From owner-evolution@net.bio.net Tue May 04 23:00:00 1999 Path: biosci!biosci!not-for-mail From: Darcio Matenhauer Lehrbach Newsgroups: bionet.molbio.evolution Subject: Introns envolved in evolution Date: 5 May 1999 12:02:38 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 19 Sender: daemon@net.bio.net Approved: mevolve@valis.microbiol.washington.edu Distribution: world Message-ID: <7gq4ke$m7d@net.bio.net> NNTP-Posting-Host: net.bio.net Hi, I'd like to discuss and change informations about the evolution of organisms studied in their splicing process. The majority of prokaryotes doesn't have introns, but all the eukaryotes have. So, have introns acquired by eukaryotes genes or have it lost by prokaryotes during the evolution of them? Let's discuss! Thanks Darcio Darcio M. Lehrbach darcio@mailandnews.com darcioml@hotmail.com From owner-evolution@net.bio.net Wed May 05 23:00:00 1999 Path: biosci!biosci!not-for-mail From: D. R. Forsdyke Newsgroups: bionet.molbio.evolution Subject: Genomics = Genome sequencing?? Date: 6 May 1999 08:12:38 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 18 Sender: daemon@net.bio.net Approved: mevolve@valis.microbiol.washington.edu Distribution: world Message-ID: <7gsbh6$h3d@net.bio.net> NNTP-Posting-Host: net.bio.net The leading article in Nature (15th April) is entitled "WAKE UP CALL FOR JAPAN'S GENOMICS". On reading further one finds that it is about genome sequencing, NOT genomics. Of course, one has to have some sequence before one can begin genomics, the latter being the STUDY of sequences, and all that this entails (bioinformatic and evolutionary analysis for example). But, HOW MUCH SEQUENCE IS ENOUGH? The techological imperative seems to have taken over again. Give the guys some sequencers and a genome, and they will go on and on until the end, and then go about looking for MORE genomes. All this requires megabucks whether you count in yen or dollars! How sad that so little of this funding employed in doing REAL genomics. Sincerely, Donald Forsdyke http://post.queensu.ca/~forsdyke/bioinfor.htm From owner-evolution@net.bio.net Thu May 13 23:00:00 1999 Path: biosci!biosci!not-for-mail From: Mr Clive Delmonte Newsgroups: bionet.molbio.evolution Subject: "Junk" DNA Date: 14 May 1999 08:32:33 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 66 Sender: daemon@net.bio.net Approved: mevolve@valis.microbiol.washington.edu Distribution: world Message-ID: <7hhfmh$e6@net.bio.net> NNTP-Posting-Host: net.bio.net May I make a belated, and rather different contribution to the recent discussion about the nature and purpose of "junk" DNA ? There is the possibility that the purpose of "junk" DNA is to enable long lengths of like-sequence, repetitive DNA to recognise each other, which could explain why it is needed in such long lengths. (I suspect we might only call it "junk" DNA because we haven't yet agreed a secure purpose for it.) Long lengths of repetitive DNA capable of recognising the same, or closely similar, repeat sequences could assist in the formation of the "30 nm" fibre of compacted nucleosomes, and in the assembly of centromeres. In addition, prior to cell division, the pairing of like chromosomes could be facilitated before separation during mitosis or meiosis, for example. The 13 pairs of human chromosomes would each need closely similar repeat sequences (each with the other), and these would need to be rather different from the repeat sequences in the other pairs. Perhaps subscribers know the repeat sequences of all of the human chromosomes ? The unique pairing of Watson-Crick base pairs, AT with AT and GC with GC, was described first by Loewdin in 1963, as far as I am aware. These properties of DNA and others are explored and developed in detail in my two books (1,2). In a single posting it is impossible to develop the arguments, but those wishing to consider fresh aspects of the behaviour of DNA may care to view the newsgroup "bionet.biophysics" to which I am currently posting the second series of DNA Structure Puzzles intended to focus attention on the wide range of experimental data which is otherwise unexplained in the literature. The attachments to the DNA Structure Puzzles in "bionet.biophsyics" include sketches of how individual base pairs can themselves form pairs, as well as a sketch of a model of DNA which facilitates such pairing. To any interested subscribers, I could send e-mail attachments of the scheme for pairing