ANNOUNCING SRS release 3.1

etzold at embl-heidelberg.de etzold at embl-heidelberg.de
Wed Sep 8 09:31:22 EST 1993


 
ANNOUNCEMENT
 
  Release 3.1 of SRS (Sequence Retrieval System) is now available to anyone
  inside the academic scientific community free of charge. Commercial
  organizations should contact the author (for addresses and contact please see
  the CONTACT section of this document).


 DESCRIPTION

  Most of our knowledge about proteins and genes is presently stored in a
  variety of libraries with mostly flat file format where simple ASCII files
  contain entries in sequential order. The entry structure of varying complexity
  is divided into individual data fields which can be of free text format or
  more often contain specialized information such as keywords or authors. The
  entries of many of these libraries provide by various mechanisms
  cross-references to those of other libraries. 

  SRS (Sequence Retrieval System) is an information indexing and retrieval
  system designed for libraries with a flat file format. SRS supports the data
  structure of these libraries by providing special indices for, eg,
  implementing lists of subentities (e.g. feature tables). Indexing of
  cross-references allows a complete network of libraries to be built. In the
  network an entry from one library can be linked to every other library either
  directly or with a succession of single links between neighboring,
  cross-referenced, libraries. 

  A language ODD (Object, Design and Definition) has been designed and developed
  to structure and define the data to cope with different library formats
  subject to continuous change. Two levels of ODD programming allow for
  defining data structures and the data themselves. An ODD compiler makes the
  data available for the C programs that retrieve or build indices. A flexible 
  parser, programmed by an extended version of Backus-Naur format, has been
  developed for the extraction of keywords from data-fields. Both the ODD
  language and the programmable  parser are required by SRS since all integrated
  libraries are left in their native state and original  formats. 


 DISTRIBUTION

  ------------------------------------------------------------------
  VAX/VMS & OpenVMS
 
  1.   anonymous ftp (binary mode) to ftp.embl-heidelberg.de

       directory: /pub/software/vax/srs   files: srs3_1.bck

  Important!!! since the VMS backup will be corrupted after the transfer get
  the file "relnotes3_1.doc" with instructions for reformatting the backup
  file.


  2.   anonymous (binary mode) ftp to biomed.uio.no

       directory: disk_1:[aftp]       files: srs3_1.bck

       Additional files:
       fixrec.c    C source to produce fixrec.exe which fixes
                   the record length of the save set if you have
  	           any problems.

       fixrec.com DCL script that does the same as the above.  


  -----------------------------------------------------------------

  U**X

  1. anonymous (binary mode) ftp to ftp.embl-heidelberg.de

     directory: /pub/software/unix/srs   files: srs3_1.tar.Z

  2. gopher to gopher.embl-heidelberg.de port 70
     same directory as above
 
  3. gopher to Norwegian EMBnet node (biomaster.uio.no) port 70

     % gopher biomaster.uio.no 70
 
     Name=EMBnet: Norway Biotechnology Centre of Oslo (BIOMASTER) 
     Type=1
     Port=70 
     Path=1/ 
     Host=biomaster.uio.no
 
     Follow these menu items:
 
      1. About the Norwegian EMBnet node
      9. SRS is here
      1. srs3_1.tar.Z
 
   Also, the UNIX distribution will be available via anonymous ftp from
   nic.switch.ch presumably in the directory /mirror/embnet-ch/software
  -----------------------------------------------------------------------

 
  Note that the UNIX and the VMS releases are equivalent!
 
  
 RELEASE NOTES
 
  The Unix port has the same user interface as the VMS version and the same
  functionality, but is lacking the online help.
 
