From owner-software@net.bio.net Thu Sep 01 23:00:00 1994 Path: biosci!WAM.UMD.EDU!qfang From: qfang@WAM.UMD.EDU (Fang Qingquan) Newsgroups: bionet.software Subject: Re: Amino acid usage for various species Date: 2 Sep 1994 08:31:57 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 24 Sender: daemon@net.bio.net Distribution: world Message-ID: References: NNTP-Posting-Host: net.bio.net On Thu, 1 Sep 1994, Tony Kwan wrote: > Hello netters, > > I am looking for any source out there, whether in the literature or on the > net, that gives a comparison of the amino acid usage frequencies between > different species such as human, mouse, yeast, drosophila, and plants. > For example, I would like to know for instance the % of leucines in total > proteins for yeast and see how this number differs from mice. Any help > would be appreciated. Thanks in advance. > > -- > Tony Kwan > Dept. of Biochemistry, McGill University > kwan@medcor.mcgill.ca > > Try Staden, it can do the works you want to do. qfang@wam.umd.edu From owner-software@net.bio.net Thu Sep 01 23:00:00 1994 Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!vixen.cso.uiuc.edu!usenet.ucs.indiana.edu!indyvax.iupui.edu!indyvax.iupui.edu!nntp Newsgroups: bionet.software Subject: Re: National Instruments FTP site Message-ID: <1994Sep1.151540.7882@ivax> From: eliecht@indyvax.iupui.edu (Ed Liechty) Date: 1 Sep 94 15:15:39 -0500 Sender: -Not-Authenticated-[7777] References: <3418fm$qrk@agate.berkeley.edu> Nntp-Posting-Host: 149.166.29.61 X-Posted-From: InterNews 1.0.2b5@149.166.29.61 Xdisclaimer: No attempt was made to authenticate the sender's name. Lines: 8 Can anyone tell me the National Instruments (makers of LabVIEW and other cool stuff) FTP address? Thanks, Mintu ftp.natinst.com From owner-software@net.bio.net Thu Sep 01 23:00:00 1994 Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!news.cac.psu.edu!news.pop.psu.edu!psuvax1!news.cc.swarthmore.edu!netnews.upenn.edu!biochem.dental.upenn.edu!ellis From: ellis@biochem.dental.upenn.edu (Ellis Golub) Newsgroups: bionet.software Subject: Re: [Q] Primer0.5 code for DOS Date: 2 Sep 1994 13:47:06 GMT Organization: University of Pennsylvania Lines: 35 Distribution: world Message-ID: <347acq$kon@netnews.upenn.edu> References: <3429gr$6i0@mintaka.chpc.utexas.edu> NNTP-Posting-Host: biochem.dental.upenn.edu Keywords: PRIMER software In article <3429gr$6i0@mintaka.chpc.utexas.edu>, hsan322@chpc.utexas.edu (David S. Lapointe) writes: |> I downloaded the source code for primer 0.5 from genome.wi.mit.edu |> and compiled it with Borland C3.1. It compiled correctly but crashed |> upon entry. Even after patching the calls to malloc to check |> for success it still crashes. |> |> Does anyone have some fixes that work with DOS? |> |> Thanks in advance!! |> |> David Lapointe |> UTHSCSA |> email: lapointe@uthscsa.edu |> I had similar problems with Borland compilers, and was running Primer only on our SGI system where it compiles fine. Recently, when looking for a more recent version (and not finding any) I did see a compiled version for PC's. I downloaded this and it runs fine. Hope this helps Ellis ============================================================================== Ellis Golub Phone: (215) 898-4629 Biochemistry Department FAX: (215) 898-3695 University of Pennsylvania ellis @ biochem.dental.upenn.edu School of Dental Medicine 4001 Spruce Street Philadelphia, PA 19104-6003 =============================================================================== From owner-software@net.bio.net Thu Sep 01 23:00:00 1994 Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!spool.mu.edu!heifetz.msen.com!zib-berlin.de!rs1-hrz.uni-duisburg.de!news.rz.uni-duesseldorf.de!amber.biophys.uni-duesseldorf.de!micha From: micha@amber.biophys.uni-duesseldorf.de () Newsgroups: bionet.software Subject: Re: UNIX GCG Site: How much CPU power? Date: 2 Sep 1994 21:36:08 GMT Organization: Biophysics Dept., Univ. Duesseldorf Lines: 89 Message-ID: <3485sm$4ju@news.rz.uni-duesseldorf.de> References: <1994Aug29.220115.34484@hulaw1.harvard.edu> Reply-To: micha@amber.biophys.uni-duesseldorf.de NNTP-Posting-Host: amber.biophys.uni-duesseldorf.de X-Newsreader: TIN [version 1.2 PL2] Keith Robison (robison@mito.harvard.edu) wrote: : Our department is considering upgrading the central computer which is : used to run GCG. We will definitely go with a UNIX box. I was wondering : if folks would be kind enough to share their experiences with how : fast a machine you need. : Key points which I can think of are: : 1) Architecture & speed (Sun, HP, SGI, Alpha, etc) DEC AXP 5000/800 (>180 MHz CPU clock ..) 128 MB with 1 GB system disk internal 4 GB external disk for user programs, data, GCG programs and data ( FULL ) - fast SCSI, DEC disk another 4 GB to come RSN ... and VAXStation 4000/60 ( ?? speed ?? ) with 1 GB disk total for user stuff. (VMS-Cluster, for the sake of completeness :-) ) Due to space limitations we built only the embl database, with a second disk the others may follow ... Fragmentation can't be avoided, as we are running very disk-intensive RNA folding stuff here. :-( Most user accounts are being moved to the VAXStation now, batch stuff on the AXP. : 2) How many total users in department 20-30 users, most of them seldom active. : 3) A reasonable guess as to the number of simultaneous users 3-5 most of the time, 1-2 batch jobs (AXP side). Interactive users won't notice batch jobs running ... Connection to the system by telnet or DECNet; network bandwidth saturated only by X ( online rotation of protein models ) or cluster disk traffic ( backup from one disk to another on a different system ). : 4) Is your current configuration working? (i.e. are people : happy with response time) perfectly happy, to one exception: DEC GKS graphics on DECWindows (not the display itself, that's much too fast to look at: screen update within one video frame, it's the menu window creation times that drive you crazy or make impatient users click around on anything below, with the obvious results :-( ). I expect the VMS process creation stuff is responsible for that, better results on unix. Stability: the AXP is running since march, fairly stable set aside the ethernet cluster problems (and one SCSI controller failure) : 5) Any relevant comments Lots of X applications ( the user interface to come ) will keep the X server busy ( takes o lot of our cpu time, 30 minutes per day ..). And 'fast' disks seem to be the only bottleneck (besides process create times) on our box. One comment on the only Unix gcg system I know as a user: Our computing center set up a Convex GCG package on their C210, with heavy interactive load and some quantum chemists running MO packages of up to 100 Meg core size. One 'benchmark' example: 360 Nt. query fasta against em_ro, AXP: 36 seconds cpu time, 2 min. 11 sec elapsed time ( disk-limited ) Convex: > 450 seconds cpu time, at 20 % cpu quota, -> > half an our elapsed time. No trace of vector processing speed here ( BLAST results may vary, as I recall ). Another Convex GCG system is the DKFZ-Heidelberg service - when we stopped working there, they had load averages > 15 ( our Convex freezes at above 12 ), same hardware platform there! I think we could beat this with our VAXStation ... One thing that stands _against_ a Unix system (from my point of view, as a 'on-leg manual') is the fact that on VMS we have GenHelp and even GenManual ( VMSHelp style ) and on Convex GCG they have the man pages, that is raw-formatted versions of the original VMS help sources (all help level keys preserved :-) ) piped thru the man system: you asked for help? Here you get it - find your relevant piece of information with grep !! We finally formatted the help files into HTML for a WWW server ... (support your local computing center) : Please post or E-mail; I will post a summary of E-mailed responses. : Keith Robison : Harvard University : Department of Cellular and Developmental Biology : Department of Genetics / HHMI : robison@mito.harvard.edu Michael Schmitz Biophysics Uni-Duesseldorf, Germany From owner-software@net.bio.net Thu Sep 01 23:00:00 1994 Path: biosci!daresbury!s-crim1!mbgjb From: mbgjb@s-crim1.dl.ac.uk (G.J. Barton) Newsgroups: bionet.software Subject: Re: ANNOUNCING-SCANPS (Scan Protein Sequence) Date: 2 Sep 1994 15:14:14 GMT Organization: Lab of Molecular Biophysics, University of Oxford. Lines: 6 Sender: mbgjb@s-crim1 (G.J. Barton) Distribution: world Message-ID: <347fg6$i1i@mserv1.dl.ac.uk> References: <3449q8$n17@mserv1.dl.ac.uk> NNTP-Posting-Host: s-crim1.dl.ac.uk Keywords: protein databank scanning Further to my previous announcement. I have now added executables for IRIX 4.0.1 to the distribution available by ftp from geoff.biop.ox.ac.uk or on the URL=http://geoff.biop.ox.ac.uk. Geoff. Barton From owner-software@net.bio.net Thu Sep 01 23:00:00 1994 Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!spool.mu.edu!heifetz.msen.com!zib-berlin.de!rs1-hrz.uni-duisburg.de!news.rz.uni-duesseldorf.de!amber.biophys.uni-duesseldorf.de!micha From: micha@amber.biophys.uni-duesseldorf.de () Newsgroups: bionet.software Subject: Re: Help: Mosaic and Entrez? Date: 2 Sep 1994 20:24:16 GMT Organization: Biophysics Dept., Univ. Duesseldorf Lines: 60 Distribution: world Message-ID: <3481lv$4ju@news.rz.uni-duesseldorf.de> References: <19940829133414.bloksber@thomashaw-at.css.msu.edu> Reply-To: micha@amber.biophys.uni-duesseldorf.de NNTP-Posting-Host: amber.biophys.uni-duesseldorf.de X-Newsreader: TIN [version 1.2 PL2] Leonard N. Bloksberg (bloksber@pilot.msu.edu) wrote: : . : I would like some help getting set up to use MOSAIC and ENTREZ please. : . Congratulations ! But some questions regarding your present setup ... : My boss has recently asked me to set up the lab to use MOSAIC and ENTREZ. We : are running a 386DX25 and a 486SX25 (both Zenith boxes) on ethernet. We also What operating system are you running on those boxes - Unix, Linux, or (uh :-( ) DOS/Windoze ? We are running Mosaic on Linux and, if absolutely necessary, on Windows (anything from 3.1 to 3.11/WfW), but on 486DX/33 boxes. The following applies to windows (no problems with Linux so far :-) ) Even using a 486DX, things can become real painful if you are stuck with only 4 MB ram ( Mosaic loads, but sometimes gets confused, or crashes when starting an external viewer ... ). 