base pairs, and of the framework of the overall structure within which such pairing is facilitated. -------------------------------------------------------- 1 Towards a New Structural Molecular Biology, by Clive Delmonte (1991) ISBN 0 9512276 0 2 "...I find much of Delmonte's critique of other workers sound enough to raise doubt in my mind about the bulk of the classical work in this area. ...the book was an eye-opener." Prof. Steven Benner at Eidgenossische Technische Hochscule, Zurich ------------------------------------------- "...the widely accepted Watson-Crick model is inadequate to explain many important pieces of data, and in some cases defies intuitive biological and physical logic as a predictive model..I commend you on your recognition of inconsistencies in the story of DNA..you have the potential of changing molecular biology." Prof. Robert Hopkins at the School of Applied and Natural Sciences in the University of Houston at Clear Lake, Texas ---------------------------------------------- 2 Advances in AFM & STM Applied to the Nucleic Acids, by Clive Delmonte (1997) ISBN 0 9512276 2 9, Library of Congress TX 4-856-037 ----------------------------------------------- Clive Delmonte --- From owner-evolution@net.bio.net Mon May 17 23:00:00 1999 Path: biosci!biosci!not-for-mail From: Chris Botka Newsgroups: bionet.molbio.evolution Subject: distances in years Date: 18 May 1999 12:18:17 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 24 Sender: daemon@net.bio.net Approved: mevolve@valis.microbiol.washington.edu Distribution: world Message-ID: <7hsedp$ks@net.bio.net> NNTP-Posting-Host: net.bio.net I have a user who has constructed a tree using PAUP. She would now like to represent the distances between the sequences in years. I am not sure that this is possible, or how accurate it might be, but I vaguely remember seeing a figure or 2 where the relationships between sequences in a tree were described using a divergence estimate in years. If anyone could direct me to a source where this is discussed, or a program that would make this estimate, I would appreciate it. Thanks, Chris ______ Christopher W Botka Phone: (415)476-5379 Sequence Analysis Consulting Service Fax: (415)502-1755 UCSF Computer Graphics Lab Office: Lib-111 Internet: botka@cgl.ucsf.edu Mail Drop: Box 0446 http://www.sacs.ucsf.edu/ NeXT/MIME mail OK From owner-evolution@net.bio.net Tue May 18 23:00:00 1999 Path: biosci!biosci!not-for-mail From: Brian Foley Newsgroups: bionet.molbio.evolution Subject: Re: distances in years Date: 18 May 1999 17:20:07 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 25 Sender: daemon@net.bio.net Approved: mevolve@valis.microbiol.washington.edu Distribution: world Message-ID: <7ht03n$8rn@net.bio.net> NNTP-Posting-Host: net.bio.net Chris Botka wrote: > > I have a user who has constructed a tree using PAUP. She would now > like to represent the distances between the sequences in years. If you have the phylogenetic distances from PAUP or PHYLIP or any other method, you also need to know the rate of change per year for this gene in this organism to calculate time from genetic distance. Otherwise, the fossil record or other physical evidence can be used to put dates on a tree. Keep in mind that the distance vs time plot is not linear. An organism that evolves at roughly 1% per year will not change 100% in 100 years. The variable sites will be mutated many times, while invariant sites do not change at all. -- ____________________________________________________________________ |Brian T. Foley btf@t10.lanl.gov | |HIV Database (505) 665-1970 | |Los Alamos National Lab http://hiv-web.lanl.gov/index.html | |Los Alamos, NM 87544 U.S.A. | |____________________________________________________________________| From owner-evolution@net.bio.net Tue May 18 23:00:00 1999 Path: biosci!biosci!not-for-mail From: Mike Syvanen Newsgroups: bionet.molbio.evolution Subject: Re: distances in years Date: 19 May 1999 13:06:54 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 36 Sender: daemon@net.bio.net Approved: mevolve@valis.microbiol.washington.edu Distribution: world Message-ID: <7hv5ku$8uh@net.bio.net> NNTP-Posting-Host: net.bio.net Chris Botka wrote: > I have a user who has constructed a tree using PAUP. She would now > like to represent the distances between the sequences in years. > > I am not sure that this is possible, or how accurate it might be, > but I vaguely remember