From owner-proteins@net.bio.net Fri Jan 01 22:00:00 1993 Path: biosci!HP720A.CSC.CUHK.HK!s911896 From: s911896@HP720A.CSC.CUHK.HK Newsgroups: bionet.molbio.proteins Subject: (none) Message-ID: <64522.s911896@mailserv.cuhk.hk> Date: 2 Jan 93 09:55:14 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 14 Dear nectters, I have a question, below. What are the transcriptional factors of hormone receptor genes, such as the estrogen receptor gene(in human or other animals). Moreover, please give me a clue about how to find related paper. I am looking forward to hearing your as-soon-as-possible reply. thank you in advance. Sincerely, Qiu Yaowu Chinese University of Hong Kong From owner-proteins@net.bio.net Sat Jan 02 22:00:00 1993 Path: biosci!agate!ames!haven.umd.edu!uunet!usc!rpi!ghost.dsi.unimi.it!univ-lyon1.fr!chx400!ulci20!isrec-sun1.unil.ch!vjongene From: vjongene@isrec-sun1.unil.ch (Victor Jongeneel) Newsgroups: bionet.molbio.proteins Subject: Re: (none) Message-ID: <1993Jan4.070858.19631@ulci20.unil.ch> Date: 4 Jan 93 07:08:58 GMT References: <01GT49BSR4G890MT7R@vax.csc.cuhk.hk> Sender: news@ulci20.unil.ch Distribution: bionet Organization: University of Lausanne CH (Switzerland) Lines: 32 X-Newsreader: TIN [version 1.1 PL8] S911896@VAX.CSC.CUHK.HK wrote: : Dear nectters, : If you know what are the transcriptional factors of GCN4, steroid binding : protein gene, or other growth regulatory factor genes, please let me known : as soon as possible. I am doing related analyses. : Thank you for your great helps. : Sincerely, : Qiu Yaowu : Chinese university of Hong Kong The primary sequences of most known transcription factors, and much detailed information about them, are documented in David Ghosh's Transcription Factor Database (TFD). The database and its documentation are available by anonymous ftp from ncbi.nlm.nih.gov in /repository/TFD. This should answer both of your questions (and much more). Good luck! -- C. Victor JONGENEEL vjongene@isrec-sun1.unil.ch Ludwig Institute for Cancer Research Chemin des Boveresses 155 FAX: +41-21-653-4474 CH-1066 EPALINGES Tel: +41-21-316-5994 Switzerland "Where the cows moo and the people vote" From owner-proteins@net.bio.net Sat Jan 02 22:00:00 1993 Path: biosci!VAX.CSC.CUHK.HK!S911896 From: S911896@VAX.CSC.CUHK.HK Newsgroups: bionet.molbio.proteins Subject: (none) Message-ID: <01GT49BSR4G890MT7R@vax.csc.cuhk.hk> Date: 4 Jan 93 02:42:00 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 12 Dear nectters, If you know what are the transcriptional factors of GCN4, steroid binding protein gene, or other growth regulatory factor genes, please let me known as soon as possible. I am doing related analyses. Thank you for your great helps. Sincerely, Qiu Yaowu Chinese university of Hong Kong From owner-proteins@net.bio.net Sun Jan 03 22:00:00 1993 Path: biosci!agate!spool.mu.edu!uunet!munnari.oz.au!manuel.anu.edu.au!dgg900 From: dgg900@anusf.anu.edu.au (David G Green) Newsgroups: bionet.molbio.proteins Subject: Symposium on molecular evolution Keywords: molecular evolution Message-ID: <1ialpeINNluq@manuel.anu.edu.au> Date: 5 Jan 93 00:46:38 GMT Organization: ANU Supercomputer Facility Lines: 162 NNTP-Posting-Host: 150.203.5.2 Originator: dgg900@anusf Robertson Symposium -------------------------------- FRONTIERS OF MOLECULAR EVOLUTION -------------------------------- Research School of Biological Sciences Australian National University Canberra, 27-29 January 1993 Molecular biology, the "new biology", lies at the heart of genetic engineering and other advances that affect our welfare. Molecular biology is also revolutionizing our understanding of evolution. Questions such as where and when did human beings first appear? and where and how did the AIDS virus arise? are now intertwined with the goal of understanding the structure and function of biological macromolecules. The study of the origins and changes of these macromolecules, especially DNA, RNA and proteins, forms the new science of molecular evolution. The programme and speakers as follows. RUBISCO ======= Paul Curmi University of NSW "Structural & Dynamic Transitions in Rubisco: A Comparison of Activated and Non-Activated Forms" Steven Gutteridge DuPont, Delaware "Mechanistic Implications of some High Resolution Structures of Ribulose-P2 Carboxylase/Oxygenase from the Cyanobacterium Synechococcus PCC6301" Matthew Morell ANU To be advised A SUPERFAMILY OF MEMBRANE TRANSPORTER ===================================== Carl Doige UC Berkeley "Structural and Functional Studies of the Histidine Permease: A Model System for the Superfamily of Traffic ATPases" Chris Higgins Oxford To be advised Tony Howells ANU "Structure/Function Studies on the ATP-Binding Transmembrane Permeases Involved in Drosophila Eye Pigmentation" PROTEIN STRUCTURE; DETERMINATION AND PREDICTION =============================================== Lisa Palmer Biosym "A comparison of the structural homology between HIV-1 PR and other members of the aspartyl protease family" Gregory Petsko Brandeis To be advised Willy Taylor Mill Hill "Protein structure prediction" HUMAN ORIGINS ============= Simon Easteal ANU To be advised Masatoshi Nei Penn. State To be advised Naoyuki Takahata Mishima "On the origin of modern Homo sapiens" EMERGING VIRUSES ================ Charles Calisher Colorado State "Recent Opportunities for the Emergence or Reemergence (if not the evolution) of Viruses" Fernando Garcia-Arenal Madrid "Emergence of New Plant Virus Systems: Two Examples" Paul Sharp Dublin "Origins and evolution of AIDS viruses" EVOLUTION OF DEVELOPMENTAL REGULATORY GENES =========================================== Donna Cohen ANU "Transcription Factor AP-1: A Universal Regulator From Yeast to Mammals." Richard Harvey Walter & Eliza Hall Institute To be advised David Miller James Cook "Homeobox gene structure and organization in the lower metazoa" Nipam Patel Carnegie "A molecular analysis of the evolution of insect segmentation" Rob Saint University of Adelaide "Molecular evolution of cell cycle genes" SEQUENCE ANALYSIS AND PHYLOGENETIC RECONSTRUCTION ================================================= Lloyd Allison Monash "Estimating Parameters and Evolutionary Distances in the Inference of Evolutionary Trees" Dan Faith CSIRO Wildlife "Methods in phylogenetic reconstruction" David Green ANU "The Chicken or the Egg - The How and Why of Multiple Sequence Alignment." Alex Reisner ANGIS "The role of networks and databases in sequence analysis" Mike Steel Christchurch "Spectral analysis - a new approach for tree reconstruction" THE MOLECULAR TREE OF LIFE ========================== Mark Chase Chapel Hill To be advised Charles Marshall UCLA "The relative importance of molecular and morphological data in understanding the evolutionary relationships among animals" Erko Stackebrandt University of Queensland To be advised ------------------------------------------------------- Robertson Symposium: Frontiers of Molecular Evolution 27-29 January 1993 SYMPOSIUM REGISTRATION NAME: __________________________________________________ STUDENT? yes / no ADDRESS: __________________________________________________ __________________________________________________ TELEPHONE: (____)______________ FAX: (____)________________ E-MAIL: _________________________ ACCOMMODATION For participants