8 MB seem sufficient... Seems your hardware is rather on the minimum side, but try it ! : have a MAC IIci in the lab which is not hooked up to ethernet, but maybe : could be if necessary. Is this hardware sufficient for minimal or normal : opperation of these systems? What hardware will I need to set us up, and : what software will I need to access these systems? Any help, or offer to Our experience is with TCP/IP networking alone, using the public domain packet driver suite and the 'winpkt' stub to make the packet drivers accessible from windows. ( for WfW, you need a ODI driver instead of the PD packet driver ) Mosaic (current release 2.0a6) is a 32bit application, so you need the win32s extension package to get it running. For a TCP/IP application, you need a windows-emulation of unix socket communication to access the network. We are running the trumpet winsock package for this. And finally, WinMosaic (or FTP, telnet, ..) on top of this ! All stuff should be available on your favourite anonymous ftp server, in case of emergency use 'archie' to locate the stuff. The usual archiving tool is pkzip ... Look for 'wmos20a6.zip', 'win32s.zip' and the like ! : answer questions as I try to get us online, will be appreciated. My boss : has mentioned that there may be an oportunity to get a new box in the near : future to accomodate increased computing needs in the lab, and would like : me to keep that in mind as I get us set up. While very nice, I am not sure : it is necessary. Thanks in advance for any help. I am rather sure you are not going to like the speed of mosaic on a 25Mhz PC! And a bigger box might as well run a www server ... : . : Dr. Leonard N. Bloksberg : bloksber@pilot.msu.edu : . : . : . Just ask again if there are problems, Michael Schmitz Biophysics Dept., Uni Duesseldorf URL: http://www.biophys.uni-duessedorf.de/ From owner-software@net.bio.net Thu Sep 01 23:00:00 1994 Newsgroups: bionet.software Path: biosci!bcm!cs.utexas.edu!uunet!newsflash.concordia.ca!CC.UMontreal.CA!megasun.BCH.UMontreal.CA!tim From: tim@megasun.BCH.UMontreal.CA (Tim Littlejohn) Subject: Re: GDE for HP-UX?? Message-ID: Sender: news@cc.umontreal.ca (Administration de Cnews) Organization: Universite de Montreal References: <1994Sep1.104850.2856@inet.d48.lilly.com> Distribution: local,world Date: Fri, 2 Sep 1994 17:27:32 GMT Lines: 29 In article <1994Sep1.104850.2856@inet.d48.lilly.com> roblogan@lilly.com writes: >I will have access to a HP-UX workstation in the near future and hope to run >the GDE package on this machine. Has anyone ever compiled GDE for the HP-UX >operating system(currently v9.0) or can anyone advise me where I might find >instructions for installing the source code release? Any advice would be >greatly appreciated and apologies if this is a topic that has been covered in >the past. Thanks!! GDE, source and some binaries (but not for HP-UX) can be obtained by anonymous ftp or gopher to: megasun.bch.umontreal.ca If anyone has any HP-UX binaries they would like to contribute to this repository, please get in touch with me and I'll put them up here. Tim -- ============================================================================== Tim Littlejohn E-mail: tim@bch.umontreal.ca Snail Mail: Departement de biochimie Phone: (514) 343-6111, x5149 Universite de Montreal Fax: (514) 343-2210 C.P. 6128, Centre-ville Montreal (Quebec), H3C 3J7 CANADA ============================================================================== From owner-software@net.bio.net Thu Sep 01 23:00:00 1994 Path: biosci!bcm!cs.utexas.edu!usc!howland.reston.ans.net!spool.mu.edu!heifetz.msen.com!zib-berlin.de!rs1-hrz.uni-duisburg.de!news.rz.uni-duesseldorf.de!amber.biophys.uni-duesseldorf.de!micha From: micha@amber.biophys.uni-duesseldorf.de () Newsgroups: bionet.software Subject: Re: [Q] Primer0.5 code for DOS Date: 2 Sep 1994 21:44:39 GMT Organization: Biophysics Dept., Univ. Duesseldorf Lines: 25 Message-ID: <3486cl$4ju@news.rz.uni-duesseldorf.de> References: <3429gr$6i0@mintaka.chpc.utexas.edu> Reply-To: micha@amber.biophys.uni-duesseldorf.de NNTP-Posting-Host: amber.biophys.uni-duesseldorf.de X-Newsreader: TIN [version 1.2 PL2] David S. Lapointe (hsan322@chpc.utexas.edu) wrote: : I downloaded the source code for primer 0.5 from genome.wi.mit.edu : and compiled it with Borland C3.1. It compiled correctly but crashed : upon entry. Even after patching the calls to malloc to check : for success it still crashes. I think you are on the right track: the 64k memory bug! : Does anyone have some fixes that work with DOS? A DOS-addicted colleague of mine produced a gcc compiled version of primer for DOS and uses it regularly (He even promised to try and test my energy rule mods for primer on DOS for comparison, so he is still hacking) Unfortunately I have no copy of his program, but I will ask him after weekend. Maybe there are special hardware tricks to think of (memory model, math coprocessor ... )? If not, I try to send a uuencoded primer.exe by e-mail. : Thanks in advance!! : David Lapointe : UTHSCSA : email: lapointe@uthscsa.edu Michael Schmitz Biophysics Dept., Univ. Duesseldorf (Germany) From owner-software@net.bio.net Thu Sep 01 23:00:00 1994 Path: biosci!bcm!cs.utexas.edu!swrinde!gatech!newsxfer.itd.umich.edu!nntp.cs.ubc.ca!unixg.ubc.ca!stone.brc.ubc.ca!sparc.brc.ubc.ca!allen From: allen@sparc.brc.ubc.ca (Allen Delaney) Newsgroups: bionet.software Subject: Re: Amino acid usage for various species Date: 2 Sep 1994 16:28:11 GMT Organization: B. R. Centre Ltd. Lines: 9 Distribution: world Message-ID: <347jqr$19o@stone.brc.ubc.ca> References: NNTP-Posting-Host: stone.brc.ubc.ca Mike? Cherry at harvard is/was providing tables of codon frequencies for many species... they were/are available at frodo.mgh.harvard.edu:[.codon] and ftp.bio.indiana.edu:archive/molbio/data -- Allen Delaney (allen@brc.ubc.ca) Biomedical Research Centre, U.B.C., Vancouver, B.C. Canada, V6T 1Z3 From owner-software@net.bio.net Thu Sep 01 23:00:00 1994 Path: biosci!daresbury!doc.ic.ac.uk!agate!library.ucla.edu!europa.eng.gtefsd.com!news.uoregon.edu!netnews.nwnet.net!news.u.washington.edu!evolution.genetics.washington.edu!joe From: joe@evolution.genetics.washington.edu (Joe Felsenstein) Newsgroups: bionet.software Subject: Re: PPC native PAUP & MacClade -- when? Date: 2 Sep 1994 05:16:50 GMT Organization: University of Washington, Seattle Lines: 16 Message-ID: <346cg2$fq2@news.u.washington.edu> References: <1994Aug31.094238.16048@cc.ic.ac.uk> NNTP-Posting-Host: evolution.genetics.washington.edu Summary: PHYLIP available now In article , David Maddison wrote: >In article <1994Aug31.094238.16048@cc.ic.ac.uk>, s.fraser@ic.ac.uk (Simon >Fraser) wrote: > >>[a question about availability of a PowerMac versions of PAUP and MacClade]. >[an answer about forthcoming PAUP and MacClade PowerMac versions]. In case it's relevant, I can add that PHYLIP in native mode for the PowerMac is available now by anonymous ftp from the usual servers, most notably evolution.genetics.washington.edu. Not that that will get you speeds like PAUP for the PowerMac ... ----- Joe Felsenstein, Dept. of Genetics, Univ. of Washington, Seattle, WA 98195 Internet: joe@genetics.washington.edu (IP No. 128.95.12.41) From owner-software@net.bio.net Thu Sep 01 23:00:00 1994 Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!wupost!crcnis1.unl.edu!unlinfo.unl.edu!dwoodman From: dwoodman@unlinfo.unl.edu (david woodman) Newsgroups: bionet.software Subject: Maclab v/s BioPac Date: 2 Sep 1994 21:03:50 GMT Organization: University of Nebraska--Lincoln Lines: 5 Message-ID: <3483vm$8h8@crcnis1.unl.edu> NNTP-Posting-Host: unlinfo.unl.edu X-Newsreader: TIN [version 1.2 PL2] We are considering these systmes for our physiology labs. I would appreciate any information regarding your use of either or both of these and what your experience has been in terms of appropriateness for an introductory physiology course. dwoodman@unlinfo.unl.edu From owner-software@net.bio.net Thu Sep 01 23:00:00 1994 Path: biosci!daresbury!not-for-mail From: psansom@hgmp.mrc.ac.uk (Mr. P.A. Sansom) Newsgroups: bionet.software Subject: Query on LYSIS proteolysis database for PC Date: 2 Sep 1994 11:53:48 +0100 Lines: 11 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <34707s$13c@mserv1.dl.ac.uk> Original-To: bio-soft@dl.ac.uk Does anybody have any experience with the LYSIS proteolysis database for PC, available from Springer-Verlag? We are thinking of purchasing it, but want to know if it is updated, and if it will indicate cleavages in a user-defined sequence. Thanks in advance Paul Sansom The Kennedy Institute of Rheumatology 6 Bute Gardens Hammersmith London From owner-software@net.bio.net Thu Sep 01 23:00:00 1994 Path: biosci!CCVAX.UNICAMP.BR!INFOMED From: INFOMED@CCVAX.UNICAMP.BR Newsgroups: bionet.software Subject: CFP: Brazilian Symp. Informatics in Dentistry and Oral Medicine Date: 2 Sep 1994 06:38:29 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 141 Sender: daemon@net.bio.net Distribution: world Message-ID: <01HGMT90XNWI8WWEAJ@ccvax.unicamp.br> NNTP-Posting-Host: net.bio.net -------------------------------------------------------- CALL FOR PAPERS First Brazilian Symposium on Informatics in Dentistry and Oral Medicine Campinas, Brazil, 9-12 November 1994 -------------------------------------------------------- The Center for Biomedical Informatics, from the State University of Campinas, UNICAMP, announces its premier technical and scientific meeting in the field of Informatics in Dentistry and Oral Medicine, to be held at the Colegio Sagrado Coracao de Jesus, in Campinas, State of Sao Paulo, Brazil, in November, 9 to 12, 1994. This first symposium aims at providing a lively forum for specialists as well for users of computers in Dentistry, Oral Medicine and allied sciences. The symposium main activities will be: - Conferences - Panel and symposia on especific themes - Presentation of papers in oral and poster form - Software demonstration sessions - Meet-the-expert sessions - Introductory course in Informatics Submission of technical papers is invited for the following topics in the areas of Dentistry and Oral Medicine: - Clinical databases - Decision support systems - Informatics in Oral Rehabilitation - Informatics in Orthodontics - Processing of signals and images - Informatics in Preventive Dentistry - Informatics and Deontology - Automation of offices and clinics - Informatics in the support to oral surgery - Applications in teaching and research Technical Exhibit A technical exhibit, featuring new products (hardware, software, services and publications) will be held simultaneously in the symposium area. Submission of papers The congress proceedings, containing abstracts (200-400 words) will be published and made available during the meeting. The official publication languages are Portuguese, Spanish and English. Authors may submit abstracts via email. Deadlines 30 September 94 submission of full papers 10 October 94 mailing of letters of acceptance or rejection Fees Students ..................................... US$ 35,00 UNICAMP and PUCCAMP teachers and employees, members of the Sociedade Brasileira de de Informstica em Sayde (SBIS) or of the Associacao Brasileira de Ususrios de Computador em Odontologia (ABUCO) ............ US$ 90,00 Non-members .................................. US$ 140,00 Registration and Information: I SBIO Secretariat NIB/UNICAMP Universidade Estadual de Campinas P.O.Box 6005 13081-970, Campinas, SP, Brazil Fone: (0192) 39-7130 Fax: (0192) 39-4717 E-mail: palombo@fem.unicamp.br sabbatini@ccvax.unicamp.br Moustafa M. El-Guindy, PhD (President, Organizing Committee) Claudio R. Palombo, DDS (Secretariat) Renato M.E. Sabbatini (Director, Center for Biomedical Informatics) _______________________________ PRE-REGISTRATION FORM NAME: ....................................................... AGE: ..... Profession: ................................ Area: ................................................. Institution: .......................................... Postal Address: ....................................... ZIP: ............... CITY: ............................ STATE/PROVINCE: ............... COUNTRY ............... Phone: ...................... Fax: .................... Email: ................................................ Date: ....................... I intend to submit a paper ( ) YES ( ) NO Title: ....................................................... ....................................................... From owner-software@net.bio.net Thu Sep 01 23:00:00 1994 Path: biosci!PCLSP2.KUICR.KYOTO-U.AC.JP!vinz From: vinz@PCLSP2.KUICR.KYOTO-U.AC.JP (Vincenzo Nardi-Dei) Newsgroups: bionet.software Subject: Kansai-net Date: 2 Sep 1994 11:36:04 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 67 Sender: daemon@net.bio.net Distribution: world Message-ID: <9409021837.AA26168@pclsp2> NNTP-Posting-Host: net.bio.net ************************************************************* Wellcome to Kansai-net ************************************************************* This net was originaly conceived by a group of Kyoto University researchers and graduated students who felt the need of a local network to be used for all the foreigner community of scholars, scientists and technologists resident in the Kansai-area (Kyoto, Nara, Osaka and Kobe, Japan) as a mean of easy communication, excange of ideas, help and informations in the "alien" Japanese environment; but, infact, is open to all of you that are resident in Kansai and have computer access to Internet; the presence of Japanese scientists is welcome and will be surely very helpful. Kansai-net is a LOCAL network concerned with everything is about the EVERYDAY LIFE and its aim is to make it easier and more enjoyable. In this view it is supposed to be very casual and the content of messages can be anything, e.g. looking for somebody to come along to Kabuki, to go for drinking, anouncements of parties, Sayonara sales, information about bargains, flat swapping, people for mountain biking, sightseeing, were to find a good english speaking dentist, are there any Russian scientists in the area or who show me around in Kobe in Sunday... This net is not censored at all, and everything is allowed, (no strict morality here!) but elegance and courtesy are demanded. Of course, this is a non-profit net and subsequently commercial advertizing is not allowed. You can post messages by sending them to To subscribe send a message to: (Vincenzo Nardi-Dei) containing in the subject: subscribe Kansai-net (or unsubscribe) and in the text: your name and, if possible, your office address and telephone number, your nationality and your email address. Looking forward to listening soon from you all, sincerely Vincenzo Nardi-Dei (vinz@pclsp2.kuicr.kyoto-u.ac.jp) Marek Tchorzewski (marek@pclsp2.kuicr.kyoto-u.ac.jp) (Kansai-net Managers) ************************************************************* From owner-software@net.bio.net Fri Sep 02 23:00:00 1994 Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!wupost!kuhub.cc.ukans.edu!kuhub.cc.ukans.edu!nntp Newsgroups: bionet.software Subject: Re: Secondary structure prediction software Message-ID: <1994Sep2.181840.71885@kuhub.cc.ukans.edu> From: peterg@rnaworld.bio.ukans.edu (Peter Gegenheimer) Date: 2 Sep 94 18:18:39 CDT Reply-To: pgegen@kuhub.cc.ukans.edu (Peter Gegenheimer) References: <340clb$bnc@newshost.lanl.gov> Distribution: world Organization: Dept. Biochemistry, Univ. Kansas-Lawrence KS Nntp-Posting-Host: rnaworld.bio.ukans.edu X-Newsreader: IBM NewsReader/2 v1.00 Lines: 26 In <340clb$bnc@newshost.lanl.gov>, pxc@mendel.lanl.gov (Paolo Catasti) writes: >Hi, > i'm looking for some simple algorithm for secondary structure >prediction of proteins. >Any simple algorithm based on the Robson-Garnier and/or Chou/ >Fasman would be suitable. >I'm too lazy to type them down although i know where to get >them in literature. >Any more recent and fancier algorithm would be also appreciated. >Crossing my fingers and waiting for help, thanks. >Regards, >Paolo Catasti The current champion is the 'PhD' program at Heidelberg. It is accessed via an e-mail server. Send a message to: PredictProtein@EMBL-Heidelberg.de using as the subject (or text) the single word HELP. It does a prediction based on aligned sequences of all proteins (if any) in the same family as yours. o-----------------------------------------------------------------------------o | Peter Gegenheimer | pgegen@kuhub.cc.ukans.edu | | Departments of Biochemistry and of Botany | voice: 913-864-3939 | | University of Kansas | FAX : 913-864-5321 | | 2045 Haworth Hall | "The sleep of reason produces | | Lawrence KS 66045-2106 | monsters." Goya | o____________________________________________|________________________________o From owner-software@net.bio.net Fri Sep 02 23:00:00 1994 Path: biosci!biosci!not-for-mail From: micha@amber.biophys.uni-duesseldorf.de () Newsgroups: bionet.software Subject: Re: W3 Biology Research Tools Followup-To: bionet.software Date: 2 Sep 1994 18:34:00 -0700 Organization: Biophysics Dept., Univ. Duesseldorf Lines: 39 Sender: biohelp@net.bio.net Distribution: world Message-ID: <3487fj$4ju@news.rz.uni-duesseldorf.de> References: <1994Aug31.094108.5883@ciba-geigy.ch> Reply-To: micha@amber.biophys.uni-duesseldorf.de NNTP-Posting-Host: net.bio.net Nager Carl David (nager@FMI.CH) wrote: : "Pedro's Research Tools" are now available on the FMI Internet World Wide Web : (W3) server. : Pedro collects these tools on the Internet, puts them together as a : short index for biologists. The index should make it easier to get : quickly your analysis done using the fast growing size of biological : Internet resources. : Access to W3 Mirrors: : -------------------- : in : Switzerland: http://www.fmi.ch/biology/research_tools.html Page (or server) seems bogus: didn't respond just now! : US: http://www.public.iastate.edu/~pedro/research_tools.html _VERY_ fine collection, I had a lot of browsing to find part of the links myself! I hope the list grows on and on ... : Any comments welcome! : Carl David and Pedro : ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ : Bio-Informatics, FRIEDRICH MIESCHER INSTITUTE, P.O.Box 2543, CH 4002 BASEL : C.D. Nager (SWITZERLAND) : e-mail: nager@fmi.ch fax: +41 (61) 697-3976 tel: +41 (61) 697-5678 : URL: http://www.fmi.ch/ : ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ : and : --------------------------------- H2N-CH-CO-NH-CH-CO-...-NH-CH-COOH -- : Pedro M. Coutinho - Graduate Student \ \ \ : IOWA STATE UNIVERSITY R1 R2 Rn : Department of Chemical Engineering Phone: 1-515-294-9370 : 2114 Sweeney Hall Fax: 1-515-294-2689 : Ames, IA 50011-2230 E-mail: pedro@iastate.edu : U.S.A. URL: http://www.public.iastate.edu/~pedro/ : ---------------------------------------------------------------------- From owner-software@net.bio.net Fri Sep 02 23:00:00 1994 Path: biosci!UIC.EDU!U56961 From: U56961@UIC.EDU ("W. Mark Coward ") Newsgroups: bionet.software Subject: (none) Date: 2 Sep 1994 19:47:34 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 25 Sender: daemon@net.bio.net Distribution: world Message-ID: <199409030247.TAA15581@net.bio.net> NNTP-Posting-Host: net.bio.net NEW MOSAIC LIST MOSAIC-L For NCSA MOSAIC users and developers MOSAIC-L offers a forum to communicate with those who use and develop NCSA Mosaic applications. To Subscribe: Send a message to either: listserv@uicvm.bitnet listserv@uicvm.uic.edu In the first line of the message (not in the subject) enter the following: subscribe mosaic-l your_account@node Your Name for example, subscribe mosaic-l jsmith@uic.edu Joe Smith From owner-software@net.bio.net Fri Sep 02 23:00:00 1994 Path: biosci!LUCIFER.MEDS.CWRU.EDU!dean From: dean@LUCIFER.MEDS.CWRU.EDU (David Dean Ph.D.) Newsgroups: bionet.software Subject: New List: Craniofacial Biology Research Date: 3 Sep 1994 07:05:28 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 23 Sender: daemon@net.bio.net Distribution: world Message-ID: <9409031404.AA17429@lucifer.MEDS.CWRU.Edu> Reply-To: dean@lucifer.MEDS.CWRU.Edu NNTP-Posting-Host: net.bio.net New List: CRANIOFACIAL BIOLOGY RESEARCH The CBR-L discourse focuses on the growth and development of the human head. Topics of interest include queries, observations, and research reports on normal craniofacial morphology, ontogeny (growth and development) and teratology, as well as variation owing to gender, demographics, ethnicity, pathology, or phylogeny. The discussion should be of interest to clinical (plastic and oral surgery, orthodontics, human genetics, epidemiology) and basic (developmental biology, medical imaging, anthropometrics, physiology, anatomy) scientists. The list sponsor is the Craniofacial Biology Research Group at Case Western Reserve University, Cleveland, OH. To subscribe send mail to majordomo@po.cwru.edu with body: SUBSCRIBE CBR-L Queries may be sent to the list administrator: David Dean From owner-software@net.bio.net Fri Sep 02 23:00:00 1994 Path: biosci!bcm!cs.utexas.edu!sdd.hp.com!saimiri.primate.wisc.edu!news.doit.wisc.edu!ie.engr.wisc.edu!mlaudon From: mlaudon@ie.engr.wisc.edu (Matthew Finley Laudon) Newsgroups: bionet.software Subject: 10th Conf. Mathematical and Computer Modelling - Boston (cfp) Date: 3 Sep 1994 17:08:33 GMT Organization: University of Wisconsin - Madison, College of Engineering Lines: 64 Message-ID: <34aaih$djq@news.doit.wisc.edu> NNTP-Posting-Host: ie.engr.wisc.edu Announcement and Call for Papers TENTH INTERNATIONAL CONFERENCE ON MATHEMATICAL AND COMPUTER MODELLING AND SCIENTIFIC COMPUTING 5-8 July 1995 Boston Marriott Hotel Copley Place Boston Massachusetts, U.S.A ------------------------- The Tenth International Conference on Mathematical and Computer Modelling and Scientific Computing is scheduled to take place 5-8 July 1995 at the Boston Marriott Hotel Copley Place in Boston, Massachusetts, U.S.A. Plenary lectures by world-renowned scientists and technical sessions on many recent developments in engineering and sciences comprise a long-standing tradition at the ICMCM's. The objective of the conference is to bring together researchers, educators, planners, and model users from various disciplines including the traditional and emerging areas of engineering and sciences for cross fertilization and exchange of information. Authors are invited to contribute their work for presentation at the conference in the form of one-page abstracts typed single-space before 15 January 1994. Early submissions are encouraged. The abstracts will be processed as they come in, and decisions on selection will be promptly communicated to the authors by FAX not later than 31 February 1995. Abstracts may be submitted by FAX by dialing to U.S.A.: (314)-364-3351. ------------------------- The topics of interest are broadly categorized into: Modelling and Computation in Engineering and Sciences; Computational Sciences and Technologies; Applied Mathematics and Modelling Methodologies; Systems Theory; Computational Control; Self-Organizing Systems, Fuzzy and Neuro-Control, Neural Networks Theory and Applications; Biomedical Sciences; Computational Physics; Computational Chemistry; Computational Biology; Environmental Sciences and Engineering; Econometrics and Decision Sciences; Defense Related Problems; Resources; Model Validations; Educational Issues, etc. Papers presented at the 10th ICMCM will be published as a special issue of the journal MATHEMATICAL MODELLING AND SCIENTIFIC COMPUTING, Volume 6 1995. (ISSN 1067-0688) All abstracts and inquiries must be sent to the address below in St. Louis, Missouri, U.S.A. Address for correspondence: Scientific Program Committee, 10th ICMCM P. O. Box 31670 St. Louis, MO 63131 U.S.A. Telephone: (314)-341-4585 (Prof. X.J.R. Avula) FAX: (314)-364-3351 E-mail: avula@umr.edu From owner-software@net.bio.net Fri Sep 02 23:00:00 1994 Path: biosci!news.Stanford.EDU!agate!howland.reston.ans.net!gatech!news-feed-1.peachnet.edu!news.duke.edu!godot.cc.duq.edu!hudson.lm.com!africa.lm.com!not-for-mail From: kub@telerama.lm.com (Joe) Newsgroups: bionet.software Subject: PC reads Mac file/disk. Date: 3 Sep 1994 13:10:20 -0400 Organization: Telerama Public Access Internet, Pittsburgh, PA Lines: 9 Message-ID: <34aals$jtc@africa.lm.com> NNTP-Posting-Host: africa.lm.com X-Newsreader: TIN [version 1.2 PL2] I am looking for a