kristoff@NET.BIO.NET (Dave Kristofferson) (11/19/89)
Dear GenBank Database Users:
Below is an example of how to FTP the weekly data update files from
the GenBank On-line Service computer, genbank.bio.net. Note that
these update files are typically 1 - 4 megabytes in size, so you may
want to use the On-line Service mail server if you only need access to
individual entries. Instructions for using the server can be obtained
by sending a message containing the word HELP (leave the Subject line
blank) to the address retrieve@genbank.bio.net.
If you have any questions, please send e-mail to
consultant@genbank.bio.net. I was out of town part of last week and
will be away through November 28th, so questions directed to me will
not be addressed until after I get back.
Sincerely,
Dave Kristofferson
GenBank On-line Service Manager
kristoff@net.bio.net
----------------------------------------------------------------------
Example of FTPing new weekly data updates from GenBank
(last update 11/18/89 - D.K.)
**********************************************************************
In the following example NET<n> is the Unix prompt on the computer
used for this example. Your computer's system prompt will be
different. Details of the ftp protocol may also be different on your
local computer; so please consult your local systems manager if the
following commands are not recognized on your local computer.
Comments in the example below are set off by ***'s as here or by ;'s
at the end of a line. Input is underlined and <cr> means press the
return key. NOTE that our UNIX system is CASE-SENSITIVE. Use lower
case input unless specifically noted otherwise below.
**********************************************************************
NET<1>ftp genbank.bio.net<cr> ;FTP to the computer genbank.bio.net
-----------------------
Connected to genbank.bio.net.
220 GENBANK.BIO.NET FTP server (SunOS 4.0) ready.
Name (genbank.bio.net:kristoff): anonymous<cr> ;use name "anonymous"
-------------
331 Guest login ok, send ident as password.
Password: <cr> ;use your user name as a
------------ ;password, e.g., kristoff
;in my case.
230 Guest login ok, access restrictions apply.
ftp> ls<cr> ;list the directory contents
------
200 PORT command successful.
150 ASCII data connection for /bin/ls (134.172.3.252,2591).
.hushlogin
Public
bin
dev
etc
lib
pub
usr
226 ASCII Transfer complete.
50 bytes received in .68 seconds (0.072 Kbytes/s)
**********************************************************************
The GenBank new data is actually kept a few subdirectories down under
pub/db/gb-newdata. EMBL new data is under pub/db/embl-newdata. For
the sake of brevity we simply change directly to the pub/db directory.
**********************************************************************
ftp> cd /pub/db<cr>
--------------
250 CWD command successful.
ftp> ls<cr> ;show GenBank and EMBL subdirectories
------
200 PORT command successful.
150 ASCII data connection for /bin/ls (134.172.3.252,2592).
alu
embl-newdata
gb-newdata
readme.doc
seqanalref
226 ASCII Transfer complete.
55 bytes received in .16 seconds (.34 Kbytes/s)
**********************************************************************
Finally we change into the GenBank new data subdirectory. The above
steps could have been omitted and one could simply use "cd
pub/db/gb-newdata" to switch to this directory after logging in. The
ls command below shows the names of the new data files. Note that the
file names all start with "gb" for GenBank followed by the month and
the day for the file in question (each file contains the previous
week's data), and finally an extension of .seq is used to indicate
that the file contains nucleic acid sequence data. A similar
file naming convention is used for EMBL data as can be seen by using
the ls command in the directory pub/db/embl-newdata.
**********************************************************************
ftp> cd gb-newdata<cr>
-----------------
250 CWD command successful.
ftp> ls<cr>
------
200 PORT command successful.
150 ASCII data connection for /bin/ls (134.172.3.252,2593).
gb1030.seq
gb1106.seq
gb1113.seq
226 ASCII Transfer complete.
36 bytes received in .16 seconds (.22 Kbytes/s)
**********************************************************************
Next use the "get" command to retrieve the desired file. These files
are anywhere from 1 - 4 Megabytes. Transfer time will be limited most
likely by the speed of your local Internet connection. The GenBank
connection runs at 1.54 Mbps so it will not be the rate limiting step
in most cases. The "get" command retrieves the file over the Internet
into your directory on your local computer.
**********************************************************************
ftp> get gb1106.seq<cr> ;get data for week ending Nov. 11th.
------------------
200 PORT command successful.
150 ASCII data connection for gb1106.seq (134.172.3.252,2595) (1510609 bytes).
226 ASCII Transfer complete.
local: gb1106.seq remote: gb1106.seq
1535022 bytes received in 19 seconds (80 Kbytes/s)
**********************************************************************
After the first transfer is complete you can retrieve other files or
use the "bye" or "quit" command to end the session.
**********************************************************************
ftp> bye<cr>
-------
221 Goodbye.