requiring accommodation during the conference on-campus rooms are available in Bruce Hall, one of the residential colleges. Single Rooms only, $32 Bed and Breakfast. Hotel/motel accommodation can be organised if requested. REGISTRATION Registration fees to cover lunches, morning and afternoon tea, and the conference dinner, will be A$100 (students $60). Registration $A_________ Accommodation Tuesday night Wednesday night Thursday night Friday night $A_________ TOTAL $A_________ For more details contact: ________________________________________________________ Tanya Joce, Conference Secretary RSBS, ANU PO Box 475 Phone: 61 6 249 4211 Canberra ACT 2601 Fax: 61 6 249 4437 Email: david.green@anu.edu.au From owner-proteins@net.bio.net Sun Jan 03 22:00:00 1993 Path: biosci!agate!spool.mu.edu!darwin.sura.net!welchgate.welch.jhu.edu!danj From: danj@welchgate.welch.jhu.edu (Dan Jacobson) Newsgroups: bionet.molbio.proteins Subject: Re: FAQ?? (for internet/compuserve mail) Message-ID: <1993Jan4.203003.3699@welchgate.welch.jhu.edu> Date: 4 Jan 93 20:30:03 GMT Organization: Johns Hopkins Univ. Welch Medical Library Lines: 565 Eric Mansell writes: >I know this must be asked all the time, but is >there a faq or other info around anywhere on how >to get mail to/from internet to compuserve, prodigy, etc.? Yes this type of information is available and has been posted before. This one is a copy of a note that Rob Harper posted. Best of luck, Dan Jacobson danj@welchgate.welch.jhu.edu ========================================================================= Below are copies of two guides to Inter-Network mail. I am not the author. Please send comments or corrections to the original authors whose names are included below. This file will be placed on nic.funet.fi for downloading via anonymous ftp from the directory /pub/sci/molbio/biodocs ********************* John J. Chew Article ************************ Inter-Network Mail Guide - Copyright 1990 by John J. Chew $Header: netmail,v 1.12 90/07/06 20:38:28 john Exp $ For those of you who were wondering what happened to the June 1990 issue, there wasn't one, because of a lack of important changes to the data, and because I've been busy with other things. Even worse (:-), there will not be an August 1990 issue as I will be temporarily between net addresses as I take a nice long holiday between jobs on different continents. If you have information to add or requests for subscriptions, send them as usual to me at and they should catch up to me with some delay wherever I end up. I'm off to enjoy my summer now, bye! -- John COPYRIGHT NOTICE This document is Copyright 1990 by John J. Chew. All rights reserved. Permission for non-commercial distribution is hereby granted, provided that this file is distributed intact, including this copyright notice and the version information above. Permission for commercial distribution can be obtained by contacting the author as described below. INTRODUCTION This file documents methods of sending mail from one network to another. It represents the aggregate knowledge of the readers of comp.mail.misc and many contributors elsewhere. If you know of any corrections or additions to this file, please read the file format documentation below and then mail to me: John J. Chew . If you do not have access to electronic mail (which makes me wonder about the nature of your interest in the subject, but there does seem to be a small such population out there) you can call me during the month of July at +1 416 979 7166 between 11:00 and 24:00 EDT (UTC-4h) and most likely talk to my answering machine (:-). DISTRIBUTION (news) This list is posted monthly to Usenet newsgroups comp.mail.misc and news.newusers.questions. (mail) I maintain a growing list of subscribers who receive each monthly issue by electronic mail, and recommend this to anyone planning to redistribute the list on a regular basis. (FTP) Internet users can fetch this guide by anonymous FTP as ~ftp/pub/docs/ internetwork-mail-guide on Ra.MsState.Edu (130.18.80.10 or 130.18.96.37) [Courtesy of Frank W. Peters] (Listserv) Bitnet users can fetch this guide from the Listserv at UNMVM. Send mail to LISTSERV@UNMVM with blank subject and body consisting of the line "GET NETWORK GUIDE". [Courtesy of Art St. George] HOW TO USE THIS GUIDE Each entry in this file describes how to get from one network to another. To keep this file at a reasonable size, methods that can be generated by transitivity (A->B and B->C gives A->B->C) are omitted. Entries are sorted first by source network and then by destination network. This is what a typical entry looks like: #F mynet #T yournet #R youraddress #C contact address if any #I send to "youraddress@thegateway" For parsing purposes, entries are separated by at least one blank line, and each line of an entry begins with a `#' followed by a letter. Lines beginning with `# ' are comments and need not be parsed. Lines which do not start with a `#' at all should be ignored as they are probably mail or news headers. #F (from) and #T (to) lines specify source and destination networks. If you're sending me information about a new network, please give me a brief description of the network so that I can add it to the list below. The abbreviated network names used in #F and #T lines should consist only of the characters a-z, 0-9 and `-' unless someone can make a very convincing case for their favourite pi character. These are the currently known networks with abbreviated names: applelink AppleLink (Apple Computer, Inc.'s in-house network) bitnet international academic network bix Byte Information eXchange: Byte magazine's commercial BBS bmug Berkeley Macintosh Users Group compuserve commercial time-sharing service connect Connect Professional Information Network (commercial) easynet Easynet (DEC's in-house mail system) envoy Envoy-100 (Canadian commercial mail service) fax Facsimile document transmission fidonet PC-based BBS network geonet GeoNet Mailbox Systems (commercial) internet the Internet mci MCI's commercial electronic mail service mfenet Magnetic Fusion Energy Network nasamail NASA internal electronic mail peacenet non-profit mail service sinet Schlumberger Information NETwork span Space Physics Analysis Network (includes HEPnet) sprintmail Sprint's commercial mail service (formerly Telemail) thenet Texas Higher Education Network #R (recipient) gives an example of an address on the destination network, to make it clear in subsequent lines what text requires subsitution. #C (contact) gives an address for inquiries concerning the gateway, expressed as an address reachable from the source (#F) network. Presumably, if you can't get the gateway to work at all, then knowing an unreachable address on another network will not be of great help. #I (instructions) lines, of which there may be several, give verbal instructions to a user of the source network to let them send mail to a user on the destination network. Text that needs to be typed will appear in double quotes, with C-style escapes if necessary. #F applelink #T internet #R user@domain #I send to "user@domain@internet#" #I domain can be be of the form "site.bitnet", address must be <35 characters #F bitnet #T internet #R user@domain #I Methods for sending mail from Bitnet to the Internet vary depending on #I