program that will read/convert a mac file (preferably from a Mac formated diskette) and convert it to PC format. If ya know of any please EMAIL me as I don't get to this newsgroup often. Thanks in advance. -- EMAIL Joe at: kub@telerama.lm.com From owner-software@net.bio.net Sat Sep 03 23:00:00 1994 Path: biosci!daresbury!trane.uninett.no!eunet.no!nuug!EU.net!howland.reston.ans.net!agate!barrnet.net!nntp.crl.com!crl2.crl.com!not-for-mail From: fats@crl.com (FATS Inc) Newsgroups: bionet.software Subject: Info needed on CARIS, Universal System Date: 3 Sep 1994 20:11:32 -0700 Organization: CRL Dialup Internet Access Lines: 9 Message-ID: <34bdt4$el0@crl2.crl.com> NNTP-Posting-Host: crl2.crl.com Keywords: CARIS, GPS, software, Universal System Dear all: Is there someone know a software package CARIS? It is said the package is from Universal Sysyem, a company in Canada. I want know where I can get detail information about CARIS, from model number to price. Would you help me? Wen From owner-software@net.bio.net Sat Sep 03 23:00:00 1994 Newsgroups: bionet.software Path: biosci!agate!spool.mu.edu!uwm.edu!news.alpha.net!mvb.saic.com!news.cerf.net!ljcrf.edu!elya From: elya@ljcrf.edu (Elya S. Kurktchi) Subject: Is there a list of Macintosh-based programs available? Message-ID: Organization: La Jolla Cancer Research Foundation Date: Sun, 4 Sep 1994 13:52:21 GMT Lines: 9 Is there a list of Macintosh-based programs available (shareware, freeware, commercial)? If so, please email me regarding how I can retrieve it. Thanks. Elya. From owner-software@net.bio.net Sat Sep 03 23:00:00 1994 Newsgroups: bionet.software Path: biosci!agate!spool.mu.edu!heifetz.msen.com!zib-berlin.de!news.th-darmstadt.de!terra.wiwi.uni-frankfurt.de!zeus.rbi.informatik.uni-frankfurt.de!news.dfn.de!urmel.informatik.rwth-aachen.de!newsserver.rrzn.uni-hannover.de!news From: Joachim Heymer Subject: Re: PC reads Mac file/disk. Message-ID: <94090410510500006@unics.rrzn.uni-hannover.de> Sender: news@newsserver.rrzn.uni-hannover.de (News Service) Reply-To: nexejhey@unics.rrzn.uni-hannover.de Organization: Molecular Biology References: <34aals$jtc@africa.lm.com> Date: Sun, 4 Sep 1994 10:51:05 GMT X-Mailer: rnMac v1.3b5 Lines: 16 In article <34aals$jtc@africa.lm.com>, Joe writes: > > I am looking for a program that will read/convert a mac file (preferably > from a Mac formated diskette) and convert it to PC format. > > If ya know of any please EMAIL me as I don't get to this newsgroup often. > A cheap and easy way is to use APPLE FILE EXCHANGE. It is part of the Macintosh system software. JOACHIM From owner-software@net.bio.net Sun Sep 04 23:00:00 1994 Newsgroups: bionet.software Path: biosci!daresbury!bioftp.unibas.ch!comp.bioz.unibas.ch!eggenber From: eggenber@comp.bioz.unibas.ch (Florian Eggenberger) Subject: WWW Introduction for Biologists Message-ID: <1994Sep5.112915.28@comp.bioz.unibas.ch> Sender: usenet@comp.bioz.unibas.ch (NEWS transaction account) Nntp-Posting-Host: bioy.embnet.unibas.ch Organization: EMBnet Switzerland [Basel] Date: Mon, 5 Sep 1994 11:29:15 GMT Lines: 164 Biocomputing, Basel University Teleteaching 1994, 2nd Course ANNOUNCEMENT: WWW INTRODUCTION ============================== This is an announcement of a series of postings starting October 10, 1994, on the newsgroup bionet.software.www in order to provide an introduction to the WorldWideWeb (WWW) project. The goal is to answer the very basic questions as what is the World-Wide Web, what is availble on the Web, what software is required to access the Web, and how to get and install the software. It is, in this course, not intended to guide people who want to provide information to the Web. A separate course/topic discussion early next year will be targeted to information providers, however,this requires that the client software is properly preinstalled, as the Web will be used for explanations. Details on that series will be announced in early 1995. The postings of this second teleteaching '94 project "WWW introduction" are aimed to biologists who have access to the Internet and are interested in obtaining and setting up the programs needed to access the Web.Previous experience with network retrieval tools are not essential but knowledge in the use of FTP is advantageous. Anyone who is interested in receiving these introductionary postings but cannot read the newsgroup bionet.software.www can subscribe to the BIOSCI email service as described in the appendix. The newsgroup bionet.software.www is also accessible in a marked-up ar- chive at EMBnet Switzerland which might be of interest to those who did already successfully implement a suitable browser. This WWW introduction course will be based on the updated version of the WWW introduction teleteaching project which was contributed by our site by myself in January 1994. Florian Eggenberger EMBnet Switzerland ACKNOWLEDGEMENTS ---------------- EMBnet Switzerland is a project funded by the University of Basel, the Swiss National Science Foundation, and industrial contributions from Di- gital Equipment and Silicon Graphics (in alphabetical order). Information on services for Switzerland available by email from: info@ch.embnet.org APPENDIX -=-=-=-= The BIO-WWW/bionet.software.www Newsgroup +++++++++++++++++++++++++++++++++++++++++ Availability on the network (specifically, World Wide Web): *********************************************************** bionet.software.www is archived, as all bionet newgroups, at the net.bio.net FTP site, and available to be used like any other bionet newsgroup (see explanations below). The bionet.software.www newsgroup, additionally, keys contributions in 'html' documents so that links are readily resolved in the 'hypertext' system, and may point to the contribution of the originator, or the subject of the message, respectively. This server runs at the Biocomputing Faci- lity of Basel University. The following is the Reply-To: "J.C. Riveros Salcedo" NNTP-Posting-Host: net.bio.net Would anyone help to find the program called ANOSIM. It is used in comparison of dominance curves and other ecological mesasurements of similarity. Any help would be greatly appreciated. Please answer to my e-mail box because I'am not subscripted to this list. Thanks. JC -- J.C. Riveros Salcedo jc%psj@upch.edu.pe P.O. Box 11-0730, Lima-11, Peru o/ Fax +(51 14) 633048 /@ Tel +(51 14) 625410 < \ Hom +(51 14) 729336 From owner-software@net.bio.net Sun Sep 04 23:00:00 1994 Path: biosci!agate!spool.mu.edu!news.cs.indiana.edu!mozo.cc.purdue.edu!macg203t.bio.purdue.edu!user From: shall@bilbo.bio.purdue.edu (GUIDO Shopping Network) Newsgroups: bionet.software Subject: GUIDO Shopping Net Followup-To: bionet.software Date: Mon, 05 Sep 1994 11:10:03 -0800 Organization: Purdue University Lines: 129 Message-ID: NNTP-Posting-Host: macg203t.bio.purdue.edu A new shopping network on the internet! To purchase items, e-mail: shall@bilbo.bio.purdue.edu. New address will soon be available via CompuServe. If interested in services, e-mail you interests to the same address for fee schedule and info. For a fee, this net will post your items, maintain the correspondence, and advise you of interested parties. Fees are due prior to posting and non-refundable. Your items will remain on the net for 90 days without additional charge. This service enables you to post items to the net without having to check constantly for reponses and reply. Reference number is shown in item description. The GSN will check your account twice daily (more often for an additional charge) and advise you via e-mail or modem if there is an interested party. 800 number and credit card services soon! Other GSN services available: Wake-up calling service Tutoring services network Coming soon: Complete for sale network services including purchase by credit cards with payment sent directly to seller. Catalog sales via e- mail! CHECK OUT THESE SERVICES AND OTHER INFO UNDER GUIDO SHOPPING NET (GSN). GSN WILL POST TO ALL CATEGORIES AS NEW PERTINENT ITEMS COME ON LINE. temp address: shall@bilbo.bio.purdue.edu Some items now available on the GUIDO Shopping Network (GSN): Include reference number after description. TEXTBOOKS $25 your choice (used, but in good condition): Math: Advanced Engineering Mathematics #1750 Differential Equations #326 Calculus #215 Business Calculus #567 Linear Algebra #125 Physics: College Physics #643 University Physics #644 Genetics: Genetics #212 Population Genetics #213 Medical: Lab Manual Anatomy and Physiology ($10) #432 Textbook of Surgery by Sabiston ($80) #538 Medical Physiology #539 Chemistry: General Chemistry #876 Organic Chemistry #877 Physical Chemistry #511 Biology: General Biology #854 Limnology #762 Comparative Physiology Schaums Outlines - $5.00 each: Organic Chemistry #901 Physical Chemistry #902 Advanced Calculus #903 Advanced Mathematics #904 Vector Analysis #905 COMPUTERS AND SOFTWARE: Texas Instruments High Speed Line Printer Cost $2,000 new. Now $200 in good shape. Free with printer: Franklin Apple Clone and Monochrome Monitor!!! #21 Think C 5.0 for the MacIntosh (new and complete) $60 #22 FPU for Mac LCII $50 #319 C Programming Primer (new) $25 #101 Hypercard 2.0 Handbook (new) $25 #102 Learn C on the MacIntosh (new with disk) $30 #103 Parallel Distributed Processing Hanbooks with MacIntosh software (new) $40 #25 Microsoft Fortran Complier V. 3 (complete) $40 #56 FURNITURE: Oak entertainment center, very nice! $250 obo. #402 MOTORCYCLE GEAR: Black cold-weather touring jacket XL $30 #598 Burgundy hi-performance motorcycle helmet L-XL. mint condition. $60 #599 PET SUPPLIES: 10 and 20 gallon aquaria $5 and up. #602 ------------------------------------------------------------------------- [GSN endsample 940905.1102.] From owner-software@net.bio.net Sun Sep 04 23:00:00 1994 Path: biosci!agate!howland.reston.ans.net!EU.net!sunic!news.funet.fi!ousrvr.oulu.fi!ojtv From: ojtv@cc.oulu.fi (Olli Vuolteenaho) Newsgroups: bionet.software Subject: GeneJockey II: verify by typing? Date: 5 Sep 1994 13:41:27 GMT Organization: University of Oulu, Department of Physiology Lines: 9 Message-ID: <34f767$86a@ousrvr.oulu.fi> NNTP-Posting-Host: sun3.oulu.fi Mime-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit X-Newsreader: TIN [version 1.2 PL2] It seems that key re-assignments for nucleotide sequence entry don't work when verifying the sequence by typing. If this is true it makes the fine feature mostly useless, or have I missed something? (I'm using an LC 475, System 7.1, GeneJockey II v1.2). Olli Vuolteenaho Dept. Physiology, University of Oulu FIN-90220 Oulu, Finland olli.vuolteenaho@oulu.fi From owner-software@net.bio.net Sun Sep 04 23:00:00 1994 Newsgroups: bionet.software Path: biosci!agate!spool.mu.edu!howland.reston.ans.net!pipex!lyra.csx.cam.ac.uk!warwick!uknet!gdt!aber!localhost!azw From: azw@aber.ac.uk (Andy Woodward) Subject: ATCC Catalogues on the WWW Message-ID: Lines: 17 Sender: news@aber.ac.uk (USENET news service) Nntp-Posting-Host: pcfcfa.dbs.aber.ac.uk Organization: The University of Wales, Aberystwyth X-Newsreader: Trumpet for Windows [Version 1.0 Rev B] Date: Mon, 5 Sep 1994 14:48:53 GMT Does anyone know the http for this? I am Dr A.M. Woodward Biological Sciences University College of Wales Aberystwyth Dyfed SY23 3DA U.K. Tel. 0970 623111x4188 Fax 0970 622354 FTP 144.124.112.30 From owner-software@net.bio.net Mon Sep 05 23:00:00 1994 Path: biosci!galaxy.ucr.edu!ihnp4.ucsd.edu!swrinde!howland.reston.ans.net!EU.net!Germany.EU.net!news.dfn.de!uni-muenster.de!pbio16.uni-muenster.de!user From: tiedtke@vnwz00.uni-muenster.de (Uwe