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Matthias Hage dok248 at GENIUS.EMBNET.DKFZ-HEIDELBERG.DE
Wed Oct 2 07:47:05 EST 1991


FASTA and Sequence Mail Server at the DKFZ

In September 1990 the DKFZ (German Cancer Research Centre in Heidelberg)
established GENIUSnet. GENIUSnet provides hardware and software infra-
structure for German scientists in the field of biocomputing.

Academic users have free of charge access not only to a wealth of
up-to-date databases e.g. all major DNA and protein sequence databases,
OMIM and recently GDB, but they can also use adequate sequence analysis
tools (e.g. GCG, Clustal, Fasta) as well as e-mail facilities. All
services can be accessed online over national networks and run on a
dedicated Convex C210 under the UNIX operating system.

Additionally, we provided two E-Mail server for database searching with
Fasta and downloading of protein and DNA sequence entries, for users who
have only poor online access to our system.

However these servers are NOT restricted to GENIUSnet users. Everybody
on the international nets is invited to take advantage of our server
facilities.

Like with all other e-mail server, you start by sending an e-mail with
all necessary information for your inquiry to a dedicated account on the
GENIUSnet computer and also receive the results as an e-mail. 



To use the sequence server write an e-mail to the following adress:

    netserv at genius.embnet.dkfz-heidelberg.de


You can use the following commands (always write the commands in the
mail BODY, do NOT use the subject line for stating any commands):

help
get nuc:seq.name     or     get prot:seq.name
get nuc:acc.no       or     get prot:acc.no

HELP returns information on how to use the sequence server.

GET returns the relevant sequence. After the ":" you can either state
the desired sequence by its sequence name (=databank entry name) or by
its accession number. 

For DNA/RNA sequences we scan the EMBL and GenBank databanks as well as
EmNew, which contains the latest EMBL entries (The DKFZ is the German
EMBnet node and therefore receives daily updates of the latest EMBL
databank entries). For Protein sequences Swissprot and NBRF/PIR are
scanned.


To use the Fasta server write an e-mail to the following adress:

    mfasta at genius.embnet.dkfz-heidelberg.de


Again several commands are available, choose:

help

in the mail body (not in the subject line) to start. You will then
receive a detailed description of the available other commands, as well
as an explanation of the output.


If you are only interested in picking up the latest EMBL databank
entries, you can also run an anonymous ftp session on our system:

ftp genius.embnet.dkfz-heidelberg.de    (ftp 192.54.49.66)
login as: anonymous
password: your user-id

change to the directory: cd pub/embnet
In pub/embnet you will find all EMBL DNA sequence entries which were
published since the shipping of the latest EMBL databank release
(because the directory pub/embnet contains quite a few entries, we
disabled the general ls (list) command as well as the usage of ls with
wildcards, however you can use ls with ls "seqname").

Or change to the directory: pub/embnet/new 
to get only the very latest EMBL databank entries. Each day, the content
of this directory is erased and only the newly arrived sequences are
placed in it (ls is completely functional in this directory).

In both directories we keep a file called "acc_numb.lis" which contains
a sorted list of all accession numbers and the corresponding sequence
names.

Please feel free to send comments or further inquiries about GENIUSnet, 
the e-mail server or ftp to my e-mail adress.

Matthias Hage
GENIUSnet Manager


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  Matthias Hage                            DKFZ, Molekulare Biophysik 
  Phone: +49-6221-422372                   Im Neuenheimer Feld 280    
  FAX:   +49-6221-401271                   D-6900 Heidelberg, Germany 
                                                                     
  Internet:   dok248 at genius.embnet.dkfz-heidelberg.de                 
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