what mail software is running at the Bitnet site in question. In the #I best case, users should simply be able to send mail to "user@domain". #I If this doesn't work, try "user%domain@gateway" where "gateway" is a #I regional Bitnet-Internet gateway site. Finally, if neither of these #I works, you may have to try hand-coding an SMTP envelope for your mail. #I If you have questions concerning this rather terse note, please try #I contacting your local postmaster or system administrator first before #I you send me mail -- John Chew #F compuserve #T fax #R +1 415 555 1212 #I send to "FAX 14155551212" (only to U.S.A.) #F compuserve #T internet #R user@domain #I send to ">INTERNET:user@domain" #F compuserve #T mci #R 123-4567 #I send to ">MCIMAIL:123-4567" #F connect #T internet #R user@domain #I send to CONNECT id "DASNET" #I first line of message: "\"user@domain\"@DASNET" #F easynet #T bitnet #R user@site #C DECWRL::ADMIN #I from VMS use NMAIL to send to "nm%DECWRL::\"user@site.bitnet\"" #I from Ultrix #I send to "user@site.bitnet" or if that fails #I (via IP) send to "\"user%site.bitnet\"@decwrl.dec.com" #I (via DECNET) send to "DECWRL::\"user@site.bitnet\"" #F easynet #T fidonet #R john smith at 1:2/3.4 #C DECWRL::ADMIN #I from VMS use NMAIL to send to #I "nm%DECWRL::\"john.smith@p4.f3.n2.z1.fidonet.org\"" #I from Ultrix #I send to "john.smith@p4.f3.n2.z1.fidonet.org" or if that fails #I (via IP) send to "\"john.smith%p4.f3.n2.z1.fidonet.org\"@decwrl.dec.com" #I (via DECNET) send to "DECWRL::\"john.smith@p4.f3.n2.z1.fidonet.org\"" #F easynet #T internet #R user@domain #C DECWRL::ADMIN #I from VMS use NMAIL to send to "nm%DECWRL::\"user@domain\"" #I from Ultrix #I send to "user@domain" or if that fails #I (via IP) send to "\"user%domain\"@decwrl.dec.com" #I (via DECNET) send to "DECWRL::\"user@domain\"" #F envoy #T internet #R user@domain #C ICS.TEST or ICS.BOARD #I send to "[RFC-822=\"user(a)domain\"]INTERNET/TELEMAIL/US #I for special characters, use @=(a), !=(b), _=(u), any=(three octal digits) #F fidonet #T internet #R user@domain #I send to "uucp" at nearest gateway site #I first line of message: "To: user@domain" #F geonet #T internet #R user@domain #I send to "DASNET" #I subject line: "user@domain!subject" #F internet #T applelink #R user #I send to "user@applelink.apple.com" #F internet #T bitnet #R user@site #I send to "user%site.bitnet@gateway" where "gateway" is a gateway host that #I is on both the internet and bitnet. Some examples of gateways are: #I cunyvm.cuny.edu mitvma.mit.edu. Check first to see what local policies #I are concerning inter-network forwarding. #F internet #T bix #R user #I send to "user@dcibix.das.net" #F internet #T bmug #R John Smith #I send to "John.Smith@bmug.fidonet.org" #F internet #T compuserve #R 71234,567 #I send to "71234.567@compuserve.com" #I note: Compuserve account IDs are pairs of octal numbers. Ordinary #I consumer CIS user IDs begin with a `7' as shown. #F internet #T connect #R NAME #I send to "NAME@dcjcon.das.net" #F internet #T easynet #R HOST::USER #C admin@decwrl.dec.com #I send to "user@host.enet.dec.com" or "user%host.enet@decwrl.dec.com" #F internet #T easynet #R John Smith @ABC #C admin@decwrl.dec.com #I send to "John.Smith@ABC.MTS.DEC.COM" #I (This syntax is for All-In-1 users.) #F internet #T envoy #R John Smith (ID=userid) #C /C=CA/ADMD=TELECOM.CANADA/ID=ICS.TEST/S=TEST_GROUP/@nasamail.nasa.gov #C for second method only #I send to "uunet.uu.net!att!attmail!mhs!envoy!userid" #I or to "/C=CA/ADMD=TELECOM.CANADA/DD.ID=userid/PN=John_Smith/@Sprint.COM" #F internet #T fidonet #R john smith at 1:2/3.4 #I send to "john.smith@p4.f3.n2.z1.fidonet.org" #F internet #T geonet #R user at host #I send to "user:host@map.das.net" #I American host is geo4, European host is geo1. #F internet #T mci #R John Smith (123-4567) #I send to "1234567@mcimail.com" #I or send to "JSMITH@mcimail.com" if "JSMITH" is unique #I or send to "John_Smith@mcimail.com" if "John Smith" is unique - note the #I underscore! #I or send to "John_Smith/1234567@mcimail.com" if "John Smith" is NOT unique #F internet #T mfenet #R user@mfenode #I send to "user%mfenode.mfenet@nmfecc.arpa" #F internet #T nasamail #R user #C #I send to "user@nasamail.nasa.gov" #F internet #T peacenet #R user #C #I send to "user%cdp@arisia.xerox.com" #F internet #T sinet #R node::user or node1::node::user #I send to "user@node.SINet.SLB.COM" or "user%node@node1.SINet.SLB.COM" #F internet #T span #R user@host #C #I send to "user@host.span.NASA.gov" #I or to "user%host.span@ames.arc.nasa.gov" #F internet #T sprintmail #R [userid "John Smith"/organization]system/country #I send to "/C=country/ADMD=system/O=organization/PN=John_Smith/DD.ID=userid/@Sp rint.COM" #F internet #T thenet #R user@host #I send to "user%host.decnet@utadnx.cc.utexas.edu" #F mci #T internet #R John Smith #I at the "To:" prompt type "John Smith (EMS)" #I at the "EMS:" prompt type "internet" #I at the "Mbx:" prompt type "user@domain" #F nasamail #T internet #R user@domain #I at the "To:" prompt type "POSTMAN" #I at the "Subject:" prompt enter the subject of your message #I at the "Text:" prompt, i.e. as the first line of your message, #I enter "To: user@domain" #F sinet #T internet #R user@domain #I send to "M_MAILNOW::M_INTERNET::\"user@domain\"" #I or "M_MAILNOW::M_INTERNET::domain::user" #F span #T internet #R user@domain #C NETMGR@NSSDCA #I send to "AMES::\"user@domain\"" #F sprintmail #T internet #R user@domain #I send to "[RFC-822=user(a)domain @GATEWAY]INTERNET/TELEMAIL/US" #F thenet #T internet #R user@domain #I send to UTADNX::WINS%" user@domain " END ----- Date: 8 Jul 91 07:56:37 GMT From: rsw@cs.brown.EDU (Bob Weiner) Subject: Basic guide on how to send e-mail [I don't profess that this will work for those who know nothing about computers, but I do think it is a good, short example of how to explain a problem like e-mail addressing to a novice computer user. It does not discuss X.400 based e-mail but should at some future time.] ************************ Bob Weiner Article *********************** Internet / Usenet Mail Addressing Guide Bob Weiner rsw@cs.brown.edu July 8, 1991 This document discusses how to address mail to or from both Usenet (via UUCP = UNIX to UNIX Copy Protocol) and the Internet (via SMTP = Simple Mail Transfer Protocol). Mail through the Internet can reach Usenet, Compuserve, MCI Mail, and many research and corporate organizations throughout the world. It assumes you have a mail reader and composer program with its own documentation, on a computer which can connect to Usenet or the Internet. The mail address is what you will put or receive on the message line that begins with the literal string: "To:". ************************ Sending Worldwide E-mail ************************ Here is how you mail to someone else. (Items within <> or in all capitals are field names for which you must give literal values. Items in [] are optional fields, which are only included in certain electronic mail addresses. An | symbol means choose one from the set of alternatives separated by the symbol. A host is a computer) From an Internet Host - To an Internet Host ------------------------------------------- If a user's organizational address is registered on the Internet, he will have an address of the form: @.