, supplied by Chris Sander and
                  Reinhard Schneider (Protein Design Group, EMBL). The database
                  is a merger of 3-D structure information from the Protein
                  Data Bank (PDB) and sequence information from SwissProt
                  (see Proteins 9, 56-68 (1991)).
                  There is one file for each PDB protein containing
                  all protein sequences deemed homologous to this protein,
                  in the form of multiple sequence alignments.
                  Example: get PROTEINDATA:1PPT.HSSP (for pancreatic polypeptide

                  The DSSP database of secondary structures has been extended
                  by extracting secondary structure assignments for
                  28 proteins for which only C(alpha) coordinates have been
                  deposited. This was done with the aid of a model building proc
                  that adds backbone coordinates to a  C(alpha) trace (L.Holm
                  and C.Sander, J.Mol.Biol. 218, 183-194 (1991)).
                  Example:  get  PROTEINDATA:3p21.dssp_ca (for p21 ras)

                  Use DIR PROTEINDATA command to get for more information
                  about PDB, DSSP and HSSP-related data files and programs.

    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):


    PROGRAPH.UAA        (N) Protein sequence analysis package (K. Hoffmann)

    CUTCOST.UAA         (U) Program to determine the cheapest source for
                            restriction enzymes v2.31 (C.G. Meinhof)


    Plota protein sequence analysis package (A. Luttke, P. Markiewicz) (N)
    PLOTA_AADATA.HQX        Sequence editor
    PLOTA_DOT.HQX           Dot matrix comparison
    PLOTA_GGR.HQX           Secondary structure prediction
    PLOTA_GOR.HQX           Secondary structure prediction
    PLOTA_HEL.HQX           Helical wheel
    PLOTA_HYD.HQX           Hydropathy analysis
    PLOTA_HYD5.HQX          Hydropathy analysis (averaging)
    PLOTA_KAS.HQX           Chain flexibility and antigenicity
    PLOTA_KKD.HQX           Prediction of membrane spanning regions
    PLOTA_POW.HQX           Power spectrum plot
    PLOTA_SIG.HQX           Signal peptide prediction
    PLOTA_SIM.HQX           Dissimilarity plot
    PLOTA_TMH.HQX           Hydrophobic moment analysis

    DBCONV.HQX          (N) Tool for reformatting "line-type" databases to
                            tab-delimited format (J.R. Valverde)

    EMBL-SEARCH.HQX     (N) Simple database retrieval program demonstrating
                            the use of the EMBL CD-ROM indices (R. Fuchs)

    SEQSPEAK.HQX        (N) Sequence data entry with acoustic feedback
                            (K. Conover)

    TRNA-SEARCH.HQX     (N) Identification of tRNA genes and plotting of RNA
                            structure (R.D. Shortridge)

    DNATRANSLATOR.HQX   (U) Version 0.99.1 of the phylogenetic analysis
                            HyperCard stack (D.J. Eernisse)

    MACMOLECULE.HQX     (U) 3D models of biomolecules v1.5 (E. Myers et al.)

    MACPATTERN.HQX      (U) Protein pattern searching with Prosite, v1.2.5
                            (R. Fuchs)

    MACTARGSEARCH.HQX   (U) Program to search DNA sequences with sequence
                            profiles v2.0 (J.A. Goodrich, W.R. McClure,
                            M.L. Schwartz)


    HOMOCHART.UUE       (N) Nice plotting of multiple alignments (R. Smith)

    OVERSEER.UUE        (N) Nucleic acid sequence database analysis package
                            (P. Sibbald)


    BOXSHADE.UUE        (N) Nice plotting of multiple aligments (K. Hoffmann)

    DBCONV.HQX          (N) Tool for reformatting "line-type" databases to
                            tab-delimited format (J.R. Valverde)

    OVERSEER.UUE        (N) Nucleic acid sequence database analysis package
                            (P. Sibbald)

    SCRUTINE.UAA        (U) Scrutineer protein sequence database analysis
                            package, version May 1991 (P. Sibbald)

<4> Other updates

    DOC        - BIOSCI.DOC      April 1991 version of the BIOSCI
                                 bulletin-board description.
               - ORDERFORM.TXT   EMBL Data Library subscription form 1991/2
               - ORDERINFO.TXT   EMBL Data Library subscription information
                                 for 1991/2
               - CDROM_INDEX.HQX Description of binary indices provided on
                                 current EMBL CD-ROMs for access to sequence
                                 database files. This is a Macintosh MS Word 4.0
                                 document compressed and converted to ascii by
    ALIGN      - DS6900.UUE      Alignment of pseudoeta-globin genes and
                                 surrounding sequences from primates and goat.
                                 by W. Bailey, Wayne State Univ, Detroit.

<5> Summary of Directories of the EMBL File Server

    Databases (* = new or updated):

*   EMBL Nucleotide Sequence Database                              NUC
      (Rel. 27, May 91 + new data from EMBL/GenBank/DDBJ)
*   Eukaryotic Promotor Database (Rel. 27, May 91)                 EPD
*   SwissProt Protein Database (Rel. 18, May 91)                   PROT
*   Prosite pattern database (Rel. 7.00, May 91)                   PROSITE
*   ENZYME database (Rel. 5, May 91)                               ENZYME
    Brookhaven Protein Structure Database (Rel. 54, Nov 90)        PROTEINDATA
*   REBASE, Restriction Enzyme Database (Rel. 9106, Jun 91)        REBASE
*   tRNA sequence and gene sequence database (1991)                TRNA
*   TFD, Transcription Factor Database (Ver 3.0, Jun 91)           TFD
*   The E.coli Database (Rel. 7, May 91)                           ECD
    Drosophila Genetic Map Database (Rel. 9012, Dec 90)            DROSOPHILA
    Listing of Molecular Biology Databases, LiMB (Rel. 2.0)        LIMB
*   Sequence analysis bibliography (SEQANALREF Rel. 17, Jun 91)    REFLIST
*   Functional Analysis of Nucleotide Sequences bibliography       REFLIST
      (FANS_REF Rel. 3.4, Apr 91)
    Alu sequence database and alignment                            ALU


    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(es)
    given above.

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