seeing a figure or 2 where the relationships > between sequences in a tree were described using a divergence > estimate in years. > > If anyone could direct me to a source where this is discussed, or a > program that would make this estimate, I would appreciate it. > > Thanks, > > Chris Don't even try to calibrate a PAUP tree with years. I have looked into this and it shouldn't be done. ( I presume you are trying to calibrate a PAUP phylogram and not a cladogram.) This is what you should do. Construct a nearest-neighbor or some other distance tree (you can use the topology from the PAUP output if you wish, but most packages will find the best topology for you). You can then try to calibrate that tree following Brian Foley's suggestions. Mike Syvanen From owner-evolution@net.bio.net Wed May 19 23:00:00 1999 Path: biosci!biosci!not-for-mail From: Mike Syvanen Newsgroups: bionet.molbio.evolution Subject: Re: distances in years Date: 20 May 1999 14:07:19 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 21 Sender: daemon@net.bio.net Approved: mevolve@valis.microbiol.washington.edu Distribution: world Message-ID: <7i1ti7$93q@net.bio.net> NNTP-Posting-Host: net.bio.net Andrew Rambaut wrote: > > > I guess by PAUP tree you mean parsimony tree. PAUP (4) can do NJ and ML > trees which are suitable for calibration. Of course if he has a > hypothesis to test he will need some measure of error which PAUP can't > do. > > Andrew Thanks for the information. Since PAUP means "phylogenetic analysis using parsimony" I've always equated it with parsimony, but that is obviously an ambiguous usage now. Mike Syvanen From owner-evolution@net.bio.net Wed May 19 23:00:00 1999 Path: biosci!biosci!not-for-mail From: Andrew Rambaut Newsgroups: bionet.molbio.evolution Subject: Re: distances in years Date: 20 May 1999 08:05:16 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 15 Sender: daemon@net.bio.net Approved: mevolve@valis.microbiol.washington.edu Distribution: world Message-ID: <7i18bc$ge3@net.bio.net> NNTP-Posting-Host: net.bio.net In article <7hv5ku$8uh@net.bio.net>, Mike Syvanen wrote: > Don't even try to calibrate a PAUP tree with years. I have looked into > this and it shouldn't be done. ( I presume you are trying to calibrate a PAUP > phylogram and not a cladogram.) This is what you should do. Construct > a I guess by PAUP tree you mean parsimony tree. PAUP (4) can do NJ and ML trees which are suitable for calibration. Of course if he has a hypothesis to test he will need some measure of error which PAUP can't do. Andrew From owner-evolution@net.bio.net Thu May 20 23:00:00 1999 Path: biosci!biosci!not-for-mail From: Mark Dowton Newsgroups: bionet.molbio.evolution Subject: Bootstrap trees and PAUP Date: 20 May 1999 17:44:43 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 22 Sender: daemon@net.bio.net Approved: mevolve@valis.microbiol.washington.edu Distribution: world Message-ID: <7i2a9r$3v6@net.bio.net> NNTP-Posting-Host: net.bio.net I've always thought you could save the shortest trees found after each bootstrap replicate, then generate a majority rule consensus tree with these, and that this should be the equivalent of the 'bootstrap tree' (by bootstrap tree, I mean the one that is output by PAUP at the completion of a bootstrap analysis). One problem with this is that if some replicates generate many equally parsimonious trees (say 100), while others only generate a single (or a few) most parsimonious tree(s), the maj. rule tree will be overly influenced by those replicates in which many equally parsimonious trees are found. I was under the impression that this was also a problem (although admittedly minor in most cases) with the bootstrap tree, but a friend tells me that the PAUP bootstrap tree corrects this. Is this the case? -- Mark Dowton Dept Biology Wollongong University Wollongong, NSW, 2522 AUSTRALIA Mark_Dowton@uow.edu.au From owner-evolution@net.bio.net Thu May 20 23:00:00 1999 Path: biosci!biosci!not-for-mail From: Andrew Rambaut Newsgroups: bionet.molbio.evolution Subject: Re: distances in years Date: 21 May 1999 10:15:34 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 12 Sender: daemon@net.bio.net Approved: mevolve@valis.microbiol.washington.edu Distribution: world Message-ID: <7i44bm$qb1@net.bio.net> NNTP-Posting-Host: net.bio.net In article <7i1ti7$93q@net.bio.net>, Mike Syvanen wrote: > Thanks for the information. Since PAUP means "phylogenetic analysis > using parsimony" I've always equated it with parsimony, but that is obviously > an ambiguous usage now. Yes, its called PAUP* where the * refers to a note saying "and maximum likelihood" or something. Andrew From owner-evolution@net.bio.net Thu May 20 23:00:00 1999 Path: biosci!biosci!not-for-mail From: Matt Kane Newsgroups: bionet.molbio.evolution Subject: SMITHSONIAN POSTDOCS IN MOLECULAR SYSTEMATICS & EVOLUTION Date: 21 May 1999 10:15:22 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 53 Sender: daemon@net.bio.net Approved: mevolve@valis.microbiol.washington.edu Distribution: world Message-ID: <7i44ba$q9f@net.bio.net> NNTP-Posting-Host: net.bio.net POSTDOCTORAL POSITIONS IN MOLECULAR SYSTEMATICS AND EVOLUTION ------------------------------------------ The Laboratory of Molecular Systematics at the National Museum of Natural History, Smithsonian Institution, invites applications for 1- and 2-year postdoctoral fellowships. Fellows are expected to conduct research in close collaboration with one of three LMS senior scientists, whose areas of research are given below. Stipends currently are $27,000 per year plus benefits. Awards are made on the basis of competitive review of written research proposals, qualifications and training. Applications from female and minority applicants are encouraged. The application deadline is 15 January 2000. To begin the application process, send curriculum vitae, names and phone numbers of 3 references and a short statement of research interests to Dr. Matthew D. Kane, Biological Sciences Program Administrator at kane@lms.si.edu or at Laboratory of Molecular Systematics, Smithsonian Institution Support Ctr., 4210 Silver Hill Rd. Suitland, MD 20746; Telephone: (301) 238-3444, x108. MICHAEL J. BRAUN, Director, Laboratory of Molecular Systematics; Curator, Vertebrate Zoology. Research specialties: genetic analysis of avian hybridization and speciation, molecular systematics and population genetics of birds, use of ancient DNA in evolutionary research. DAVID L. SWOFFORD, Principle Investigator, Laboratory of Molecular Systematics; Curator, Vertebrate Zoology. Research specialties: theory and methodology of phylogenetic inference from morphological, genetic, and molecular data; systematics of fishes. ELIZABETH A. ZIMMER, Principal Investigator, Laboratory of Molecular Systematics; Curator, Botany. Research specialties: molecular systematics of flowering plants; structure and differential expression of multigene families (particularly in interspecific hybrids); development of molecular markers across a range of species divergence; and molecular basis of morphological and developmental adaptations. Dr. Matthew D. Kane Laboratory of Molecular Systematics National Museum of Natural History Smithsonian Institution Museum Support Center 4210 Silver Hill Road Suitland, MD 20746 Telephone: (301) 238-3444 EX. 108 Fax: (301) 238-3059 email:kane@lms.si.edu From owner-evolution@net.bio.net Fri May 21 23:00:00 1999 Path: biosci!biosci!not-for-mail From: oneiro@asu.edu Newsgroups: bionet.molbio.evolution Subject: estimated divergence times Date: 21 May 1999 17:54:49 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 22 Sender: daemon@net.bio.net Approved: mevolve@valis.microbiol.washington.edu Distribution: world Message-ID: <7i4v8p$qmp@net.bio.net> NNTP-Posting-Host: net.bio.net I am not sure if this answers your question, but nor am i sure that anyone else did either. Perhaps you might try Kumar S, et al. A molecular timescale for vertebrate evolution. Nature. 1998 Apr 30;392(6679):917-20. PMID: 9582070; UI: 98241226. or Hedges SB, et al. Continental breakup and the ordinal diversification of birds and mammals. Nature. 1996 May 16;381(6579):226-9. PMID: 8622763; UI: 96208645. Pubmed has a lot on the subject I think. Hope this helps, or at least doesn't wast your time. -Roman Johnson _______________________________________________________________________________ "Think you can, think you can't; either way you're right." -Henry Ford From owner-evolution@net.bio.net Sat May 22 23:00:00 1999 Path: biosci!biosci!not-for-mail From: Joe Felsenstein Newsgroups: bionet.molbio.evolution Subject: Re: Bootstrap trees and PAUP Date: 23 May 1999 10:51:44 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 20 Sender: daemon@net.bio.net Approved: mevolve@valis.microbiol.washington.edu Distribution: world Message-ID: <7i9f7g$4kr@net.bio.net> NNTP-Posting-Host: net.bio.net