geoffk@usage.csd.unsw.oz.au (Geoff Kornfeld) (04/17/91)
Is fileserv%gunbrf still operational? I've sent several requests for searches there but I've had no replies. Alternatively, is there another site that has the same facility (search through GenBank,EMBL,PIR databases for keyword matches (rather than sequence,accesion no, or locus matches) )? Thanks in advance, Geoff Kornfeld
kristoff@genbank.bio.net (David Kristofferson) (04/18/91)
Regarding keyword searches, these can be done on the free GenBank
On-line Service (GOS) irx account which is described in the following
information.
Sincerely,
Dave Kristofferson
GenBank Manager
kristoff@genbank.bio.net
----------------------------------------------------------------------
The GenBank On-Line Service
The GenBank On-Line Service (GOS) provides access to the most recent
quarterly releases of the GenBank and EMBL nucleic acid sequence databases,
as well as the data added to each of these since their most recent releases
(in the New Data databases). In addition, the Swiss-Prot protein sequence
database and GenPept, a database of peptide sequences derived by the
automatic translation of annotated coding regions of entries in the
GenBank databases, are available. Users can query the databases by
annotation keywords, search for sequence similiarity, and retrieve entries
of interest. The GOS is available through e-mail servers, anonymous FTP,
anonymous interactive login, and login to established, password-protected,
individual accounts. Access to all GOS services is available to both
commercial and non-commercial users at the same cost. On-line help is
available for all aspects of this Service. User manuals, information
on costs, and application forms may be requested from GenBank at
GENBANK@GENBANK.BIO.NET.
INTERACTIVE ACCESS
Interactive access to the GOS databases is provided through the SprintNet
public data network and via remote login over the Internet. At present,
the IRX (Information Retrieval Experimental Workbench) program is the
primary interactive database retrieval program. Three usage classes are
available for the GOS; these classes are described below.
Class 0 Accounts
Anonymous users of the interactive system are provided with 20 minute
sessions using the IRX retrieval program. With this program, entries
in any of the on-line databases can be located by searching for a
keyword or combination of keywords appearing in any of the fields of
the entries' annotations. Located entries can be displayed on the
terminal or downloaded to the user's computer with the Kermit
file-transfer program. (The Kermit program is available for a wide
variety of computers from numerous software bulletin boards, user
groups, and from Columbia University. MS-DOS and Macintosh versions
are available from GenBank on request.) New users of the IRX program
should read the on-line introduction which can be displayed by
answering 'Y' to the first question the program asks ("Do you want
help?").
To use the GOS Class 0 account, one must have a supported terminal or
a computer with software for emulating one of those terminals (see the
list in the Example at the end of this message) and a modem capable of
communicating at 300, 1200, 2400, or 9600 baud. Instructions for
dialing to access the GenBank computer are shown in the example below.
After completing the login procedure shown in the example, the IRX
database query program is immediately started.
Class 1 Accounts
To gain access to additional services, users of the GOS may wish to
establish accounts on the GOS computer. These accounts provide access
to the GOS computer, 1 Mbyte of disk space for user files, access to
IRX, the GenBank relational database management system, and
interactive and batch mode use of FASTA and TFASTA (a version of FASTA
that compares a peptide sequence with a nucleic acid sequence database
by translating the database sequences in up to six reading frames "on
the fly"). Class 1 accounts also provide electronic mail access for
contacting other users of the GOS and users of computers connected to
the Internet and other computer networks. Access to a wide variety of
electronic bulletin boards is also provided. Newsgroups that may be
of special interest are the bionet.journals.contents newsgroup which
provides on-line versions of the tables of contents of several
important journals before publication and bionet.sci-resources which
provides on-line copies of the NIH Guides to Grants and Contracts.
Several other newsgroups are available for exchange of information on
experimental protocols and other areas of scientific interest.
Class 2 Accounts
For an additional fee, Class 2 users are provided with access to the
IntelliGenetics Suite of sequence analysis programs and databases
formatted for those programs. Additional databases (e.g., the PIR Protein
Sequence Database, KeyBank(TM), and VectorBank(TM)) are also available to
Class 2 users. Class 2 users also have access to all the facilities
available to Class 1 users.