[.][.] for example: bert@ladder.princeton.edu where is a computer name and is a recursive specification of a logical location, that is, it may contain subdomains as in: = DOMAIN_IDENTIFIER | SUBDOMAIN_IDENTIFIER. Organization should always be one of the following: net for network gateways, e.g. uu.net edu for educational institutions, e.g. brown.edu org for non-profit organization, e.g. osf.org com for commercial firms, e.g. hp.com gov for government entities, e.g. nasa.gov mil for war gamers, e.g. army.mil uucp for non-interneters, Usenet hosts, e.g. novavax.uucp arpa obsolete, refers to the Arpanet that evolved into the Internet. Country is typically a two letter country code for mail outside of the US: ca Canada fr France se Sweden dk Denmark ch Switzerland One example of a self-deprecating Internet mail address might be: nerdy@wimpy.eecs.berkeley.edu This addresses a message to the , nerdy, at the , wimpy, in the EE Computer Science department , eecs, at UC Berkeley, berkeley, which is obviously an educational institution, edu. To send, simply place the user's address in the 'To:' field of your mail message. From a Usenet Host - To a Usenet Host ------------------------------------- Now consider that you are a user whose computer is registered on the UUCP Usenet, who has only a dialup connection to the network and you want to mail to another such user. Let's say you actually wanted to communicate with someone earning a lot of money, call him smiley@bucks. His machine bucks communicates directly with a registered machine, cash. So you could send to him with the following address: uunet!cash!bucks!smiley The host 'uunet' is a very important one; it serves as a mail gateway between Usenet and the Internet, so it knows how to properly address mail for practically every Internet domain and registered UUCP host in the world. This is why your mail must go through it, because locally your mail host will never be as smart as uunet. If your host computer can't send directly to uunet, you will have to precede the above path with one that starts with a machine that your's communicates directly with and ends with a machine name that communicates with uunet, plus another '!', e.g. nearby!farther!uunet!cash!bucks!smiley From an Internet Host - To a Usenet Host ---------------------------------------- If your machine is on the Internet and the other is on Usenet, you can use something like: bucks!smiley@uunet.uu.net From a Usenet Host - To an Internet Host ---------------------------------------- If your machine is on Usenet only and the other is on the Internet, you can use something like either of the following: nearby!farther!uunet!ladder.princeton.edu!bert nearby!farther!uunet!bert@ladder.princeton.edu From an Internet Host - To a Compuserve User -------------------------------------------- To mail to a Compuserve user with an ID of aaaaa,bbbb: aaaaa.bbbb@compuserve.com Note that the comma in the ID becomes a period in the Internet address. From an Internet Host - To an MCI Mail Customer ----------------------------------------------- @mcimail.com *********************************** Why me? Can't I just lick a stamp? *********************************** Once you realize that you can get a message from across the country in under 2 hours depending on how frequently you poll a dial-up computer or within a few minutes on the Internet, you'll learn to enjoy the convenience of this facility. The main benefits of electronic mail are that: it always sits and waits until the addressee has time for it; it decreases work interruptions, allowing more time and thoughtful responses to other people's thoughts and questions; it provides data that you can work with and modify, unlike facsimiles and voice mail; it is the backbone of many large organizations wide-area communications strategies for the 90's and thus a safe investment of time and money; logical, non-location dependent addressing is much simpler and reliable than postal addressing; automatic mail forwarding is also available; e-mail is a very cost effective means of messaging. By the way, UUCP mail is a 1970's technology, although it has advanced a great deal. (UUCP mail addresses use the '!', which is called a 'bang' rather than an exclamation point because networking people don't have much time to read and because they love to save syllables. Internet mail dates back even farther than UUCP mail. Domain-based mail addressing became a phenomenon in the mid-1980's. ============================================================================== Bob Weiner rsw@cs.brown.edu -- Explaining Real Computers to Real People From owner-proteins@net.bio.net Sun Jan 03 22:00:00 1993 Path: biosci!NBRF.GEORGETOWN.EDU!POSTMASTER From: POSTMASTER@NBRF.GEORGETOWN.EDU Newsgroups: bionet.molbio.proteins Subject: Announcement of PIR Service Interruption Message-ID: <01GT4JA0RKZM8WW0W2@NBRF.Georgetown.Edu> Date: 4 Jan 93 19:32:43 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 20 Announcement of Temporary Interruption of Access to The Protein Identification Resource The National Biomedical Research Foundation will (once again) be attempting to repair a hardware problem on Tuesday 5 January. From 12:00 EST Tuesday 5 January through about 17:00 EST Wednesday 6 January it will not be possible for users to access the Protein Identification Resource Network Server. The On-line System is currently unavailable but should be back up when the system is restored. We regret any inconvenience this temporary loss of service will cause. ------------------------------------------------------------------------ Dr. John S. Garavelli Database Coordinator Protein Information Resource National Biomedical Research Foundation Washington, DC 20007 POSTMAST@GUNBRF.BITNET POSTMASTER@NBRF.GEORGETOWN.EDU From owner-proteins@net.bio.net Mon Jan 04 22:00:00 1993 Path: biosci!agate!spool.mu.edu!uwm.edu!zaphod.mps.ohio-state.edu!moe.ksu.ksu.edu!hobbes.physics.uiowa.edu!news.iastate.edu!sanger.bb.iastate.edu!zsha From: zsha@iastate.edu (Zhengyu Sha) Newsgroups: bionet.molbio.proteins Subject: protein transportation Message-ID: Date: 6 Jan 93 02:09:32 GMT Sender: news@news.iastate.edu (USENET News System) Organization: Iowa State University, Ames IA Lines: 1 Could somenetter tell me how a periplasmic protein without a leader sequence is transported across the inner membrane in bacteria. I am specifically interested in the Catalase HP I in the E.coli but the mechanisms involving other proteins are helpful too. From owner-proteins@net.bio.net Tue Jan 05 22:00:00 1993 Path: biosci!agate!dog.ee.lbl.gov!hellgate.utah.edu!caen!uunet!zaphod.mps.ohio-state.edu!magnus.acs.ohio-state.edu!ldruhan From: ldruhan@magnus.acs.ohio-state.edu (Lawrence J Druhan) Newsgroups: bionet.molbio.proteins Subject: help Keywords: help Message-ID: <1993Jan6.173536.13082@magnus.acs.ohio-state.edu> Date: 6 Jan 93 17:35:36 GMT Sender: news@magnus.acs.ohio-state.edu Distribution: oh Organization: The Ohio State University Lines: 7 Nntp-Posting-Host: top.magnus.acs.ohio-state.edu help - I want to use cassette mutagenesis to create a point mutation but the base that must be changed is in the overhang region of one of the restriction sites the cassette will use. There is still 3 bases that can base pair. Will this work? Please reply via e-mail. Thanks in