In article <7i2a9r$3v6@net.bio.net>, Mark Dowton wrote: >... One problem with this is that if some replicates >generate many equally parsimonious trees (say 100), while others only >generate a single (or a few) most parsimonious tree(s), the maj. rule tree >will be overly influenced by those replicates in which many equally >parsimonious trees are found. > >I was under the impression that this was also a problem (although >admittedly minor in most cases) with the bootstrap tree, but a friend >tells me that the PAUP bootstrap tree corrects this. Is this the case? I am virtually certain that PAUP corrects for this (I know that PHYLIP does too). One counts the trees when there are 100 of them as 0.01 of a tree each, in doing the consensus tree. -- Joe Felsenstein joe@genetics.washington.edu Dept. of Genetics, Univ. of Washington, Box 357360, Seattle, WA 98195-7360 USA From owner-evolution@net.bio.net Sun May 23 23:00:00 1999 Path: biosci!biosci!not-for-mail From: Francisco M. De La Vega Newsgroups: bionet.molbio.evolution Subject: CALL-FOR-PAPERS: SNP Data Analysis & Management at PSB'2000 Date: 24 May 1999 11:04:01 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 111 Sender: daemon@net.bio.net Approved: mevolve@valis.microbiol.washington.edu Distribution: world Message-ID: <7ic4ah$lm8@net.bio.net> NNTP-Posting-Host: net.bio.net Human Genome Variation: Analysis, Management and Application of SNP Data A session of the Pacific Symposium on Biocomputing 2000, Honolulu, Hawaii, January 5-9, 2000 Recently there has been considerable interest in using single nucleotide polymorphisms (SNP) for the understanding of complex diseases and for pharamacogenetics. The human genetics community, both private and academic, is engaged in large scale SNP discovery efforts and assay development. With the imminent development of high throughput methodologies for automating the SNP discovery and screening process, it is likely that many if not all of the common polymorphisms will be identified and characterized in the next several years. As is often the case, data production may outpace current data management and analysis capabilities. New, specialized SNP databases are being designed and implemented to capture the impending flood of polymorphism data. Comprehensiveness of the captured data and the exploration of its intellectual content is essential. Computational methods and tools to handle and analyze polymorphism data flow will certainly play an important role in this challenge. Call for Participation The PSB 2000 session "Human Genome Variation: Analysis, Management and Application of SNP Data" aims to provide a timely forum in this area, bringing together computer scientists, bioinformatics specialists and biologists, from academia and industry, to address the forthcoming problems in the utilization of SNP information. We encourage academic, industrial and government scientists to submit manuscripts. In addition to a session for oral presentation of novel peer-reviewed contributions, there will be a panel discussion devised to foster exchange between industry and academic scientists. Participants are invited to discuss their issues with other peers in this panel session. Posters and computer demonstrations are also requested to complement the session. Topics The contributions should pose and discuss a specific problem that the biocomputing community will need to address, describe models, or propose specific solutions to a problem. Sequence polymorphisms will be the common theme, but the computational or theoretical contributions can span areas ranging from population genetics and evolution to data visualization and management. Among the anticipated topics are: Automation of large scale SNP genotyping. Data management and integration for SNP genotyping systems. Evolutionary aspects of genome variability and SNP analysis. Ontologies for human genome variation. SNP database mining and knowledge discovery. Statistical methods for SNP analysis. Tools for high throughput SNP discovery and screening. Visualization and analysis of SNP data. Submissions PSB will publish accepted full papers in an archival proceedings indexed in MEDLINE. All contributed papers will be rigorously peer-reviewed by at least three referees. A limited number of papers will be selected for a 30-minute oral presentation to the full assembled conference. Accepted poster abstracts will be distributed at the conference