Path: utzoo!utgpu!news-server.csri.toronto.edu!rpi!zaphod.mps.ohio-state.edu!uwm.edu!bionet!kristoff From: kristoff@genbank.bio.net (David Kristofferson) Newsgroups: bionet.general Subject: Re: Fileserv at GUNBRF Message-ID: Date: 17 Apr 91 17:02:00 GMT References: <1368@usage.csd.unsw.oz.au> Organization: GenBank Online Service Lines: 210 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 ) 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