  Release 3.1 remains compatible with indices built with older releases.
  Indices cannot yet be shared amongst different operating systems (exeptions:
  VMS-OpenVMS, IRIX-SunOS-Solaris)
 
 In the distribution of SRS 3.1 the following database are supported:
  
   Databank name             format supported           where to get it from
  
   SWISSPROT (1)                   GCG                        EMBL
   PIR (1)                         native                     MIPS
   EMBL(1)                         GCG                        EMBL
   GENBANK (1)                     GCG                        NCBI
   NRL3D (1)                       native                     MIPS
   PDB (1)                         native                     EMBL
   HSSP (1)                        native                     EMBL
   PROSITE (1)                     native                     EMBL
   PROSITEDOC (1)                  native                     EMBL
   BLOCKS (1)                      native		      NCBI
   EPD (1)                         native		      NCBI
   ECD (1)                         native                     EMBL
   OMIM (1)                        native                     Welch Lab
   MIMMAP (1)                      EMBL	    	              EMBL
   ENZYME (1)                      native                     EMBL
   REBASE (1)                      native                     EMBL
   CPGISLE (1)                     EMBL 		      EMBL
   SEQANALREF (2)                  EMBL                       EMBL
   SEQANALRABS (2)                
   LIT                             native                     EMBL
   LITT                            EMBL                       expasy.chuge.ch
   NAKAI                           GCG                        GCG
   LIMB                            native                     EMBL
   FASTA (1)                       GCG
   BLAST (1)                       native
   PROFILE (1)                     GCG
  
 
  SRS indexes the libraries in the native format - reformatting is NOT required.
  All indices for a library need typically 20% of the size of the library 
  itself.
  
  Indexed are fields such as "Definition", "Title", "Authors", "Reference",
  "Accession"; note that the feature tables in the sequence libraries are 
  indexed in a way that a search on that index retrieves not the complete entry 
  but ONLY the feature (eg, intron, transmembrane helix). The sequence of 
  retrieved features can be extracted if the feature is only defined by begin 
  and end position; more complicated "locations" as found in EMBL and GenBank
  (join, reverse...) will be supported by the next release. 
  
  SRS allows indexing of crossreferences and thus the construction of a 
  library network; all libraries listed above marked with "(1)" are part
  of that network - any entry or set of these from one library can be linked
  to any other library within the network (provided a link exists); multistep
  links (eg, PDB->EMBL) are resolved automatically into a succession of 
  single links (eg, PDB->SwissProt->EMBL). All links are bidirectional.
  The databanks Seqanalref and Seqanalrabs (abstracts of articles listed in
  Seqanalref) marked with "(2)" are linked in a separate network. 
  
  Output files from Fasta, Blast, Profilesearch can be converted to
  indexable library and linked to the sequence libraries; This allows
  navigating from reported homologies to the sequence library searched and to 
  all other libraries marked "(1)" such as Prosite, Hssp, PDB... This facility 
  is still in a somewhat experimental stage and will be improved soon.
  
  SRS is well adapted to the GCG package (writes sequences with CGC format,
  reads and writes the FOSN format) but can also used in other environments 
  since it supports the PIR sequence format as well (others will be added).
  
  Two new commands make the maintenance of SRS quite simple:
    srscheck: checks all indices and writes a shell script with all commands
              needed for updating the system
    srsupdate: executes that shell-script (or DCL file)
  
  SRS is flexible since all interior information is programmed in a special 
  purpose information definition language (ODD - Object Definition and Design) 
  Formats can be changed or libraries added without recompilation of the 
  C-code. A Maintenance manual describes in detail the use of that language.
  
  
 REFERENCES
  
     Etzold T. and Argos P., SRS - an indexing and retrieval tool for flat 
     file data libraries. Comput. Appl. Biosci. 9:49-57(1993).
  
     Etzold T. and Argos P., Transforming a set of biological flat file 
     libraries to a fast access network. Comput. Appl. Biosci. 9:59-64(1993).
  


 ACKNOWLEDGEMENTS
  
  The U**X port of the SRS was made possible thanks to the collaboration
  and hard work of Lukas Rosenthaler and Reinhard Doelz from the Swiss
  EMBnet node.


 CONTACTS

  Thure Etzold      etzold at embl-heidelberg.de, Tel: 0049-6221-387529
  Rodrigo Lopez     rodrigol at biotek.uio.no,    Tel: 0047-22958756     
  Reinhard Doelz    doelz at urz.unibas.ch



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