E-MAIL SERVERS
In addition to providing interactive access, GenBank currently offers two
electronic mail servers, one for sequence similarity searching and one for
database entry retrieval. These are freely available to anyone who can
send mail to an Internet address. The following networks have gateways to
the Internet: BITNET, EARN, NETNORTH and JANET. Users of computers on
these networks may need to change the format of the addresses given below
to send the message through a forwarding gateway. Users should consult
their computer system managers or administrators to determine the proper
forwarding gateway and address form. Questions regarding the use of the
e-mail servers (or other aspects of the GOS) may be addressed to:
CONSULTANT@GENBANK.BIO.NET.
FASTA Server
The GenBank FASTA Server receives mail messages containing a nucleic acid
or protein query sequence with instructions for the search. The server
then performs a FASTA sequence similarity search against the specified
database, and returns the results by electronic mail.
To use the FASTA Server, send an electronic mail message containing the
formatted query sequence to the following Internet address:
SEARCH@GENBANK.BIO.NET. To receive instructions for formatting the query
sequence, send a mail message to this address containing the word "Help"
as the only line of the message.
Entry Server
E-mail access to sequence database entries is provided for three reasons:
1) to enable users of the FASTA Server to retrieve entries identified by
sequence similarity searches; 2) to enable users of the Class 0
interactive system described above, who access it by network remote login
(e.g., telnet) to retrieve copies of entries of interest; and 3) to enable
readers of journals that identify published sequences by accession number
to retrieve computer-readable versions of those sequences. To retrieve a
database entry, send a mail message containing only the entry name or the
accession number (not both) to the address: RETRIEVE@GENBANK.BIO.NET. The
on-line databases are searched and the entry (if any) which corresponds to
the supplied entry name or accession number will be returned by electronic
mail. To receive instructions on using the Entry Server, send a mail
message to the RETRIEVE address (above) containing the word "Help" as the
only line of the message. Because of the order in which the databases are
searched, if both GenBank and EMBL data banks contain entries with the
same primary accession number (the usual case), a query on the accession
number will result in the GenBank version of the entry being returned. If
the EMBL-format version of the entry is required, it can be retrieved from
the EMBL file server at NETSERV@EMBL.BITNET.
ANONYMOUS FTP
In addition to interactive access and electronic mail servers, GenBank
also provides files for anonymous FTP (File Transfer Protocol),
including GenBank and EMBL new data and contributed software. Each week
the new entries created in the GenBank database are collected into an
update file. The file has a name in the form of gbMMDD.seq, where MM is the
number of the month and DD is the date of file creation. Likewise, new
EMBL entries are collected into files with names in the form of emMMDD.seq.
The weekly update files are kept in the new data directories until they
are superseded by a new quarterly release of the database.
To access any of the files available for anonymous FTP, one should use
the FTP protocol to connect to GENBANK.BIO.NET [134.172.1.160], using
"anonymous" as the Username and one's surname as the Password.
===============================================
Example. Login to the free GOS IRX account
ATDT14159616860 Use ATDP for pulse dialing phone.
CONNECT 2400 Connect to 2400 baud modem
Trying GENBANK.BIO.NET (1434.172.1.160)...Open
SunOS/BSD UNIX (genbank.bio.net)
login:genbank Typing 'genbank' allows you to access the GenBank
computer.
Password:4nigms This is the password for the GenBank computer; it
MUST be entered in lowercase characters.
Last login... This message includes a date showing the last
anonymous login, as well as other system
information.
SunOS Release 4.0.3 (GENBANK)
The following is a list of commonly used terminals
Designation Terminal Type
adm3a Lear Siegler (ADM)
aaa-48 Ann-Arbor Ambassador in 48 line mode
aaa-60 Ann-Arbor Ambassador in 60 line mode
dm3025 Datamedia 3025a
h19 Heath H19 or Zenith
hp2621 Hewlett Packard HP2621
hp2648-iv Hewlett Packard HP2648A
sun Sun Microsystems Workstation console
tvi912 Televideo 912, 920
tvi950 Televideo 950
vi200 Visual 200
vt100 Digital Equipment VT100 (default)
vt102 Digital Equipment VT102
vt200 Digital Equipment VT200
Press Return to select vt100, or enter the appropriate terminal
(type the designation of the appropriate terminal type followed by <CR>)
After completing the login procedure shown above, the IRX sequence entry
searching program is immediately started.
===============================================
Further information about the GenBank On-line Service may be obtained by
contacting GenBank at:
GenBank
c/o IntelliGenetics Inc.
700 East El Camino Real
Mt. View, CA 94040
(415) 962-7364
genbank@genbank.bio.net