From: doelz@comp.bioz.unibas.ch (Reinhard Doelz)
Newsgroups: bionet.software
Subject: Re: embl/gopher
Date: 30 Aug 92 07:04:29 GMT
Reply-To: doelz@urz.unibas.ch
Distribution: bionet
Organization: EMBnet Switzerland [BASEL]

In article <9208281632.AA01723@labsun1.med.uottawa.ca>, baird@LABSUN1.MED.UOTTAWA.CA (stephen baird) writes:
|>     Does anybody know a gopher hole that one can search and retrieve
|> sequences from the EMBL database like the great IUBIO gopher hole?	


Name=BIOFTP EMBnet Switzerland
Type=1
Port=70
Path=1/EMBNet BioInformation Resource Switzerland/
Host=bioftp.unibas.ch    

                   EMBNet BioInformation Resource Switzerland

      1.  About EMBnet/
 -->  2.  Database/
      3.  Hints/
      4.  Info on this EMBNet Information Resource.
      5.  Other EMBnet Hosts/
      6.  Software/

                                    Database

 -->  1.  EMBL CD-ROM release/
      2.  ENZYME database/
      3.  GENBANK sequence archive in Indiana (USA)/
      4.  NEW since last EMBL release/
      5.  PIR International sequences in Houston (USA) /
      6.  PROSITE dictionary/
      7.  SWISS-PROT CD-ROM release/
      8.  UPDATES since last EMBL release/


The setup is somewhat different from Don Gilbert's gopher hole. First, 
I keep TWO different subsets of EMBL updates. One which is containing 
all NEW sequences (hence, obviously, item (4) on the list), and 
then all entries which have been there before but got changed for 
one or the other reason (item 8). The NEW sequences are called XEMBL, 
and the updates are called XXEMBL. Therefore, if you select item (1), 
you see 

 -->  1.  Simultaneous search in all XXEMBL XEMBL EMBL sections  <?>
      2.  search for a key word in FUN section                   <?>
      3.  search for a key word in INV section                   <?>
      4.  search for a key word in MAM section                   <?>
      5.  search for a key word in ORG section                   <?>
      6.  search for a key word in PHG section                   <?>
      7.  search for a key word in PLN section                   <?>
... 
and all the other EMBL sublibraries. This way, the search can take a bit 
longer, because you in fact initiate 15 gopher searches simultaneously on 
the Indigo (which is mostly running at load 2 anyhow). 'Long' means about 
20 seconds if you search for something which is quite abundant. However, 
as you may know, WAIS type full-text searches are not quite exhaustive, 
and frequently give some trouble if you look for trivial words (e.g., 
'protein'). 
I have not strictly limited the number of answers, therefore you get 
up to 60 pages of results. 

Regards 
Reinhard 


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                   EMBNet BioInformation Resource Switzerland

      1.  About EMBnet/
      2.  Database/
      3.  Hints/
      4.  Info on this EMBNet Information Resource.
 -->  5.  Other EMBnet Hosts/
      6.  Software/

      1.  List of all EMBnet nodes.
      2.  Node Detailed Info/
      3.  more GOPHERs (biological and others)/
 -->  4.  national_EMBnet_hosts/
      5.  non-national_EMBnet_hosts/


      1.  Belgium.
      2.  Denmark.
      3.  Finland.
      4.  France.
      5.  Germany.
      6.  Greece.
      7.  Israel.
      8.  Italy.
      9.  Netherlands.
      10. Norway.
      11. Spain.
      12. Sweden.
 -->  13. Switzerland.
      14. UK.


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