advance - Lawrence Druhan druhan.1@osu.edu From owner-proteins@net.bio.net Tue Jan 05 22:00:00 1993 Path: biosci!uwm.edu!zaphod.mps.ohio-state.edu!magnus.acs.ohio-state.edu!news From: news@magnus.acs.ohio-state.edu Newsgroups: bionet.molbio.proteins Subject: help Message-ID: <1993Jan6.134049.9110@magnus.acs.ohio-state.edu> Date: 6 Jan 93 13:40:49 GMT Distribution: usa Organization: The Ohio State University Lines: 1 Nntp-Posting-Host: bottom.magnus.acs.ohio-state.edu This article was probably generated by a buggy news reader. From owner-proteins@net.bio.net Tue Jan 05 22:00:00 1993 Path: biosci!agate!ames!saimiri.primate.wisc.edu!zaphod.mps.ohio-state.edu!menudo.uh.edu!menudo.uh.edu!usenet From: ramin@brain.bchs.uh.edu (ramin homayouni) Newsgroups: bionet.molbio.proteins Subject: Electrospray tandem mass spec for protein sequencing Message-ID: <1ig168INNfvt@menudo.uh.edu> Date: 7 Jan 93 01:31:52 GMT Organization: University of Houston Lines: 14 NNTP-Posting-Host: brain.bchs.uh.edu Hello netters, I have recently heard from a colleague that protein sequences may be determined by using electrospray tandem mass spectroscopy. My knowledge in this field is extremely poor. So I'm wondering if anyone would suggest some references which review this technique and discuss the pros and cons of using this technique in comparison with traditional methods of protein sequencing. Also, does anyone know of a service which will sequence a protein using electrospray tandem mass spec? ANY input on this topic will be greatly appreciated. Thank you in advance. Please reply to : Ramin@brain.bchs.uh.edu From owner-proteins@net.bio.net Thu Jan 07 22:00:00 1993 Path: biosci!NBRF.GEORGETOWN.EDU!POSTMASTER From: POSTMASTER@NBRF.GEORGETOWN.EDU Newsgroups: bionet.molbio.proteins Subject: Announcement of PIR Technical Development News Message-ID: <01GTA16BI8O68WVZBL@NBRF.Georgetown.Edu> Date: 8 Jan 93 17:54:21 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 28 Announcement of the Protein Information Resource Technical Development News We have on-going efforts to standardize the PIR databases, improving their parsability and compliance with CODATA and other format standards. During the next year the combined staffs of the PIR-International will be imposing and enforcing many new rules and requirements on the distributed versions of the database. Some of these rules and requirements may affect the currently existing software designed to read the PIR databases in "NBRF format". Notification of the broader aspects of these changes will be placed in our newsletters and in announcements posted on the BioSci Newsgroups PROTEINS and BIONEWS. However, some people may wish to be informed about the technical aspects of these changes before they appear in a database release. For that reason we will be setting up an electronic mailing list to inform software developers and others interested in the technical aspects of these database changes. If you would be interested in being placed on this mailing list, please send a brief electronic mail note to me at one of the network addresses below. ------------------------------------------------------------------------ Dr. John S. Garavelli Database Coordinator Protein Information Resource National Biomedical Research Foundation Washington, DC 20007 POSTMAST@GUNBRF.BITNET POSTMASTER@NBRF.Georgetown.Edu From owner-proteins@net.bio.net Thu Jan 07 22:00:00 1993 Path: biosci!TRMETU.BITNET!CONSULT1 From: CONSULT1@TRMETU.BITNET (TAYLAN) Newsgroups: bionet.molbio.proteins Subject: NATO ADVANCED STUDY INSTITUTE Message-ID: <9301081246.AA15250@net.bio.net> Date: 8 Jan 93 12:46:23 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 118 Please, distribute to related persons/organizations NATO ADVANCED STUDY INSTITUTE ----------------------------- MOLECULAR ASPECTS OF OXIDATIVE DRUG METABOLIZING ENZYMES AND THEIR SIGNIFICANCE IN ENVIRONMENTAL TOXICOLOGY, CHEMICAL CARCINOGENESIS,AND HEALTH JUNE 20 -- JULY 2 , 1993 KUSADASI-TURKEY ORGANIZED BY: Emel ARINC (TURKEY), Wolfgang KLINGER (GERMANY), John B. SCHENKMAN (USA), John J. STEGEMAN(USA) The primary aim of Institute will be on the recent advances in biochemical, regulatory and molecular aspects of oxidative drug metabolizing enzymes. Mainly cytochrome P450 dependent and Flavin containing monooxygenases will be covered. Significance of these enzymes in genotoxicology, environmental toxicology, chemical car- cinogenesis will be discussed. Therapeutic P450 inhibitors and cytochrome P4501A1 induction in fish and its potential use in bio- chemical monitoring will be considered as special topics of interest. LECTURERS: Richard F. ADDISON (CANADA) Wolfgang KLINGER (GERMANY) Diana ANDERSON (UK) Sergei V. KOTELEVTSEV (RUSSIA) Emel ARINC (TURKEY) David KUPFER (USA) Johannes DOEHMER (GERMANY) Anthony Y.H. LU (USA) Yoshiaki FUJII-KURIYAMA (JAPAN) Franz OESCH (GERMANY) John W. GORROD (UK) Richard M. PHILPOT (USA) Helmut GREIM (GERMANY) John B. SCHENKMAN (USA) Ernest HODGSON (USA) John J. STEGEMAN (USA) Eric F. JOHNSON (USA) Hugo Vanden BOSSCHE (BELGIUM) Chung S. YANG (USA) SESSIONS Session I : BIOCHEMISTRY AND MOLECULAR BIOLOGY OF THE MICROSOMAL CYTOCHROME P450 ISOZYMES Session II : FLAVIN CONTAINING MONOOXYGENASES Session III : METABOLISM AND TOXICITY OF DRUGS AND OTHER XENOBIOTICS Session IV : GENOTOXICOLOGY, PREDICTIVE TESTS, CHEMICAL CARCINOGENESIS AND CYTOTOXICITY Session V : THERAPEUTIC AGENTS AND CYTOCHROME P450 Session VI : ECOTOXICOLOGICAL ASPECTS OF CYTOCHROME P450 AND BIOCHEMICAL MONITORING OF AQUATIC POLLUTANTS Lectures, poster sessions, oral presentations and discussions will be held from 9:00 h. to 12.30 h. and from 16.30 h. till 19:00 h. Approximately 75 participants will be admitted. The Institute is located in a five-star KORUMAR Hotel which has its own beach and Con- ference rooms in KUSADASI, on the Aegean Coast. PARTICIPANTS The Advanced Study Institute will accomodate about 75 graduate stu- dents, post-doctoral fellows and senior scientists from universities, govermental organizations and the industry. Instructions for Applications ------------------------------ Persons wishing to attend the Institute should fill out the enclosed "Application Form" and send it to Director of ASI. Those applying for financial assistance will be required to include a statement giving rea- sons in support of their application and a letter of recommendation from a senior scientist active in the field. Scientific contributions by par- ticipants in poster sessions and in oral presentations (15 min.) are welcome. Abstracts not exceeding one page must be in English. DEADLINE FOR APPLICATION and ABSTRACT SUBMISSION: FEBRUARY 20, 1993 FINANCES: Participants are expected to cover their own travel and living expenses. A limited number of grants covering (part of) these expenses will be available for participants from NATO countries. NO REGISTRATION FEE IS DUE. Upon acceptance, a non-returnible deposit of 100 U.S. dollars will be requested from the successful candidates. Deposits will be reimbursed at the end of the course to the participants. The total cost including half-board, coffe servings, abstract book, and some activities is 550 US dollars per person sharing a double room. Accomodations for the par- ticipiants' family members are available at the same cost as for