Baumert) Newsgroups: bionet.software Subject: Looking for enzyme kinetics SW (DOS) Followup-To: bionet.software Date: 6 Sep 1994 13:10:55 GMT Organization: University of Muenster Lines: 13 Message-ID: NNTP-Posting-Host: pbio16.uni-muenster.de Hi, I'm looking for free DOS-software (anonFTP) that can handle enzyme kinetics datas generating Lineweaver-Burk-plots etc. on DOS not Windows! With kind regards, -- Uwe Baumert Institute for General Zoology and Genetics University of Muenster Schlossplatz 5 D-48149 Muenster, Germany e-mail: tiedtke@vnwz01.uni-muenster.de From owner-software@net.bio.net Mon Sep 05 23:00:00 1994 Path: biosci!agate!howland.reston.ans.net!EU.net!uknet!daresbury!not-for-mail From: ptaylor@hgmp.mrc.ac.uk (Dr. P.L. Taylor) Newsgroups: bionet.software Subject: Re: GeneJockey II: verify by typing? Date: 6 Sep 1994 16:04:39 +0100 Lines: 20 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <34i0e7$335@mserv1.dl.ac.uk> Original-To: bio-soft@dl.ac.uk >It seems that key re-assignments for nucleotide sequence entry don't >work when verifying the sequence by typing. If this is true it >makes the fine feature mostly useless, or have I missed something? >(I'm using an LC 475, System 7.1, GeneJockey II v1.2). >Olli Vuolteenaho >Dept. Physiology, University of Oulu >FIN-90220 Oulu, Finland >olli.vuolteenaho@oulu.fi You are perfectly correct, Olli. Key re-assignment does not work when verifying a sequence by typing. I will fix this in the next release. Thank you for pointing this out. Phil Taylor | MRC Reproductive Biology Unit | Centre for Reproductive Biology | 37 Chalmers Street mbplt@seqnet.dl.ac.uk | Edinburgh EH3 9EW ptaylor@hgmp.mrc.ac.uk | Scotland. From owner-software@net.bio.net Mon Sep 05 23:00:00 1994 Path: biosci!galaxy.ucr.edu!ihnp4.ucsd.edu!agate!howland.reston.ans.net!europa.eng.gtefsd.com!news.umbc.edu!haven.umd.edu!purdue!mozo.cc.purdue.edu!news From: "Curt Ashendel" Newsgroups: bionet.software Subject: Re: PC reads Mac file/disk. Date: Mon, 5 Sep 94 12:42:10 EST Organization: Purdue University Lines: 33 Message-ID: <58300.ashendel@aclcb.purdue.edu> Reply-To: NNTP-Posting-Host: ashendel.medchem.purdue.edu X-Minuet-Version: Minuet1.0_Beta_16 X-POPMail-Charset: English To: kub@telerama.lm.com On 3 Sep 1994 13:10:20 -0400, Joe wrote: >I am looking for a program that will read/convert a mac file (preferably >from a Mac formated diskette) and convert it to PC format. There is a shareware program I found at oak.oakland.edu/pub/ms-dos (I think it was in the disk utility section) in a zipped file called MACSEE22.ZIP. I have not tried it, but it may be the answer you are looking for. Quoting from its doc file: MacSEE V2.2 for DOS and Windows REEVEsoft MacSEE is a utility that will allow you to read/write Macintosh format diskettes on your PC. This includes 1.44 MB High Density Macintosh diskettes and Macintosh hard disks including SyQuest removable hard drives formatted on a Mac. It does not include 800K Mac disks as a standard PC floppy drive can't make heads or tails of what is written on those disks. Please note that this unregistered version 2.2 is being released into Shareware as a demonstration version. It adds bug fixes and features to version 2.1 (also shareware) and may be freely distributed provided that all files included remain intact and unmodified. Curt Ashendel Purdue University West Lafayette, IN ashendel@aclcb.purdue.edu From owner-software@net.bio.net Mon Sep 05 23:00:00 1994 Path: biosci!agate!howland.reston.ans.net!EU.net!Austria.EU.net!newsfeed.ACO.net!swidir.switch.ch!scsing.switch.ch!sun.rediris.es!news.uam.es!samba.cnb.uam.es!jenfedaque From: jenfedaque@samba.cnb.uam.es Newsgroups: bionet.software Subject: Protein similarity percent matrix Date: 5 Sep 94 20:58:37 WET Organization: C.N.Biotecnologia, CSIC Lines: 12 Message-ID: <1994Sep5.205837.1@samba.cnb.uam.es> NNTP-Posting-Host: samba.cnb.uam.es Hello all, I need a program that calculates percent similarities between proteins, from a multiple alignment. (Or better a program that makes the alignment by itself and produces also a matrix of similarities). Please, answer directly to: josefina@farmacia.ub.es Thanks, Josefina From owner-software@net.bio.net Mon Sep 05 23:00:00 1994 Path: biosci!CAP.GWU.EDU!winfield From: winfield@CAP.GWU.EDU ("Robert J. Winfield") Newsgroups: bionet.software Subject: software reccomendation Date: 6 Sep 1994 02:17:34 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 7 Sender: daemon@net.bio.net Distribution: world Message-ID: References: NNTP-Posting-Host: net.bio.net anyone have some reccomendations for software to replace PCGene? The version wife has will only handle 14,000 bases and she needs something that will work with at least 48k bases in 1 file winfield@cap.gwu.edu From owner-software@net.bio.net Mon Sep 05 23:00:00 1994 Path: biosci!daresbury!trane.uninett.no!nac.no!eunet.no!nuug!EU.net!uunet!news.delphi.com!usenet From: Patrick G Swann Newsgroups: bionet.software Subject: info needed re met.simulation SCAMP Date: Mon, 5 Sep 94 21:23:15 -0500 Organization: Delphi (info@delphi.com email, 800-695-4005 voice) Lines: 5 Message-ID: <5i+yWhT.swannp@delphi.com> NNTP-Posting-Host: bos1b.delphi.com I'm looking for a program to simulate product yields from multi-sequence (possibly branching) pathways given initial substrates and kinetic constants. I' ve heard that SCAMP can do this and am interested in any information regarding availability. Many Thanks. From owner-software@net.bio.net Mon Sep 05 23:00:00 1994 Path: biosci!bcm!cs.utexas.edu!sdd.hp.com!vixen.cso.uiuc.edu!news.uoregon.edu!netnews.nwnet.net!news.u.washington.edu!strom From: strom@u.washington.edu (Mark Strom) Newsgroups: bionet.software Subject: Re: ATCC Catalogues on the WWW Date: 6 Sep 1994 20:24:25 GMT Organization: University of Washington Lines: 28 Message-ID: <34ij5p$r8e@news.u.washington.edu> References: NNTP-Posting-Host: stein3.u.washington.edu azw@aber.ac.uk (Andy Woodward) writes: (ATCC Catalogues on the WWW) >Does anyone know the http for this? Try gopher://merlot.gdb.org/11/Database-local/cultures/atcc This is located at the BioGopher at John Hopkins University (gopher://gopher.gdb.org/). >I am Dr A.M. Woodward > Biological Sciences > University College of Wales > Aberystwyth > Dyfed > SY23 3DA > U.K. > Tel. 0970 623111x4188 > Fax 0970 622354 > FTP 144.124.112.30 -- Mark S. Strom, Ph.D. phone (206) 860-3379/fax (206) 860-3394 F/NWC3, NWFSC/NMFS/NOAA URL http://listeria.nwfsc.noaa.gov/home-page.html 2725 Montlake Blvd. E. email: strom@u.washington.edu Seattle, WA 98112-2097 mstrom@sci.nwfsc.noaa.gov From owner-software@net.bio.net Mon Sep 05 23:00:00 1994 Path: biosci!agate!overload.lbl.gov!dog.ee.lbl.gov!ihnp4.ucsd.edu!library.ucla.edu!europa.eng.gtefsd.com!howland.reston.ans.net!gatech!newsxfer.itd.umich.edu!uunet!zib-berlin.de!informatik.tu-muenchen.de!lrz-muenchen.de!ipp-garching.mpg.de!alf.biochem.mpg.de!krasel From: krasel@alf.biochem.mpg.de (Cornelius Krasel) Newsgroups: bionet.software Subject: Superimposing crystal structures? Date: 6 Sep 1994 18:01:23 GMT Organization: Rechenzentrum der Max-Planck-Gesellschaft in Garching Lines: 25 Message-ID: <34iapjINNu6t@sat.ipp-garching.mpg.de> NNTP-Posting-Host: alf.biochem.mpg.de X-Newsreader: TIN [version 1.1 PL8] [Article crossposted from bionet.xtallography] Hello netters, I would like to superimpose different crystal structures in PDB format. I know that there are programs who can do that, but I would like to do it on a Linux box (e.g. to view the superimposed structures later in Rasmol). I understand that I have to minimize the RMS between different points (e.g. Calpha) but I am not sure _how_ to do this. I am especially unsure if commonly used algorithms can account for the relative orientation of a three-dimensional structure to another. (As you might see, my mathematical background is virtually nonexistant :-) Can anybody give me some hint (or even better, lead me to some piece of C source code)? Thanks in advance, --Cornelius. -- /* Cornelius Krasel, Abt. Lohse, Genzentrum, D-82152 Martinsried, Germany */ /* email: krasel@alf.biochem.mpg.de fax: +49 89 8578 3795 */ /* "People are DNA's way of making more DNA." (Edward O. Wilson, 1975) */ From owner-software@net.bio.net Mon Sep 05 23:00:00 1994 Newsgroups: bionet.software Path: biosci!agate!howland.reston.ans.net!pipex!uknet!gdt!aber!gepasi.dbs.aber.ac.uk!prm From: prm@aber.ac.uk (Pedro Mendes) Subject: Re: info needed re met.simulation SCAMP Message-ID: Keywords: metabolic simulation Lines: 71 Sender: news@aber.ac.uk (USENET news service) Nntp-Posting-Host: pcfchb.dbs.aber.ac.uk Organization: The University of Wales Aberystwyth X-Newsreader: Trumpet for Windows [Version 1.0 Rev B] References: <5i+yWhT.swannp@delphi.com> Date: Tue, 6 Sep 1994 14:16:53 GMT Patrick G Swann writes: >I'm looking for a program to simulate product yields from multi-sequence >(possibly branching) pathways given initial substrates and kinetic constants. >I' ve heard that SCAMP can do this and am interested in any information >regarding availability. Many Thanks. SCAMP is available by ftp from ftp://bmsdarwin.brookes.ac.uk/pub/software/atari/scamp/scamp25g.zip or ftp://bmsdarwin.brookes.ac.uk/pub/software/ibmpc/scamp/scamp25g.zip Alternatively if you want to use MS-Windows, you can use GEPASI, available from the same site: ftp://bmsdarwin.brookes.ac.uk/pub/software/ibmpc/gepasi/gep208c.zip with the source code in ftp://bmsdarwin.brookes.ac.uk/pub/software/ibmpc/gepasi/gsrc208c.zip below is a short description of GEPASI: GEPASI 2.0 is a package for the simulation and modelling of biochemical pathways and chemical reactions. It was made for research but can also be used for educational purposes. With GEPASI you build models of pathways and simulate their dynamics and steady state for given sets of parameters. GEPASI generates the coefficients of Metabolic Control Analysis for steady states. There is also a facility to assist in the study of the effects of several parameters on the properties of the model pathway. GEPASI can be used to simulate systems with stable states, limit cycles and choatic behaviour. There is no manual included but the context-sensitive help includes a short tutorial on metabolic modelling and references to review articles and books about computer simulation in biochemistry, metabolic control analysis, enzyme kinetics and numerical analysis. Also included in the package is the file GEPASI.WRI containing a cut-down version of a paper in "Modern trends in Biothermokinetics" (1993), edited by S. Schuster, M. Rigoulet, R. Ouhabi and J.-P. Mazat (Plenum Press) with a short description of GEPASI. A more detailed paper on GEPASI has been published in journal "Computer Applications in the Biosciences". The full reference is: Mendes P., (1993) GEPASI: a software package for modelling the dynamics, steady states and control of biochemical and other systems. Comput. Appl. Biosci. 