Generic Protein Sequence

Reinhard Doelz doelz at comp.bioz.unibas.ch
Fri Mar 4 03:06:09 EST 1994


In article <71476.ewright at fox.nstn.ns.ca>, ewright at FOX.NSTN.NS.CA ("Edwin Wright") writes:
|> Is it possible to construct a generic protein sequence from the existing
|> protein database?
As the codon table is ambiguous, you will end up in several possibilities.
Most protein database entriues have a crosslink to EMBL or GENBANK. 
You might want to us SRS (Sequence Retrieval System) from Thure Etzold
for this purpose. We are collaborating with Thure and a _preliminary_
version of the GOPHER gateway to SRS is currently in the test phase. 
This gateway is capable of mapping data entries into other databases.
The result is printed in GCG format (GCG Inc, commercial software). 

If you have Access to GOPHER, you might try the following. 

>>>> NOTE <<<<
The following is DEVELOPMENTAL, and there is NO GUARANTEE that this interface
will stay at the same links, location, or format. 

      1.  About Gopher, and this bioftp site/
      2.  Biology subject tree in Gopher/
      3.  DIBUG [Discover Insight Biosym User Group] Mailing list/
 -->  4.  EMBNet BioInformation Resource Switzerland/
      5.  GCG Software Manual/
      6.  Infoservers in European Countries/
      7.  and if you have suggestions or problems....  [ 7Jan94, 1kb].
      8.  development site of GOPHER (U Minnesota)/
      9.  selected USENET News/

      1.  About EMBnet/
 -->  2.  Database/
      3.  Hints/
      4.  Info on this EMBNet Information Resource  [ 7Jan94, 4kb].
      5.  Other EMBnet Hosts and Sources of Information/
      6.  Software/

      1.  About these searches  [18Jan94, 1kb].
      2.  EMBL/
      3.  EMBL updates/
 -->  4.  Experimental/
      5.  FLYBASE /
      6.  GENBANK (Indiana)/
      7.  More DNA searches/
      8.  Protein databases (NIH)/
      9.  general database searches (HOPKINS)/

 -->  1.  Experimental SRS gateway/

 -->  1.  Start to compost query on gopher.embnet.unibas.ch/
      2.  Expert mode: Query directly getz at gopher.embnet.unibas.ch <?>

      1.  Use EMBL (+updates)/
 -->  2.  Use SWISSPROT /
      3.  Use PIR International/
      4.  Use NRL_3D (Xray structure sequences)/
      5.  Use PROSITE /
      6.  Use PROSITEDOC /
      7.  Use BLOCKS /

 -->  1.  Search ID in SWISSPROT/
      2.  Search Definition in SWISSPROT/
      3.  Search Accession Number in SWISSPROT/
      4.  Search Author in SWISSPROT/
      5.  Search Reference in SWISSPROT/
      6.  Search Title in SWISSPROT/
      7.  Search Keyword in SWISSPROT/
      8.  Search Feature in SWISSPROT/

      1.  Report directly from ID in SWISSPROT <?>
      2.  Report MEDLINE entry from ID in SWISSPROT <?>
 -->  3.  Report EMBL entry from ID in SWISSPROT <?>
      4.  Report PIR International entry from ID in SWISSPROT <?>
      5.  Report NRL3D entry from ID in SWISSPROT <?>
      6.  Report PROSITE entry from ID in SWISSPROT <?>
      7.  Report PROSITEDOC entry from ID in SWISSPROT <?>
      8.  Report BLOCKS entry from ID in SWISSPROT <?>


 lqqqqqqqqqqqqqqqqqqqReport EMBL entry from ID in SWISSPROTqqqqqqqqqqqqqqqqqqqk
 x                                                                            x
 x Words to search for  calm_human                                            x
 x                                                                            x
 x                                       [Cancel ^G] [Accept - Enter]         x
 x                                                                            x
 mqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqj


 -->  1.  Query result overview.
      2.  File of Sequence Names .
      3.   embl:GGCALMA .
      4.   embl:GGCAM .
      5.   embl:GGCAM1 .
      6.   embl:GGCAM2 .
      7.   embl:GGCAM3 .
      8.   embl:GGCAM4 .
      9.   embl:GGCAM5 .
      10.  embl:GGCAM6 .
      11.  embl:HSCAM .
      12.  embl:HSCAMA .
      13.  embl:RNCAM .
      14.  embl:RNCAMA .
      15.  embl:RNCAMI1 .
      16.  embl:RNCAMI2 .
      17.  embl:RNCAMI3 .
      18.  embl:RNCAMII3 .
      19.  embl:RNCAMIII .
      20.  embl:RNRCM1 .
      21.  embl:XLCAMA .
      22.  embl:XLCAMB .
      23. This search produced  20 hits.


and the result is, 

  report of query "Q1 = [SWISSPROT-ID:calm_human*]>EMBL"

////////////////////////////////////////////////////////////////////////////////
        ...searching "CALM_HUMAN*"
      CALM_HUMAN                                                   1 entries
    library "swissprot": found 1 entries
  found "CALM_HUMAN*" in 1 entries
  
retrieved 1 entries from index "id"
Mapped to "embl" -> 20 entries

//////////////////////////////////////////////////////////////////////////////// 
  set "Q1" has 20 entries of type "Seq-ID"
  time of query:  4-Mar-1994  

....

Maybe this helps.

Regards
Reinhard 



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clude that other  software products cannot possibly do a similar job. 




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