Path: funic!fuug!mcsun!uunet!zaphod.mps.ohio-state.edu!uwm.edu!bionet!gunbrf.bitnet!POSTMAST From: POSTMAST@gunbrf.bitnet Newsgroups: bionet.molbio.proteins Subject: PIR Network Server Announcement Message-ID: <9108010710.AA01734@genbank.bio.net> Date: 1 Aug 91 07:07:00 GMT Sender: news@genbank.bio.net Distribution: bionet Lines: 261 Announcement of the Protein Identification Resource BITNET Network Request Service Five commands and access to two new sequence databases have been added to the network request service. The new commands are FEATURE, HOST, QUIT, SUPERFAMILY and TAXONOMY. They are described below in more detail. The two new databases are NRL_3D which contains the sequence information extracted from the Brookhaven Protein Data Bank, and GBNEW which contains the weekly update sequences from GenBank (TM). These databases are automatically available through all the commands that can use them. The National Biomedical Research Foundation Protein Identification Resource has a full-function network fileserver and database query system. This automatic network server, operating since August 1990, is capable of handling database queries, sequence searches and sequence submissions, in addition to fileserver requests. To use this server, request commands should be directed to FILESERV@GUNBRF on BITNET. The FILESERVer recognizes the following commands sent either in a mail message, or (if the sender is on BITNET) in command messages or in a file: Command Action ------- ----------------------------------------------- ACCESSION list entry codes and titles by accession number AUTHOR list entry codes and titles by author BASES list accessible databases DEPOSIT deposit entry for database submission END DEPOSIT terminate deposit entry FEATURE list entry codes and titles by feature table entry GET return entry by entry code HELP return HELP instructions HOST list entry codes and titles by host species INDEX list SENDable files JOURNAL list entry codes and titles by journal citation KEYWORD list entry codes and titles by keyword QUIT ignore the remaining text (E-mail signature blocks) RETURN change return address for gateway mail SEARCH search for sequence by FASTA procedure END SEARCH terminate sequence for searching SEND send file SPECIES list entry codes and titles by species SUGGEST leave suggestion or correction for PIR staff END SUGGEST terminate suggestion text SUPERFAMILY list entry codes and titles by superfamily name TAXONOMY report taxonomy for scientific or common name TITLE list entry codes and titles by title Multiple commands can be sent with one command on each line of a mail message or file. Commands should NOT be sent on the Subject line of a mail message. Receipt of command messages and files will be acknowledged immediately. Mail messages will be acknowledged by return mail. For help in using any of the commands, send a request of the form HELP topic for example HELP SEARCH In addition to the commands, help instructions are also available on the following topics: Gateway_Access IBM-VM_BITNET On-Line_Access VAX-VMS_BITNET Because of inter-network gateway communication protocols, there are limitations on requests sent through gateways. Users not on BITNET or INTERNET who will be accessing BITNET through local or inter-network gateways should read and carefully follow these instructions before sending requests. Only mail message requests (not command messages or files) can be sent through gateways. Because the addresses posted on gateway mail do not always work for the return, before you send requests through inter-network gateways it is strongly recommended that you first contact Dr. John S. Garavelli at POSTMASTER@GUNBRF on BITNET. We will confirm a return address for you and may instruct you to use the RETURN command to insure that your request output will reach you. It is not usually necessary to do this if you are on BITNET or INTERNET, unless your system employs a local remailer or your mail program applies a non-standard return address (for example a personal name on the FROM: line). The BITNET network and the inter-network gateways impose strict file size limits. Poorly posed database queries may result in output so extensive that it could not be returned by network mail. Therefore, an output limit of 1000 lines for each command and 3000 lines total for each request is imposed by the PIR FILESERVer. The DEPOSIT command must, and the SEARCH and SUGGEST commands may, be followed by their respective END commands when text appears on intervening lines. The DEPOSIT command requires, and the SEARCH command optionally uses, parameters that appear on the same line as the command. Because of the complexity of these commands, users should obtain and carefully read the help instructions on these commands before attempting to use them. Here is a brief synopsis of each server command. ACCESSION number This command will return a list of entry codes and titles for entries with accession numbers matching the left portion of the accession number provided. AUTHOR name This command will return a list of entry codes and titles for entries with an author matching the portion of the author name provided. BASES This command will return a list of the accessible databases and the number of entries each contains. Currently, this selection of databases cannot be changed during network access. The databases available and their abbreviations for code specification are as follows: Abbreviation Database Update Schedule PIR1 PIR Annotated and Classified Entries quarterly PIR2 PIR Preliminary Entries approximately bimonthly PIR3 PIR Unverified Entries weekly NRL_3D Brookhaven Data Bank Sequences quarterly N NBRF Nucleic GB GenBank (TM) as received GBNEW GenBank (TM) New Entries weekly EMBL EMBL as received Access to these and additional databases can be provided to on-line users. DEPOSIT FORM or DEPOSIT AUTHORIN submission text END DEPOSIT This command will allow the submission of protein sequence entries prepared in a standard format. The PIR accepts submissions in the electronic version of the GenBank/EMBL/PIR Data Submission Form, or in the Transaction Protocol Format of the GenBank AUTHORIN program. This command MUST be followed on the same line by either FORM or AUTHORIN to indicate the type of deposit, and by the END DEPOSIT command at the end of the text of the entry. Only one DEPOSIT command should be sent with each