separately from the archival Proceedings. Please prepare your submission according to the instructions found at the Web page: http://www.cgl.ucsf.edu/psb/cfp-snp.html Dates & Deadlines Paper submissions due: July 12, 1999 Notification of paper acceptance: August 27, 1999 Camera ready of accepted papers due: September 24, 1999 Abstract deadline: October 1, 1999 Meeting: January 5-9, 2000 Conference Information The Pacific Symposium on Biocomputing (PSB 2000) is an international, multidisciplinary conference for the presentation and discussion of current research in the theory and application of computational methods in problems of biological significance. PSB 2000 will be held January 5- 9, 2000, in Honolulu, Hawaii at the Sheraton Waikiki. For more information see the official PSB 2000 Web page at : http://www.cgl.ucsf.edu/psb/ Session Chairs Francisco M. De La Vega, Synthesis and Arrays R&D, PE Biosystems, Foster City, CA, USA. E-mail: DelaveFM@pebio.com Martin Kreitman, Department of Ecology and Evolution, University of Chicago, Chicago, IL, USA. E-mail: mkre@midway.uchicago.edu From owner-evolution@net.bio.net Wed May 26 17:12:00 1999 Path: biosci!biosci!not-for-mail From: BIOSCI Administrator Newsgroups: bionet.molbio.evolution Subject: BIOSCI/bionet miniFAQ & Fundraiser Date: 26 May 1999 11:12:02 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 234 Sender: daemon@net.bio.net Approved: mevolve@valis.microbiol.washington.edu Distribution: world Message-ID: <7ihdhi$kc2@net.bio.net> NNTP-Posting-Host: net.bio.net (LAST REVISION: 30-JUL-95) This BIOSCI "miniFAQ" is designed to answer the questions that come up the *most frequently*. The main BIOSCI FAQ (Frequently Asked Questions) is accessible on the World Wide Web at URL http://www.bio.net/. If you can not find an answer to your question in this or other documentation, the BIOSCI technical support staff answers e-mail queries sent to biosci-help@net.bio.net We can only answer questions about the use of the newsgroups and mailing lists. We unfortunately do not have the staff to do Internet information searches or answer scientific questions. Please post those to the appropriate BIOSCI/bionet newsgroups. Contents: -------- 0) BIOSCI NEEDS YOUR SUPPORT!! 1) Using the WWW to access the BIOSCI/bionet newsgroups. 2) What to do about "spams," i.e., junk mail, ads, etc. 3) Examples of subscribing and unsubscribing to the mailing lists. 4) The BIOSCI user address and research interest directory. 0) BIOSCI NEEDS YOUR SUPPORT!! ------------------------------ BIOSCI's government funding has been expended, and we are now operating solely from advertising revenue that we have raised from our Web site at http://www.bio.net/. We need just a few minutes of your time to help us serve you. You can do two important things which will take very little time for you individually and will immensely help us continue to help you. First, please use our WWW system at http://www.bio.net/ to access the archives. You can post or reply to messages via your Web browser as described in item #1 below. Your usage helps attract sponsors. If you contact any of our sponsors, please be sure to thank them for supporting BIOSCI. It is critical for them to get this feedback if they are to continue their sponsorship for the long term. Second, if you work for a company or organization that provides products or services of interest to the biology community, please pass this message on to your marketing or marketing communications department or other appropriate group. Please ask them to help support BIOSCI by sponsoring our Web site and explain the uses and benefits of the system to the biology community. If they are interested, they can then contact us for further information at our tech support address, biosci-help@net.bio.net. 1) Using the WWW to access the BIOSCI/bionet newsgroups. -------------------------------------------------------- As of 10 December 1995, all BIOSCI/bionet full newsgroups are accessible through the World Wide Web (WWW) at URL http://www.bio.net. One can read and reply publicly or privately to both recent postings and archived messages through one's Web browser if it is configured properly to send e-mail. Each newsgroup is equipped with its own WAIS index. 