Sequence databases questions

Reinhard Doelz doelz at comp.bioz.unibas.ch
Sat Apr 25 02:56:00 EST 1992


In article <9204250316.AA23537 at ccwf.cc.utexas.edu>, timmer at CCWF.CC.UTEXAS.EDU (Richard T. Timmer) writes:
|>      4.  I suppose this is an extension of #2, or perhaps more
|> exactly what I was trying to ask initially.  I was curious as 
|> to the types of genetic/protein databases are accessible via 
|> Internet (FTP or Gopher) and the nature of the access (or 
|> database search services) available.
|> 

bioftp.unibas.ch holds many biological databases, and the main ones 
are accessible via GOPHER as well. gopher binaries are stored as well. 
The current release of EMBL (rel. 30), Swissprot (rel. 21) and more 
are provided as delivered in the CD ROM of EMBL. Further, Dr.Amos 
Bairoch provides a huge collection of small databases on this server by 
maintaining it remotely on the network. Recent additions include the 
yeast chromosome III sequences (DNA) in biology/EMBnet/brand_new and 
(protein) in biology/database/yeast. 

Maybe this helps. 
Regards 
Reinhard 

               Setup of the Server bioftp.unibas.ch
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                                    ~/
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               biology                                   programs 
   +-------------+-----------+------------+            source code
   |                         |            |             uu and zoo
  cd                        EMBnet     database        QUERY system
The last EMBL CD-ROM         |            | 
(resource permitting         |            +------------------------+
- drive used elsewhere)      |                                     |
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         +---------+-----------+--------------------+              |
         |         |           |                    |              |
Xembl_flat    database     Xembl_form             Xembl            |
         |         |           |                    |              |
    The current    |        The current             |              |
Xembl and XXembl   |   Xembl and XXembl             |              |
database in EMBL   |   database in PIR              |              |
flat file format   |   format (also GCG)            |              |
                   |                                |              |
    +-------+------+-+          +--------------+----+------+       |
    |       |        |          |              |           |       |
   embl    pir     swissprot  data.dir    indices.dir   (others)   |
    |       |        |          |              |           |       |
Current databases in PIR        |     indices of current scratch   |
format (also GCG suited)        |     Xembl and XXembl   files     |
                                |     database in EMBL  not needed |
                                |     format                       |  
+----+----+----+----+----+----+-+--+----+----+----+----+----+      |   
fun  inv  mam  org  phg  pln  pri  pro  rod  syn  una vrl vrt      |
Entries in EMBL format, *ONE PER FILE*. The files are named        |
using the entry code as file name. NEW in the next release;        | 
extension 'dat', update to existing release, extension 'upd'.      |
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++++++----+++++++--------++++++------------------------------------+
||||||    |||||||        ||||||                 
|||||5srna||||||gcg_codon|||||prosite          These databases are
||||aaid  |||||haemb     ||||resenzym          maintained,updated,
|||alu    ||||limb       |||smallrna           but not entirely 
||ecd     |||ngdd        ||tfd                 produced by 
|enzyme   ||pkinases     |trna                 Dr. A. Bairoch, 
epd       |+------info   references            Department of 
          fly     |      +++                   Medical Biochemistry,
+++++-----+      ++      |||                   University of Geneva,
||||news         ||      ||fans_ref            Geneva, Switzerland. 
|||clones        ||      |journals_toc         bairoch at cmu.unige.ch
||cytofeat       ||      seqanalref
|flybase         |articles
stocks           various


-- 
+----------------------------------+-------------------------------------+
|    Dr. Reinhard Doelz            | RFC     doelz at urz.unibas.ch         |
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