9, 563-571. GEPASI runs under MS-WINDOWS 3.1 and is free software, covered by the GNU General Public License. GEPASI uses GNUPLOT (either the DOS or MS-Windows versions), users should download this package and install it to be able to plot the results obtained with GEPASI. A maths co-processor is not necessary but if present will accelerate the simulations by a large factor. GEPASI 2.0 (c) 1989,1992,1993 by Pedro Mendes. NOTE: the subjects of metabolic simulation and metabolic control analysis are discussed in the usenet newsgroup bionet.metabolic-reg. Cheers, Pedro Mendes prm@aber.ac.uk From owner-software@net.bio.net Tue Sep 06 23:00:00 1994 Path: biosci!galaxy.ucr.edu!ihnp4.ucsd.edu!agate!spool.mu.edu!umn.edu!newsdist.tc.umn.edu!urvile.msus.edu!TIGGER.STCLOUD.MSUS.EDU!DEGROOTE From: degroote@TIGGER.STCLOUD.MSUS.EDU (David DeGroote) Newsgroups: bionet.general,bionet.software Subject: scheduling software Date: 7 Sep 1994 02:37:13 GMT Organization: ST. CLOUD STATE UNIVERSITY, ST. CLOUD, MN Lines: 3 Message-ID: <34j90p$vmd@urvile.MSUS.EDU> Reply-To: degroote@TIGGER.STCLOUD.MSUS.EDU NNTP-Posting-Host: tigger.stcloud.msus.edu Xref: biosci bionet.general:11051 bionet.software:9240 We are looking for software to help us schedule classes. Reply by e-mail to DEGROOTE@Tigger.stcloud.msus.edu. Will post a summary. Thanks in advance. David DeGroote From owner-software@net.bio.net Tue Sep 06 23:00:00 1994 Path: biosci!daresbury!trane.uninett.no!sunic!umdac!Peter.Lundberg From: peterl@umdix.umdc.umu.se (Peter Lundberg) Newsgroups: bionet.software Subject: Re: Newsreader for Mac Date: 7 Sep 1994 17:02:16 GMT Organization: Phys Chem, University of Umea, Sweden Lines: 9 Sender: -Not-Authenticated-[2976] Message-ID: <34krmo$5np@news.umu.se> References: <34jv0c$904@fstgds15.tu-graz.ac.at> NNTP-Posting-Host: plgmac.chem.umu.se X-Posted-From: InterNews 1.0@news.umu.se. Xdisclaimer: No attempt was made to authenticate the sender's name. Another news reader is 'InterNews' 1.0 from Dartmouth College. I think it is *better* than NewsWatcher. Try them out! 73, Peter ================================== Peter Lundberg Email: peterl@umdix.umdc.umu.se ============761.91141============= From owner-software@net.bio.net Tue Sep 06 23:00:00 1994 Path: biosci!newshost.lanl.gov!ncar!gatech!psuvax1!rutgers!mcrcr6!smithp01 From: smithp01@mcrcr6.med.nyu.edu Newsgroups: bionet.software,sci.image.processing,sci.techniques.microscopy Subject: Announcing MDPP V94.100: available from DECUS Message-ID: <1994Sep7.081203.7488@mcrcr6> Date: 7 Sep 94 08:12:03 EDT Organization: NYU Medical Center, New York, NY 10016, USA Lines: 16 Xref: biosci bionet.software:9239 sci.image.processing:8311 sci.techniques.microscopy:563 This will serve to announce that the newest version of the Micrograph Data Processing Program (MDPP) has been submitted to the DEC Users Society Library (DECUS). People interested can request distribution tapes from DECUS. There are now two separate distributions: one for Open VMS (VAX and Alpha) and one for UNIX (Ultrix and OSF/1). MDPP is an image processing package targetted principally towards problems in electron microscopy, but it contains a great many other tools as well. An overview of the package can be obtained by FTPing a brief description from the host 'mcclb0.med.nyu.edu' in the MDPP sub-directory. +----------------------------------------------------------------------------+ |Ross Smith, Research Computing Resource, Department of Cell Biology, NYU-MC| |E-Mail: SMITH@NYUMED.BITNET (BITNET), SMITH@MCCLB0.MED.NYU.EDU (Internet)| +----------------------------------------------------------------------------+ From owner-software@net.bio.net Tue Sep 06 23:00:00 1994 Path: biosci!galaxy.ucr.edu!ihnp4.ucsd.edu!agate!howland.reston.ans.net!EU.net!sunic!news.funet.fi!ousrvr.oulu.fi!mac36049.oulu.fi!user From: mhaveri@cc.oulu.fi (Matti Haveri) Newsgroups: bionet.software Subject: Re: Newsreader for Mac Date: Wed, 07 Sep 1994 16:50:33 +0300 Organization: University of Oulu Lines: 29 Message-ID: References: <34jv0c$904@fstgds15.tu-graz.ac.at> NNTP-Posting-Host: mac36049.oulu.fi Mime-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit NewsWatcher is free. It may not be sold for profit or included with software which is sold for profit, but otherwise you should feel free to use it and redistribute it. The anonymous FTP site for the program, the user document, and the Think C source code is: ftp://ftp.acns.nwu.edu/pub/newswatcher/ NewsWatcher requires a Macintosh running System 7.0 or later with 2.5 megabytes or more of memory and a hard drive. The Mac must be connected to the Internet, and MacTCP must be properly installed and configured. For dialup use, NewsWatcher works with the various SLIP and PPP programs, and with ARA together with an appropriately configured AppleTalk/IP gateway. It is strictly an online newsreader, and it does not support any other kind of dialup connection. The program requires an active full TCP/IP connection to the Internet. It does not support offline newsreading, and it does not support older kinds of dialup connections designed primarily for simple terminal emulation. We have no plans to add these features soon, if at all. If you need an offline newsreader or a newsreader which works with older kinds of dialup connections, you must use some other program. NewsWatcher was written by John Norstad of Northwestern University: mailto:j-norstad@nwu.edu -Matti Haveri From owner-software@net.bio.net Tue Sep 06 23:00:00 1994 Path: biosci!galaxy.ucr.edu!ihnp4.ucsd.edu!swrinde!pipex!warwick!bham!bcs113.bham.ac.uk!user From: J.Parkhill@bham.ac.uk (Julian Parkhill) Newsgroups: bionet.software Subject: Re: Newsreader for Mac Date: Wed, 07 Sep 1994 15:50:26 +0000 Organization: University of Birmingham Lines: 25 Distribution: world Message-ID: References: <34jv0c$904@fstgds15.tu-graz.ac.at> NNTP-Posting-Host: bcs113.bham.ac.uk In article <34jv0c$904@fstgds15.tu-graz.ac.at>, fojan@fochsg02.tu-graz.ac.at (Peter Fojan) wrote: > Hi folks, > Is there somewhere in the net a newsreader for Macintosh available. I would be > interested to get one preferred pd or shareware. Is there a site where I could > find this program? > Thanxx for the info, > Peter The best newsreader I have found is Newswatcher. Current version 2.0b9 is available by anon FTP at ftp://ftp.acns.nwu.edu/pub/newswatcher/ It is a threaded newsreader, with a host of wonderful additional functions. As an example: If you were reading this with Newswatcher, you could double-click on the URL above, and it would automatically launch Fetch to retrieve the file for you. -- Julian Parkhill - J.Parkhill@bham.ac.uk CRC Laboratories, Dept. of Cancer Studies, Medical School, University of Birmingham, Edgbaston, Birmingham, B15 2TJ, U.K. Disclaimer: If I thought anybody gave a damn about my opinions.... From owner-software@net.bio.net Tue Sep 06 23:00:00 1994 Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!pipex!uknet!daresbury!not-for-mail From: Dietmar Tietz Newsgroups: bionet.software Subject: Re: nih image where to find. Date: 7 Sep 1994 10:49:47 +0100 Lines: 37 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <34k2br$kpe@mserv1.dl.ac.uk> MIME-Version: 1.0 Original-To: Peter Fojan On 7 Sep 1994, Peter Fojan wrote: > Hi folks, > Can someone direct me to a program called nihimage for the Macintosh? > Where could I find it. Is it ftp able or how to obtain? > Thanx for the information. > Peter > > --------------------------------------------------------------------------- > | Fojan Peter | E-Mail: | > | University of Technology Graz | Fojan@fochsg02.tu-graz.ac.at | > | Institute of Biotechnology | Fojan@biote.tu-graz.ac.at | > | Petersgasse12 | PHONE:(++43) 316 873-8424 | > | A-8010 Graz / Austria | FAX: (++43) 316 811050 | > --------------------------------------------------------------------------- > Peter, You should find NIH-Image 1.55 in the /pub/nih-image directory on zippy.nimh.nih.gov. Good luck! Dietmar Tietz ****************************************************************** * Dietmar Tietz, Ph.D., Research Scientist * * Biostatistics, Justus-Liebig-University * * Ludwigstr. 27, D-35390 Giessen, Germany * * Phone: +49-(641)-702-6015 * * Fax: +49-(641)-702-5995 * * Email: Dietmar.Tietz@Uni-Giessen.de * ****************************************************************** From owner-software@net.bio.net Tue Sep 06 23:00:00 1994 Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!EU.net!Austria.EU.net!newsfeed.ACO.net!fstgds15.tu-graz.ac.at!fochsg02.tu-graz.ac.at!fojan From: fojan@fochsg02.tu-graz.ac.at (Peter Fojan) Newsgroups: bionet.software Subject: Newsreader for Mac Date: 7 Sep 1994 08:52:28 GMT Organization: Graz University of Technology, Austria Lines: 15 Distribution: world Message-ID: <34jv0c$904@fstgds15.tu-graz.ac.at> NNTP-Posting-Host: fochsg02.tu-graz.ac.at Hi folks, Is there somewhere in the net a newsreader for Macintosh available. I would be interested to get one preferred pd or shareware. Is there a site where I could find this program? Thanxx for the info, Peter -- --------------------------------------------------------------------------- | Fojan Peter | E-Mail: | | University of Technology Graz | Fojan@fochsg02.tu-graz.ac.at | | Institute of Biotechnology | Fojan@biote.tu-graz.ac.at | | Petersgasse12 | PHONE:(++43) 316 873-8424 | | A-8010 Graz / Austria | FAX: (++43) 316 811050 | --------------------------------------------------------------------------- From owner-software@net.bio.net Tue Sep 06 23:00:00 1994 Path: biosci!bcm!cs.utexas.edu!uunet!newsfeed.ACO.net!fstgds15.tu-graz.ac.at!fochsg02.tu-graz.ac.at!fojan From: fojan@fochsg02.tu-graz.ac.at (Peter Fojan) Newsgroups: bionet.software Subject: nih image where to find. Date: 7 Sep 1994 08:42:20 GMT Organization: Graz University of Technology, Austria Lines: 16 Distribution: world Message-ID: <34judc$8k2@fstgds15.tu-graz.ac.at> NNTP-Posting-Host: fochsg02.tu-graz.ac.at Hi folks, Can someone direct me to a program called nihimage for the Macintosh? Where could I find it. Is it ftp able or how to obtain? Thanx for the information. Peter -- --------------------------------------------------------------------------- | Fojan Peter | E-Mail: | | University of Technology Graz | Fojan@fochsg02.tu-graz.ac.at | | Institute of Biotechnology | Fojan@biote.tu-graz.ac.at | | Petersgasse12 | PHONE:(++43) 316 873-8424 | | A-8010 Graz / Austria | FAX: (++43) 316 811050 | --------------------------------------------------------------------------- From owner-software@net.bio.net Tue Sep 06 23:00:00 1994 Path: biosci!galaxy.ucr.edu!ihnp4.ucsd.edu!usc!howland.reston.ans.net!europa.eng.gtefsd.com!newsxfer.itd.umich.edu!zip.eecs.umich.edu!panix!news.columbia.edu!ciao.cc.columbia.edu!jk32 From: jk32@ciao.cc.columbia.edu (Jose Katz) Newsgroups: bionet.software Subject: Protein Tertiary Structure Modeling Program ? Date: 7 Sep 1994 15:21:27 GMT Organization: Columbia University Lines: 10 Message-ID: <34klpn$4po@apakabar.cc.columbia.edu> NNTP-Posting-Host: ciao.cc.columbia.edu Does anyone know if there is a program available which would help in creating a three-dimensional model of a protein (including secondary and tertiary structure) given the amino acid sequence, type of tertiary fold (e.g. alpha-beta barrel), and the segments predicted to be alpha-helices, beta-sheets or turns. The ultimate goal is to create a pdb file for display, and various types of simulations. Thank you very much. -- Ferenc Czegledy From owner-software@net.bio.net Tue Sep 06 23:00:00 1994 Newsgroups: bionet.software Path: biosci!galaxy.ucr.edu!ihnp4.ucsd.edu!swrinde!howland.reston.ans.net!wupost!monsanto.com!rcwieg.monsanto.com!user From: rcwieg@ccmail.monsanto.com (Roger Wiegand) Subject: Re: Newsreader for Mac Message-ID: Sender: news@tin.monsanto.com (USENET News System) Organization: Searle Molecular Biology References: <34jv0c$904@fstgds15.tu-graz.ac.at> Date: Wed, 7 Sep 1994 15:38:54 GMT Lines: 49 In article <34jv0c$904@fstgds15.tu-graz.ac.at>, fojan@fochsg02.tu-graz.ac.at (Peter Fojan) wrote: > Hi folks, > Is there somewhere in the net a newsreader for Macintosh available. I would be > interested to get one preferred pd or shareware. Is