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Below we give an example utilizing the METHODS-AND-REAGENTS list at both of our two BIOSCI sites: Users in the Americas and Pacific Rim countries who use the BIOSCI ------------------------------------------------------------------ node at computer net.bio.net: ---------------------------- A) Determine the "listname" which is the <=8 character mail address ^^^^^^^^^^^^^ for the group. These can be found in the BIOSCI Info. Sheet. For the METHODS-AND-REAGENTS group the mailing address is methods@net.bio.net. The listname is the portion of the address to the left of the @ sign, i.e., "methods". The listname is used with the "subscribe" and "unsubscribe" commands illustrated below. B) Mail all commands in the body of a mail message addressed to biosci-server@net.bio.net. Do NOT send commands to the newsgroup posting addresses! Leave the Subject: line blank, any text on it will be ignored. C) In the body of your message put one or more of the following commands with an "end" command on the last line, e.g., subscribe methods unsubscribe methods end Do NOT put your e-mail address or other text on these lines. The server only allows you to cancel your subscription if the address on your mail header matches the address on our mailing list. Please ask for help at biosci-help@net.bio.net if your address has changed, e.g., if you know you are on the list but the server tells you that you are not a member. Users in Europe, Africa, and Central Asia who use the BIOSCI node at -------------------------------------------------------------------- computer daresbury.ac.uk (also known as dl.ac.uk): ------------------------------------------------- To subscribe and unsubscribe to/from the BIOSCI lists, you need to specify the full USENET newsgroup name with "bionet-news." prepended. The USENET newsgroup names are listed in the BIOSCI Information sheet on the Web at http://www.bio.net/. For the METHODS-AND-REAGENTS list the USENET newsgroup name is bionet.molbio.methds-reagnts, thus the appropriate commands are sub bionet-news.bionet.molbio.methds-reagnts unsub bionet-news.bionet.molbio.methds-reagnts These commands are included in a message addressed to mxt@dl.ac.uk, NOT to the newsgroup mailing addresses. As usual, include the text in the body of the message as text on the Subject: line is ignored. To unsubscribe from all the lists at the UK node, use unsub bionet-news Please note that if the address in the list is different than the one in your mail message header, you will not be able to unsubscribe by this method. If you have problems, please mail biosci@daresbury.ac.uk. 4) The BIOSCI user address and research interest directory. ----------------------------------------------------------- Please take this opportunity to add your name, address, and research interest information to the BIOSCI User Address Database if you have not already done so. You can fill out the address form directly through our Web page at URL http://www.bio.net/adrform.html. The address database is reindexed nightly for WWW access (the URL is http://www.bio.net/). If you are not directly on the Internet but can reach it by e-mail, please use our waismail server to access the user directory. waismail use is described above. You can also request a user address form by e-mail from biosci-help@net.bio.net. Please check your database entry from time-to-time to see if your address information is still up-to-date. Because of our limited personnel resources, we ask that you resubmit a *complete* form to revise your entry; we only replace complete entries and do not have resources to edit old forms. From owner-evolution@net.bio.net Mon May 31 14:19:00 1999 Path: biosci!biosci!not-for-mail From: Kay Diederichs Newsgroups: bionet.molbio.evolution Subject: mapping completed genome projects onto phylogenetic tree Date: 31 May 1999 08:19:37 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 18 Sender: daemon@net.bio.net Approved: mevolve@valis.microbiol.washington.edu Distribution: world Message-ID: <7iu9a9$gpv@net.bio.net> NNTP-Posting-Host: net.bio.net Hi, I am interested in a mapping of all completed genome projects onto the phylogenetic tree. I´m thinking of a rather detailed picture that I could produce if I could find a tree detailed enough to find the organisms. Is there a paper with such a picture, or a website? Thanks for your help, Kay -- Kay Diederichs http://strucbio.biologie.uni-konstanz.de/~kay email: Kay.Diederichs@uni-konstanz.de Tel +49 7531 88 4049 Fax 3183 Fakultaet fuer Biologie, Universitaet Konstanz Box M656, D-78457 Konstanz, Germany