request. A separate form must be submitted for each sequence. Forms with more than one sequence and requests with more than one DEPOSIT command cannot be accepted. It is important that nucleotide sequences including authors' protein sequence translations be submitted to only to GenBank or EMBL, as appropiate, and not to the PIR FILESERVer. GenBank and EMBL forward protein sequences to the PIR International with no further effort required on the part of the author. FEATURE feature-name This command will return a list of entry codes and titles for entries in the PIR databases only with an entry in the feature table matching the portion of the feature name provided. A list of the features currently in the database can be obtained by the command SEND FEATURES. GET code This command will return the full text of an entry with the code matching the code provided. These codes are found in the lists returned by one of the search commands (ACCESSION, AUTHOR, JOURNAL, FEATURE, HOST, KEYWORD, SPECIES, SUPERFAMILY or TITLE). The format of the code is a database abbreviation, a colon, and four to ten alphanumeric characters. HOST host-name This command will return a list of entry codes and titles for entries in the PIR databases only with a host name matching the portion of the host name provided. INDEX This command will return a list of the files that can currently be sent by the PIR FILESERVER using the SEND command. JOURNAL citation This command will return a list of entry codes and titles for entries with a journal citation matching the portion of the citation provided. KEYWORD words This command will return a list of entry codes and titles for entries with any keyword, or portion of a keyword, matching the words provided. You may provide any number of groups of three or more alphanumeric characters expected in a single keyword entry. QUIT If you use a mail program which automatically attaches a signature block to every message, use this command to inform the server that all the following lines should be ignored. RETURN address If you are sending mail from a non-BITNET network through a gateway, you may need to provide a return address different from the one posted on the message in order for your output to be sent to you correctly. The RETURN command will allow you to correct your return address. SEARCH parameters sequence or SEARCH parameters sequence text END SEARCH This command will allow a sequence to be compared in a FASTA search (see W.R.Pearson & D.J. Lipman PNAS (1988) 85:2444-2448) with the PIR databases. You may send either protein or nucleotide sequences in the IUPAC standard single letter code; however,only the PIR protein sequence databases will be searched. Nucleotide sequences will be translated in six reading frames according to a selectable genetic code, and those translated protein sequences will be compared against the PIR protein sequence databases. The SEARCH command may be used in two forms, either on a single line with parameters and sequence, or on multiple lines with the parameters on the line with the SEARCH command, followed by lines with the sequence and an END SEARCH command on the line following the end of the sequence. There are two optional parameters for the SEARCH command, KTUP and NUC. The KTUP parameter sets the ktup value for the FASTA program. The NUC parameter specifies that the sequence is a nucleotide sequence, and can select the genetic code to be used for the translation of that sequence. SEND filename This command will instruct the FILESERVer to send, by separate electronic transmission, the specified file. A list of the currently available files can be obtained by using the INDEX command. SPECIES name This command will return a list of entry codes and titles for entries with the species matching the portion of a species name provided. The species name may be the Latin genus and/or species name, or a common name. Because the names of some viruses contain the common name of the host species, entry codes and titles for entries with the species of viruses infecting a species may also be listed. Please note: this is not an efficient command for performing a general query of the PIR databases especially with extensively studied species. For well- studied species, the TITLE command will be more efficient. SUGGEST text or SUGGEST text END SUGGEST This command will submit the text of your message to an NBRF staff member. You may use it to suggest modifications or improvements to our FILESERVER or corrections to the PIR database. You may either place the text on the same line with the SUGGEST command, or you may use any number of lines for the text followed by the END SUGGEST command on the line after the last line of the text. SUPERFAMILY superfamily-name This command will return a list of entry codes and titles for entries in the PIR databases only which belong to that superfamily. Since the domains of some multidomain proteins are not completely classified, the SUPERFAMILY command will not necessarily produce a complete list of all entries in a specific superfamily. A list of the superfamilies currently in the database can be obtained by the command SEND SUPERFAM. TAXONOMY taxonomic-name or TAXONOMY common-name This command will report taxonomies for entries in the taxonomic database currently being used by the PIR and shared with GenBank (TM) and EMBL. This database is maintained by Dr. Andrzej Elzanowski at the Max-Planck- Institut fur Biochemie. You should provide a fully or partially specified name of 1 to 8 words with a minimum length of 3 letters each. Names at all taxonomic levels containing those words will be reported. The organelles containing genetic material of some higher organisms also have entries in this database. TITLE title This command will return a list of entry codes and titles for entries with any portion of a title matching the word provided. You may provide any number of groups of three or more alphanumeric characters expected in a single title. PIR titles include protein names, species names and Enzyme Commission numbers, consequently this command is generally the most efficient way to perform a general query of the PIR databases. ------------------------------------------------------------------------ Dr. John S. Garavelli Database Coordinator Protein Identification Resource National Biomedical Research Foundation Washington, DC 20007 POSTMASTER@GUNBRF.BITNET