the participiants . Children at 0-6 years of age will be free of charge. For application forms, write to Dr. Emel ARINC Director of ASI Middle East Technical University ODTU TR 06531 ANKARA-TURKEY Fax: (90) (4) 210 12 79 Telex no: 42761 ODTK TR Tel: (90) (4) 210 10 00 ---> Ext. 3105 For information through E-mail contact Muzaffer TAYLAN CONSULT1@TRMETU.BITNET From owner-proteins@net.bio.net Thu Jan 07 22:00:00 1993 Path: biosci!ROCKVAX.ROCKEFELLER.EDU!masure From: masure@ROCKVAX.ROCKEFELLER.EDU Newsgroups: bionet.molbio.proteins Subject: (none) Message-ID: <9301090434.AA07352@rockvax.ROCKEFELLER.EDU> Date: 9 Jan 93 04:31:53 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 1 help From owner-proteins@net.bio.net Mon Jan 11 22:00:00 1993 Path: biosci!agate!ames!saimiri.primate.wisc.edu!caen!destroyer!news.iastate.edu!vincent1.iastate.edu!zsha From: zsha@iastate.edu (Zhengyu Sha) Newsgroups: bionet.molbio.proteins Subject: Re: protein transportation Message-ID: Date: 12 Jan 93 21:31:26 GMT References: <1iuvuiINNf0k@terminator.rs.itd.umich.edu> Sender: news@news.iastate.edu (USENET News System) Organization: Iowa State University, Ames IA Lines: 9 In <1iuvuiINNf0k@terminator.rs.itd.umich.edu> Mark A. Saper write: >I know about the periplasmic transport proteins ... these all have leader >sequences. Is the protein that you are working with known to not have a >leader sequence? I have cloned and seqed a catalase gene which I purified the enzyme from periplasmic fraction from B.abortus which is a gram-negative bacterium. N-terminal amino acid sequence of the purified enzyme show no cleavable leader sequence. The a.a. sequence predicted by the nuceotide seq. also did not show any signal-like sequences. I checked the a.a. sequence of the periplasmic catalase of E.coli HP I(Biochem.Biophys.Res.Comm. 154:392-397) in the gene bank and could not find a leader sequence too. A recent mini review in J.B. said membrane and periplasmic bacterial proteins used the uniformal secretion mechanism. In contrast, some of the extracellular proteins use self-promoted extracellular secretion mechanisms. I wonder if anyone has any idea? From owner-proteins@net.bio.net Mon Jan 11 22:00:00 1993 Path: biosci!daresbury!buzz.bmc.uu.se!corax.udac.uu.se!sunic!uunet!zaphod.mps.ohio-state.edu!howland.reston.ans.net!paladin.american.edu!gatech!destroyer!news.itd.umich.edu!nuntius From: saper@elmo.biop.umich.edu (Mark A. Saper) Newsgroups: bionet.molbio.proteins Subject: Re: protein transportation Message-ID: <1iuvuiINNf0k@terminator.rs.itd.umich.edu> Date: 12 Jan 93 17:42:42 GMT References: Organization: Biophysics Research Div., Univ. of Michigan Lines: 8 NNTP-Posting-Host: elmo.biop.umich.edu X-UserAgent: Nuntius v1.1 In article Zhengyu Sha, zsha@iastate.edu writes: >Could somenetter tell me how a periplasmic protein without a leader sequence is I know about the periplasmic transport proteins ... these all have leader sequences. Is the protein that you are working with known to not have a leader sequence? From owner-proteins@net.bio.net Sun Jan 17 22:00:00 1993 Path: biosci!agate!spool.mu.edu!howland.reston.ans.net!usc!elroy.jpl.nasa.gov!news.claremont.edu!nntp-server.caltech.edu!leda.cs.caltech.edu!mikael From: mikael@leda.cs.caltech.edu (Mikael P B Larsson) Newsgroups: bionet.molbio.proteins,bionet.neuroscience,bionet.software,bionet.xtallography Subject: interactive supercomputing Keywords: interactive supercomputing, computational engineering, Message-ID: <1jeeajINNrku@gap.caltech.edu> Date: 18 Jan 93 14:20:03 GMT Organization: California Institute of Technology Lines: 23 Xref: biosci bionet.molbio.proteins:498 bionet.neuroscience:907 bionet.software:3985 bionet.xtallography:130 NNTP-Posting-Host: leda.cs.caltech.edu computational biology, computational chemistry Hi, I am working with a new type of high speed logic and its applications for high performance computers. I am particularly interested in "interactive supercomputing". Being an electrical engineer, I have fairly naive views of what people in other disciplines might like to use a strong computer for, so I would be grateful if you could tell me what you are currently using computers for, what tasks you would like to run in interactive mode, where you would like to use models with higher resolution and so on. Pointers to the literature would also be greatly appreciated. Please reply by email. Thanks in advance Mikael Larsson Graduate Student Dept of Computer Science Caltech Pasadena From owner-proteins@net.bio.net Sun Jan 17 22:00:00 1993 Path: biosci!daresbury!doc.ic.ac.uk!pipex!uunet!olivea!news.bbn.com!hsdndev!husc-news.harvard.edu!husc.harvard.edu!ng4 From: ng4@husc10.harvard.edu (Ho Leung Ng) Newsgroups: bionet.molbio.proteins Subject: Ca2+ binding in calmodulin Message-ID: Date: 19 Jan 93 02:07:51 GMT Lines: 5 Nntp-Posting-Host: husc10.harvard.edu I forgot one thing. I am interested in the values for CaM without Ca2+ bound. Thanks Ho Leung Ng From owner-proteins@net.bio.net Sun Jan 17 22:00:00 1993 Path: biosci!daresbury!doc.ic.ac.uk!pipex!uunet!olivea!news.bbn.com!hsdndev!husc-news.harvard.edu!husc.harvard.edu!ng4 From: ng4@husc10.harvard.edu (Ho Leung Ng) Newsgroups: bionet.molbio.proteins Subject: Ca2+ binding in calmodulin Message-ID: Date: 19 Jan 93 02:03:41 GMT Lines: 6 Nntp-Posting-Host: husc10.harvard.edu Hello. For a course final project, I need to know the pKa of the charged residues in the Ca2+ binding sites in calmodulin. Would anyone know what they are (roughly) or where I can look up such information? Thanks. Ho Leung Ng From owner-proteins@net.bio.net Sat Jan 23 22:00:00 1993 Path: biosci!NET.BIO.NET!kristoff From: kristoff@NET.BIO.NET (David Kristofferson) Newsgroups: bionet.molbio.proteins Subject: BIOSCI/bionet Frequently Asked Questions Message-ID: <9301241000.AA22644@net.bio.net> Date: 24 Jan 93 10:00:02 GMT Sender: kristoff@net.bio.net Distribution: bionet Lines: 16 New users of BIOSCI/bionet may want to read the "Frequently Asked Questions" or "FAQ" sheet for BIOSCI. The FAQ provides details on how to participate in these forums and is available for anonymous FTP from net.bio.net [134.172.2.69] in pub/BIOSCI/biosci.FAQ. It may also be requested by sending e-mail to biosci@net.bio.net (use plain English for your request). The FAQ is also posted on the first of each month to the newsgroup BIONEWS/bionet.announce immediately following the posting of the BIOSCI information sheet. Sincerely, Dave Kristofferson BIOSCI/bionet Manager kristoff@net.bio.net From owner-proteins@net.bio.net Wed Jan 27 22:00:00 1993 Path: biosci!VM.UOGUELPH.CA!MCRGILAD From: MCRGILAD@VM.UOGUELPH.CA (Gilad Bernadsky) Newsgroups: bionet.molbio.proteins Subject: Short peptide sequencing Message-ID: <9301281620.AA23032@net.bio.net> Date: 28 Jan 93 16:12:51 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 23 Hi, I am sending this message for a respectful graduate student in our lab. Please reply to my E-mail address (mcrgilad@vm.uoguelph.ca). Thx, Gilad Dept. of Microbiolgy University of Guelph Canada ------------------------Original message------------------------- HELLO, I AM HAVING DIFFICULTIES SEQUENCING A SHORT (24 AMINO ACIDS) HYDROPHILIC PEPTIDE BY CONVENTIONAL MEANS (I.E. SOLID SUPPORT AND GAS PHASE). I SUSPECT THE PEPTIDE DOES NOT BIND TO THE SAMPLE MEMBRANE (WE TRIED THE MILLIPORE SEQUENET KIT). ANY SUGGESTIONS AND IDEAS WOULD BE MUCH APPRECIATED. THANKS, MARK BRAY DEPT. OF MICROBIOLOGY UNIVERSITY OF GUELPH CANADA From owner-proteins@net.bio.net Thu Jan 28 22:00:00 1993 Path: biosci!daresbury!doc.ic.ac.uk!warwick!uknet!comlab.ox.ac.uk!mikes From: mikes@bioch.ox.ac.uk (Mike Smith) Newsgroups: bionet.molbio.proteins Subject: Generating Structures from angles Message-ID: <1993Jan29.104904.10957@newton.bioch.ox.ac.uk> Date: 29 Jan 93 10:49:04 GMT Organization: Department of Biochemistry, University of Oxford Lines: 11 Originator: mikes@newton.bioch Hi there! Does anybody know of any programs (or has good ideas for programs) that would generate side-chains from angles? In particular, I am trying to calculate the coordinates of a TYR from the chi-1 and chi-2 angles, but am having difficulty doing this. Cheers Mike Smith From owner-proteins@net.bio.net Fri Jan 29 22:00:00 1993 Path: biosci!daresbury!buzz.bmc.uu.se!corax.udac.uu.se!sunic!mcsun!Germany.EU.net!gmd.de!newsserver.jvnc.net!yale.edu!spool.mu.edu!uwm.edu!psuvax1!psuvm!lxm116 From: LXM116@psuvm.psu.edu Newsgroups: bionet.molbio.proteins Subject: collagen, cross-linking data Message-ID: <93030.201032LXM116@psuvm.psu.edu> Date: 31 Jan 93 01:10:32 GMT Organization: Penn State University Lines: 7 I am posting this for a Physiology graduate student interested in data on intr- muscular connective tissue changes associated with resistance training. Looking for new or unpublished data specifically concerning crosslinking, fiber typing, and concentrations. If data available please include info on methods and molecular markers used. Any help is greatly appreciated. Send all responses to : txm137@psuvm.psu.edu From owner-proteins@net.bio.net Sun Jan 31 22:00:00 1993 Path: biosci!NBRF.GEORGETOWN.EDU!POSTMASTER From: POSTMASTER@NBRF.GEORGETOWN.EDU Newsgroups: bionet.molbio.proteins Subject: Announcements of PIR Network Request Service Message-ID: <01GU7OAL68NE9AMFK4@NBRF.Georgetown.Edu> Date: 1 Feb 93 19:55:08 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 301 Announcements of the Protein Information Resource Network Request Service Highlights 1. Summaries for PIR-International Release 35 and NRL_3D Release 11 2. The ALN Database of Protein Sequence Alignments 3. Confidentiality of Requests Submitted to the Network Request Server 4. PIR-International Technical Development Bulletin 5. GenBank and EMBL Database Sections 6. PIR Network Request Service Command Summary Announcements 1. Summaries for PIR-International Release 35 and NRL_3D Release 11 Release 35.00 of the PIR-International databases, Release 11.00 of the NRL_3D database (corresponding to Brookhaven Protein Data Bank Release 62), and Release 3.00 of the ALN database of protein sequence alignments, are now available through the PIR On-line system and Network Request Server. Distribution of the tapes of the new release has been completed and the CD-ROMs are due to be shipped shortly. Database Release Sequences Residues PIR1 35.00 10,928 3,761,590 Annotated and Classified Entries PIR2 34.00 16,662 4,453,825 Preliminary Entries PIR3 34.00 19,644 5,660,425 Unverified Entries NRL_3D 11.00 1,550 272,744 Sequences from Brookhaven PDB ALN 3.00 715 (entries) Protein Sequence Alignments Growth of the PIR databases is documented in the file DBGROWTH.LIS available through the Network Request Server. The following files are also available through the Server: entries added since Release 34.00 are listed in PADD.LIS, entries revised since Release 34.0 are listed in PREV.LIS, superfamiles recorded in PIR1 and PIR2 are listed in SUPERFAM.LIS, keywords employed in PIR1 and PIR2 are listed in KEYWORDS.LIS, features cataloged in PIR1 and PIR2 are listed in FEATURES.LIS, recognized journal abbreviations are listed in JOURNALS.LIS a description of the ALN database is in ALNBASE.LIS, titles in the ALN database are listed in ALNTITLE.LIS, titles in the NRL_3D Database are listed in NRLTITLE.LIS. 2. The ALN Database of Protein Sequence Alignments The Protein Information Resource (PIR) is developing a system for construction, storage and retrieval of alignments of protein sequences. The objective is a database of characteristic domain alignments with their known properties that might be useful for characterizing proteins of unknown structure and function as well as for describing the evolutionary relationships of multidomain proteins. In the initial phase, we have constructed a database of alignments of homologous protein sequences that are less than 55% different from each other. Groups of at least three sequences with comparable lengths and more than 50% identical were selected from Section 1, Annotated and Classified entries of the PIR-International Protein Sequence Database (PIR1). The ClustalV program of Des Higgins at EMBL was used to align the sequences initially. The alignments were checked by senior staff members at PIR and corrections were incorporated wherever necessary using the ALNED program developed at PIR. Other alignments developed as part of research projects at PIR, as well as alignments of domains and repeats have also been included. The database currently has 715 entries and can be accessed through the PIR On-line system, the Network Request Service and the ATLAS retireval system being developed at PIR. Description of an ALN database entry Each entry consists of a variable number of consecutive records. The information contained in these lines is divided into six sections. The sections are listed below in the order in which they occur in the entry. 1. TITLE The title of the alignment. 2. DATE Creation and revision dates. 3. MEMBERS The sequence identification codes of the sequences used in the alignment. 4. MEMBERS TITLES The members title lines, as found in the Protein Sequence Database. 5. ALIGNMENT (variable number of records) The alignment of sequences. The completely conserved residues are marked by '*' and partially conserved residues are marked by '.' at the bottom of the alignment. 6. MATRIX The matrix of percent differences. The upper portion of the matrix gives the number of differences between the sequences while the lower portion represents the same as percent differences. 3. Confidentiality of Requests Submitted to the Network Request Server All requests submitted to the PIR Network Request Server, including protein and nucleotide sequences submitted for FASTA search against the PIR-International protein sequence databases, are confidential within the following limitations. The requests are stored in files in a directory that is not accessible to the public through either network communication or the on-line system. Network access is only possible through the server daemon and then only in response to the network request, coded by date, time and address, that generated the file. The files are not accessible to PIR personnel except those with the computer system privileges necessary to conduct computer hardware and software maintenance. The files, other than those generated by PIR staff members, are examined only for accounting purposes and to monitor and ensure correct software performance. Accounting summaries are generated for user address distribution, numbers of requests, and numbers of commands on a monthly basis. The files may be retained for up to one month for this accounting and are then deleted. This confidentiality does not, of course, apply to protein sequences submitted through the Server for inclusion in the PIR-International database. 4. PIR-International Technical Development Bulletin We have on-going efforts to standardize the PIR databases, improving their parsability and compliance with CODATA and other format standards. During the next year the combined staffs of the PIR-International will be imposing and enforcing many new rules and requirements on the distributed versions of the database. Some of these rules and requirements may affect the currently existing software designed to read the PIR databases in "NBRF format". Notification of the broader aspects of these changes will be placed in our newsletters and in announcements posted on the BioSci Newsgroups PROTEINS and BIONEWS. However, some people may wish to be informed about the technical aspects of these changes before they appear in a database release. For that reason we will be setting up an electronic mailing list to inform software developers and others interested in the technical aspects of these database changes. This electronic bulletin serves as an "early warning system" for people who are concerned about changes in the format and standards for PIR database entries. The first bulletin was posted on 22 January. Hereafter, they should appear approximately quarterly. The first bulletin may be obtained by sending the request SEND PIRTECH.LIS to the PIR Network Request Server. If you would be interested in being placed on this mailing list, please send a brief electronic mail note to me at POSTMAST@GUNBRF.BITNET or POSTMASTER@NBRF.Georgetown.Edu. 5. GenBank and EMBL Database Sections The GenBank and EMBL entries available on the On-line system and the Network Request Server are now divided into the standard 13 libraries. The GBNEW section contains the GenBank weekly update entries. All these databases are automatically available on the Server through all the commands that can use them. Particular databases may be selected with the USE BASES command described at the end of the Server command summary. 6. PIR Network Request Service Command Summary The National Biomedical Research Foundation Protein Information Resource network request service is a full-function fileserver and database query system. Operating since August 1990 it is capable of handling database queries, sequence searches and sequence submissions, in addition to fileserver requests. To use this server, request commands should be sent to FILESERV@GUNBRF on BITNET or FILESERV@NBRF.Georgetown.EDU on Internet. The server recognizes the following commands sent either in a mail message, or (if the sender is on BITNET) in a command message or a file: Command Action ------- ----------------------------------------------- ACCESSION list entry codes and titles by accession number AND combine QUERY commands with Boolean AND AUTHOR list entry codes and titles by author BASES list accessible databases CROSS list PIR entry codes and titles corresponding to a particular nucleic sequence database entry DEPOSIT deposit entry for database submission END DEPOSIT terminate deposit entry FEATURE list entry codes and titles by feature table entry GENE list entry codes and titles for a gene name 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 MEMBER list alignments containing entry code as a member NOT combine QUERY commands with Boolean NOT OR combine QUERY commands with Boolean OR QUERY begin collecting QUERY commands END QUERY terminate collecting commands and execute QUERY QUIT ignore the remaining text (E-mail signature blocks) RETURN change return address for gateway mail SEARCH search for matching sequences 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 USE set databases, dates or formats to use in limited searches 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: Custom_Services Databases FTP Gateway_Access Help_en_Espanol Help_en_francais Hints IBM-VM_BITNET On-Line_Access PIR_Distribution VAX-VMS_BITNET Because of network gateway communication protocols, there are limitations on requests sent through gateways. Users not on BITNET or INTERNET who access the server through local or 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 addresses posted on gateway mail do not always work for the return, before you send requests through network gateways it is strongly recommended that you first contact John S. Garavelli (POSTMAST@GUNBRF on BITNET, POSTMASTER@NBRF.Georgetown.EDU on Internet). We will confirm a return address for you and may instruct you to use the RETURN command to ensure 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 nonstandard return address (for example a personal name on the FROM: line). The BITNET network and the network gateways impose strict limits on file size. 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 for each request is imposed by the PIR server. The DEPOSIT and QUERY commands, and the SEARCH and SUGGEST commands (in their multiline form) must be followed by their respective END commands after the text appearing on the intervening lines. The DEPOSIT command requires, and the SEARCH command optionally uses, parameters that appear on the same line as the command. Because these four commands are so complex, users should obtain and carefully read the help instructions before attempting to use them. The databases available through the PIR Network Server and their abbreviations for code specification are as follows: Abbreviation Database Update Schedule PIR1 PIR Annotated and Classified Entries approximately biweekly PIR2 PIR Preliminary Entries approximately weekly PIR3 PIR Unverified Entries weekly ALN PIR Alignment Entries semiannually NRL_3D Brookhaven Data Bank Sequences quarterly PATCHX MIPS PIR-Supplementary Database quarterly N NBRF Nucleic GB* GenBank (TM) as received GBNEW GenBank (TM) New Entries weekly EMBL* EMBL as received In the FASTA output of the SEARCH command the abbreviation for PATCHX is shortened to PATX and NRL_3D is shortened to NR3D; the longer abbreviation should be used to retrieve an entry with the GET command. Not all commands work with all databases; please read the information returned by the command HELP DATABASES. The GenBank (TM), GB, and EMBL databases are now divided into sections corresponding to the sections of their standard releases: -BCT Bacterial Sequences -EST EST Sequences -INV Invertebrate Sequences -MAM Other Mammalian Sequences -PHG Phage Sequences -PLN Plant Sequences -PRI Primate Sequences -RNA Struct RNA Sequences -ROD Rodent Sequences -SYN Synthetic Sequences -UNA Unannotated Sequences -VRL Viral Sequences -VRT Other Vertebrate Sequences These databases may be indivually accessed with the USE BASES command with the database abbreviation and the section abbreviation, for example USE BASES GBPRI or all sections of a given database may be accessed with the database abbreviation and an asterisk, for example USE BASES PIR* or USE BASES GB* ------------------------------------------------------------------------ Dr. John S. Garavelli Database Coordinator Protein Information Resource National Biomedical Research Foundation Washington, DC 20007 POSTMAST@GUNBRF.BITNET POSTMASTER@NBRF.Georgetown.Edu