there a site where I could > find this program? > Thanxx for the info, > Peter > -- > > --------------------------------------------------------------------------- > | Fojan Peter | E-Mail: | > | University of Technology Graz | Fojan@fochsg02.tu-graz.ac.at | > | Institute of Biotechnology | Fojan@biote.tu-graz.ac.at | > | Petersgasse12 | PHONE:(++43) 316 873-8424 | > | A-8010 Graz / Austria | FAX: (++43) 316 811050 | > --------------------------------------------------------------------------- Try Newswatcher, you'll like it. The following is from the Readme: NewsWatcher is free. It may not be sold for profit or included with software which is sold for profit, but otherwise you should feel free to use it and redistribute it. The anonymous FTP site for the program, the user document, and the CodeWarrior C source code is: ftp://ftp.acns.nwu.edu/pub/newswatcher/ The helper programs used by NewsWatcher are available via anonymous FTP at: ftp://ftp.acns.nwu.edu/pub/newswatcher/helpers/ NewsWatcher requires a Macintosh running System 7.0 or later with 2.5 megabytes or more of memory and a hard drive. The Mac must be connected to the Internet, and MacTCP must be properly installed and configured. NewsWatcher is distributed as a ³fat binary². This means that it runs in native 68K mode on Motorola 68K Macintoshes, and it runs in native PowerPC mode on Power Macintoshes. -- Thanks, Roger mailto::rcwieg@ccmail.monsanto.com From owner-software@net.bio.net Tue Sep 06 23:00:00 1994 Newsgroups: bionet.molbio.methds-reagnts,bionet.software Path: biosci!daresbury!trane.uninett.no!sunic!news.funet.fi!nntp.utu.fi!utu.fi!jarnie From: jarnie@utu.fi (Jarmo Niemi) Subject: TRACTOR, a T-track location program Message-ID: Sender: news@utu.fi (Usenet News admin) Nntp-Posting-Host: polaris.cc.utu.fi Organization: University of Turku, Finland X-Newsreader: TIN [version 1.2 PL2] Date: Wed, 7 Sep 1994 12:01:08 GMT Lines: 25 Xref: biosci bionet.molbio.methds-reagnts:18139 bionet.software:9244 The QuickBasic program TRACTOR is used to locate clones in a known sequence using only one sequencing reaction, a method generally known as "T-tracking". The program can reduce workload at the end stage of a sequencing project using the random subcloning strategy. A paper discussing the program will be published in Computer Applications in the Biosciences vol. 10, number 5. Interested parties are requested to take a look at my WWW page http://www.utu.fi/~jarnie/ or contact me at jarnie@utu.fi. The program is available by anonymous FTP at ftp.funet.fi as /pub/sci/molbio/msdos/tractor6.zip. Incidentally, the Acknowledgements section of the paper thanks among others, Dr. V. Jongeneel, Dr. S. Nedospasov, Dr. R. Harper _and_ bionet.molbio.methds-reagnts... -- Jarmo Niemi,Biochemistry,U.of Turku,jarnie@utu.fi,http://www.utu.fi/~jarnie/ "Take care of Mr. Bond. See that some harm comes to him." -Moonraker From owner-software@net.bio.net Tue Sep 06 23:00:00 1994 Path: biosci!UVVM.UVIC.CA!JCOWARD From: JCOWARD@UVVM.UVIC.CA Newsgroups: bionet.software Subject: ITCH'94 UPDATES ! Date: 7 Sep 1994 15:02:07 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 110 Sender: daemon@net.bio.net Distribution: world Message-ID: <940907.143544.PDT.JCOWARD@UVVM.UVic.CA> NNTP-Posting-Host: net.bio.net ITCH'94 - INFORMATION TECHNOLOGY IN COMMUNITY HEALTH: VICTORIA, BC, CANADA: OCTOBER 30 - NOVEMBER 2, 1994 CHANGING OPPORTUNITIES - UPDATES ! - REGISTER NOW This is the sixth International Conference addressing information technology issues in health care. The ITCH Conferences have always taken a very broad view of the definition of community health. It is meant to include all aspects of health care, acute or chronic, public or private, and hospital or non-hospital based. CONFERENCE LOCATION ITCH'94 is being held in the Victoria Conference Centre located in the "Garden" City's inner harbour. The centre is located adjacent to THE WORLD-FAMOUS EMPRESS HOTEL OVERLOOKING THE waterfront, beside the British Columbia (Canada's Pacific Rim Province) Legislature. The Greater Victoria area recently hosted the XV Commonwealth Games. PRE-CONFERENCE EVENTS Workshops: "TECHNOLOGY ASSESSMENT" "COMPUTER NETWORKING" "NURSING INFORMATICS" Student Poster Contest and Prizes: KEYNOTE & INVITED SPEAKERS Dr. Paige Sipes-Metzler - "CHALLENGES OF INFORMATION MANAGEMENT WHEN PRIORITIZING HEALTH CARE". Professor Andrew Penn - "THE SYNAPSE PROJECT: CLINICAL USE OF MEDICAL HYPERTEXT ON INTERNET'S WORLDWIDE WEB". Dr. Stephen Soumerai - "CLAIMS VERSUS CLAIMS: HOW TO TEST HYPOTHESES ABOUT DRUG POLICY USING DRUG CLAIMS DATABASES". WORLD-WIDE PARTICIPATION OF SPEAKERS Over 100 abstracts were reviewed: At least 70 papers will be presented at the Conference. Speakers are attending from Canada and the USA: As well; as far away as New Zealand, Australia, Germany, South Africa, England, The Netherlands, Italy, and France. ITCH'94 CONFERENCE TOPICS General topics include; "CLIENT-ORIENTED SYSTEMS", "INFORMATION NEEDS", "VOICE SYSTEMS", "MULTIMEDIA and EXPERT SYSTEMS", "EVALUATING UTILIZATION", "LINKING PROFESSIONALS", "THE HUMAN INTERFACE", EMERGING ABORIGINAL SETTING and SITUATIONS", and "NEW DIRECTIONS". CONFERENCE PROCEEDINGS ALL papers "PRESENTED" will be published in the Conference "Proceedings - ITCH'94". The Proceedings are included in the registration price. A copy will be given to each person as when they register on site. SPONSORS & EXHIBITORS UVic - The University of Victoria, CPHA - Canadian Public Health Association, BCMOH - British Columbia Ministry of Health, COACH - Canada's Health Informatics Association, Metro-McNair Clinical Laboratories, The School of Health Information Science at UVic, GVHS - Greater Victoria Hospital Society, IML - Island Medical Laboratories, RNABC - Registered Nurses Association of BC, BCSC - British Columbia Systems Corporation, G.S.C. Data Corporation, CHIS - Community Health Information Systems, A. Wilson and Associates, and Clinicare Corporation. FOR REGISTRATION AND INFORMATION ON "ITCH'94" PLEASE CONTACT: ITCH'94 CONFERENCE MANAGEMENT (Ms. Pat McGuire) DIVISION OF CONTINUING STUDIES UNIVERSITY OF VICTORIA PO BOX 5050, MS 8451 VICTORIA, BC, CANADA V8W-3N6 TELEPHONE: (604) 721-8470 FAX : (604) 721-8774 EMAIL: PMCGUIRE@POSTOFFICE.UVIC.CA . JAMES H. COWARD, CHE ITCH'94 - INFORMATION TECHNOLOGY IN COMMUNITY HEALTH ORGANIZING COMMITTEE, SPONSORS AND EXHIBITORS, 220, 1641 Hillside Avenue, Victoria BC V8T 5G1 PHONE: (604) 598-3681 FAX: (604) 592-6341 From owner-software@net.bio.net Wed Sep 07 23:00:00 1994 Path: biosci!galaxy.ucr.edu!ihnp4.ucsd.edu!library.ucla.edu!europa.eng.gtefsd.com!howland.reston.ans.net!xlink.net!news.urz.uni-heidelberg.de!cbb From: cbb@convex.phazc.uni-heidelberg.de (Christopher Blencowe) Newsgroups: bionet.software Subject: Re: Looking for enzyme kinetics SW (DOS) Date: 8 Sep 1994 09:17:55 GMT Organization: University of Heidelberg, Germany Lines: 19 Message-ID: <34mks3$jkj@sun0.urz.uni-heidelberg.de> References: NNTP-Posting-Host: iris.phazc.uni-heidelberg.de X-Newsreader: TIN [version 1.2 PL2] Uwe Baumert (tiedtke@vnwz00.uni-muenster.de) wrote: : Hi, : I'm looking for free DOS-software (anonFTP) that can handle enzyme kinetics : datas generating Lineweaver-Burk-plots etc. on DOS not Windows! : With kind regards, : -- : Uwe Baumert : Institute for General Zoology and Genetics : University of Muenster : Schlossplatz 5 : D-48149 Muenster, Germany e-mail: tiedtke@vnwz01.uni-muenster.de Try the book 'Enzfitter' with software package, not for free, but cheap enough and plain thing running on DOS. Sincerly, Christopher From owner-software@net.bio.net Wed Sep 07 23:00:00 1994 Path: biosci!agate!spool.mu.edu!howland.reston.ans.net!swiss.ans.net!solaris.cc.vt.edu!uunet!EU.net!sunic!news.funet.fi!news.csc.fi!news.helsinki.fi!klaava!tjvuorin From: tjvuorin@cc.Helsinki.FI (T Joonas Vuorinen) Newsgroups: bionet.software Subject: INSTALLING PROGRAM NEEDED !! Date: 8 Sep 1994 09:10:40 GMT Organization: University of Helsinki Lines: 3 Message-ID: <34mkeg$m3l@kantti.Helsinki.FI> NNTP-Posting-Host: klaava-fddi.helsinki.fi Mime-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit X-Newsreader: TIN [version 1.2 PL0] I need install program for dos i got 5-disks program which should install to hard drive E:mail me tjvuorin@cc.helsinki.fi From owner-software@net.bio.net Wed Sep 07 23:00:00 1994 Path: biosci!galaxy.ucr.edu!ihnp4.ucsd.edu!library.ucla.edu!europa.eng.gtefsd.com!newsxfer.itd.umich.edu!news.cic.net!magnus.acs.ohio-state.edu!csn!yuma!purdue!mozo.cc.purdue.edu!inet.d48.lilly.com!marvin.d50.lilly.com!user Newsgroups: bionet.software Subject: Looking for PreExperiment Sorting SW Message-ID: From: WRBensch@Lilly.com (Bill Bensch) Date: Thu, 08 Sep 1994 13:32:11 -0500 Followup-To: bionet.software Distribution: world Organization: Lilly Research Laboratories (Eli Lilly & Co) Nntp-Posting-Host: marvin.d50.lilly.com Mime-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit Lines: 18 I am looking for some software that will allow me to separate animals at the beginning of a study into groups such that the mean value for a specific variable is the same for each group. basicly, I would feed in the values for individual animals, the number of groups, and the number of animals per group, and the software would sort the animals into groups. I presenly randomly sort the animals into groups, then use JMP to visualize the distribution of the values and group means. I then repeatedly re-assign animals to different groups until the group means are close to each other. I would appreciate any pointers to any program to remove this tedium. -- William R. Bensch | Reply to: wrbensch@lilly.com Cardiovascular Research, DC 0522 | Voice: (317) 276-8499 Lilly Research Labs | FAX: (317) 277-0892 Indianapolis IN 46285 | ****My employer sponsors my research, not necessarily my opinions**** From owner-software@net.bio.net Wed Sep 07 23:00:00 1994 Path: biosci!galaxy.ucr.edu!ihnp4.ucsd.edu!swrinde!emory!gatech!nntp.msstate.edu!ukma!ndlc.occ.uky.edu!not-for-mail From: mowersp@ndlc.occ.uky.edu (Patrick Mowers) Newsgroups: bionet.software Subject: Re: info needed re met.simulation SCAMP Date: 7 Sep 1994 19:05:01 -0500 Organization: The NDLC's Internet Gateway Lines: 19 Message-ID: <34lkfd$d93@ndlc.occ.uky.edu> References: <5i+yWhT.swannp@delphi.com> NNTP-Posting-Host: ndlc.occ.uky.edu X-Newsreader: TIN [version 1.2 PL2] Patrick G Swann (swannp@delphi.com) wrote: : I'm looking for a program to simulate product yields from multi-sequence : (possibly branching) pathways given initial substrates and kinetic constants. : I' : ve heard that SCAMP can do this and am interested in any information regarding : availability. Many Thanks. You might want to try GEPASI, a freeware program that is designed for just this type of thing. It will handle upto 26 Rxns and supports a number of kinetics models such as Michaelis-Minton, etc. You can use it with gnuplot for graphing output. Both run under windows 3.1 and I believe you can get them via gopher from oakland or several other places. I have even seen GEPASI on shareware CDROMs. Good luck, Pat Mowers mowersp@ndlc.occ.uky.edu From owner-software@net.bio.net Wed Sep 07 23:00:00 1994 Path: biosci!galaxy.ucr.edu!ihnp4.ucsd.edu!usc!howland.reston.ans.net!news.cac.psu.edu!wilbur!lar11 From: lar11@wilbur.cac.psu.edu (LAWRENCE A RODRIQUEZ) Newsgroups: bionet.software Subject: Mapmaker and RI data Date: 8 Sep 1994 16:27:16 GMT Organization: Penn State University, Center for Academic Computing Lines: 13 Message-ID: <34ne14$ge6@hearst.cac.psu.edu> NNTP-Posting-Host: wilbur.cac.psu.edu X-Newsreader: TIN [version 1.2 PL2] I've had no success in obtaining an answer from the Mapmaker folks, so I thought I'd check here as to whether Mapmaker/Exp 3.0 applies an adjustment for recombinant inbred strain data so that the recombination distances generated would be comparable to a consensus mouse map. There appears to be some sort of adjustment made when I scanned the C code for the program (in the MAPS.C file). But since I'm not familiar with C, I can't say for sure. There's nothing in the manual about this. Thanks for any help. --Larry Center for Developmental and Health Genetics Penn State University From owner-software@net.bio.net Wed Sep 07 23:00:00 1994 Path: biosci!galaxy.ucr.edu!ihnp4.ucsd.edu!swrinde!emory!europa.eng.gtefsd.com!newsxfer.itd.umich.edu!gatech!taco.cc.ncsu.edu!jamarsh From: jamarsh@eos.ncsu.edu (John Allen Marsh) Newsgroups: bionet.software Subject: WANTED: DNA Strider Date: 8 Sep 1994 16:54:11 GMT Organization: North Carolina State University, Project Eos Lines: 13 Distribution: world Message-ID: <34nfjj$sb5@taco.cc.ncsu.edu> Reply-To: jamarsh@eos.ncsu.edu (John Allen Marsh) NNTP-Posting-Host: c00517-118rd.eos.ncsu.edu Keywords: DNA Strider, Mac Software Originator: jamarsh@c00517-118rd.eos.ncsu.edu Hello all, I am looking for a program called DNA Strider for Mac. I need to know who sells it and what the price is, if possible. Thanks! JAM P.S. I wanted to post this on bionet.software.sources, but the newsgroup is currently empty, and I couldn't figure out how to post to it (it appears that my software won't let me). Any help on this? -- From owner-software@net.bio.net Thu Sep 08 23:00:00 1994 Path: biosci!internet!biosci!not-for-mail From: biohelp (BIOSCI Administrator) Newsgroups: bionet.software Subject: UNSUBSCRIBING, BIOSCI ARCHIVES, ADDRESS DATABASE & BIOSCI FAQ Date: 9 Sep 1994 02:00:16 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 322 Sender: daemon@net.bio.net Distribution: world Message-ID: <199409090900.CAA18417@net.bio.net> NNTP-Posting-Host: net.bio.net Four important items follow: How to cancel e-mail subscriptions to BIOSCI newsgroups, BIOSCI archive searching, the BIOSCI FAQ, and the BIOSCI User Address Directory form. If you have not yet listed yourself in our BIOSCI user directory, please take a few minutes to complete and return the form below. If your personal information has changed since you listed yourself, please send us a complete new updated form. We can not make manual revisions to existing entries. Sincerely, Dave Kristofferson BIOSCI/bionet Manager biosci-help@net.bio.net **** How to cancel a BIOSCI e-mail subscription **** If you want to cancel your e-mail subscription to this group, PLEASE DO NOT POST YOUR UNSUBSCRIBE REQUEST TO THE NEWSGROUP ADDRESS (NOR REPLY TO A MESSAGE POSTED TO THE NEWSGROUP)!!! This would send your request to all of the readers of the newsgroup, but it might still not be seen by the BIOSCI staff - thus you would annoy many people and possibly not accomplish your goal anyway. IF YOU ARE LOCATED IN THE AMERICAS OR PACIFIC RIM COUNTRIES, please send a message to biosci@net.bio.net Instructions will be returned automatically, so the contents of your message do not matter. IF YOU ARE LOCATED IN EUROPE, AFRICA OR CENTRAL ASIA, please send a message to MXT@dl.ac.uk containing the word help in the body of the message to retrieve e-mail server instructions. Any text placed on the Subject: line of your message will be ignored, so be sure to put the "help" command in the body of the message. If you need personal assistance, a BIOSCI staff member can be contacted at either of the following addresses. Please contact the address designated for your location. Support Address Location --------------- -------- biosci@daresbury.ac.uk Europe, Africa, and Central Asia biosci-help@net.bio.net Americas and the Pacific Rim **** SEARCHING BIOSCI ARCHIVES **** The easiest way to search the BIOSCI archives is to use gopher software and connect over the Internet to net.bio.net, the U.S. BIOSCI computer. We maintain three indexes which are searchable from the main gopher menu on net.bio.net: (1) an index of all BIOSCI postings; (2) an index of individual journal article references from the Table of Contents postings on the BIO-JOURNALS newsgroup; and (3) an index of BIOSCI users including regular mail and e-mail addresses, phone/FAX numbers, research interests, and newsgroup participation. E-mail users can search the BIOSCI archives by using our waismail e-mail server. For instructions send the message help to waismail@net.bio.net. Leave the Subject: line blank (anything entered on the Subject: line is ignored). WAIS software can also be used to search the archives as described in the BIOSCI FAQ (see below). Finally, the BIOSCI archive files are accessible by anonymous FTP to net.bio.net [134.172.2.69] in the directory pub/BIOSCI. **** BIOSCI FREQUENTLY ASKED QUESTIONS (FAQ) SHEET **** 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/doc/biosci.FAQ or for retrieval by gopher to net.bio.net, port 70. It may also be requested by sending the command info faq in the body of an e-mail message to the Internet address biosci-server@net.bio.net. Please do not enter the info faq command on the Subject: line of your message since the e-mail server ignores text on the Subject: line. 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. **** BIOSCI USER ADDRESS DIRECTORY **** Please take this opportunity to add your name and address information to the BIOSCI User Address Database if you have not already done so. Below is the address form that we would like each reader of the BIOSCI/bionet newsgroups to complete and return if you would like to be listed in our database. The database serves as a directory that enables biologists, who are currently using (or even just reading) the BIOSCI newsgroups, to look up e-mail addresses and other information about our users. The address database is reindexed nightly for WAIS, waismail, and gopher access. If you have access to gopher, connect to net.bio.net to search the database. If you have access to WAIS, please use our WAIS source biologists-addresses.src. If you are not on the Internet, please use our waismail server (send the word "help" to waismail@net.bio.net to get instructions; any text on the Subject: line of your message will be ignored, so put the help command in the body of the mail message.). Please carefully follow the instructions for completing the form below and return it to either of the following two addresses (whichever is more convenient for you). Thanks in advance for taking the time to complete and return the form. Addresses for returning forms Location Network ----------------------------- -------- ------- biovote@net.bio.net U.S.A. Internet/BITNET biovote@daresbury.ac.uk U.K. JANET MAKING SURE THAT YOUR INFORMATION IS CURRENT This notice will be mailed bimonthly to each newsgroup. You should check your database entry from time-to-time to see if your address information is still up-to-date. Using Gopher to complete the form --------------------------------- If you don't want to use a text editor, you can also use Dan Jacobson's gopher site to fill out the address database form as follows. Otherwise skip this section on gopher and proceed to the instructions for filling out the form below. > To add yourself to the database just point your > gopher client at merlot.gdb.org and select the following: > > --> 15. Searching For Biologists/ > > --> 9. E-mail Addresses of Biosci-Bionet Users/ > > --> 1. Add (or Correct) Your Address to the BIOSCI User Address > Data.. > > > And fill out the form. or Rob Harper's gopher site in Europe as follows: > Europeans can point their gopher client at gopher.csc.fi and add their > information to the database. All entries will be mailed directly to > Dave for incorporation in a wais source. > > The path to the questionare is as follows. > > ---> 10. Finnish EMBnet BioBox/ > > ---> 8. FAQ Files/ > > FAQ Files > > 1. EMBnet: Information. > 2. EMBnet: Internet resources guide. > 3. A Biologist's Guide to Internet Resources/ > 4. All FAQs (Frequently Asked Questions) Searches and Archives/ > --->5. Bionauts Address Database (questionaire) IMPORTANT INSTRUCTIONS - PLEASE READ CAREFULLY Please enter all responses after the : on each line, leaving one (1) blank space after the : (i.e., before the start of your text). Please do NOT extend your responses past the end of each line (80 characters). PLEASE DO NOT alter any of the field identifiers such as "first name: ". If you have nothing to enter after a field identifier, PLEASE LEAVE IT - do not delete it even if there is no data on the line in question. Several lines are provided at the end of the form for comments, but, please adhere to the line length restriction. On the date: line, please enter the date in the DD-MM-YY format, e.g., 15-05-93 for 15 May 1993. This line will tell others when the information was last updated. Please be sure to include the 0's for single digit days or months, e.g., 15-05-93, not 15-5-93. Note that the "e-mail network: " line below is for specifying, e.g., "Internet," "BITNET," "EARN," "JANET," or whatever other network that your computer may be on. If you are uncertain about any field, please feel free to leave it blank, but please DO NOT DELETE the field identifier from the form! In the first field below, "New information or Update ...", please enter "N" if this is the first time that you have registered in the directory or "U" if you are correcting a listing that you sent to us previously. The comment: lines may be used for anything that you like but PLEASE DO NOT DELETE THEM FROM THE FORM OR ALTER THEM. One suggested use is to list the names of the newsgroups in which you participate. Please use the MAILING LIST name (see below - the latest version of the list can be requested from biosci@net.bio.net) instead of the USENET name even if you don't participate by e-mail. WAIS might get confused by the periods in the USENET names. This allows one to retrieve via WAIS or waismail the list of participants in a particular group. For example: comment: ARABIDOPSIS PLANT-BIOLOGY BIONEWS On the comment: lines use these names below ---- NOT the USENET names below MAILING LIST NAME USENET Newsgroup Name ----------------- --------------------- ACEDB-SOFT bionet.software.acedb AGEING bionet.molbio.ageing AGROFORESTRY bionet.agroforestry ARABIDOPSIS bionet.genome.arabidopsis BIOFORUM bionet.general BIO-INFORMATION-THEORY bionet.info-theory BIONAUTS bionet.users.addresses BIONEWS bionet.announce BIO-JOURNALS bionet.journals.contents BIO-MATRIX bionet.molbio.bio-matrix BIOPHYSICAL-SOCIETY bionet.prof-society.biophysics BIOPHYSICS bionet.biophysics BIO-SOFTWARE bionet.software BIOTHERMOKINETICS bionet.metabolic-reg CELL-BIOLOGY bionet.cellbiol CHLAMYDOMONAS bionet.chlamydomonas CHROMOSOMES bionet.genome.chromosomes COMPUTATIONAL-BIOLOGY bionet.biology.computational CYTONET bionet.cellbiol.cytonet DROSOPHILA bionet.drosophila EMBL-DATABANK bionet.molbio.embldatabank EMPLOYMENT bionet.jobs GDB bionet.molbio.gdb GENBANK-BB bionet.molbio.genbank GENETIC-LINKAGE bionet.molbio.gene-linkage GRASSES-SCIENCE bionet.biology.grasses HIV-MOLECULAR-BIOLOGY bionet.molbio.hiv HUMAN-GENOME-PROGRAM bionet.molbio.genome-program IMMUNOLOGY bionet.immunology INFO-GCG bionet.software.gcg JOURNAL-NOTES bionet.journals.note METHODS-AND-REAGENTS bionet.molbio.methds-reagnts MOLECULAR-EVOLUTION bionet.molbio.evolution MYCOLOGY bionet.mycology NEUROSCIENCE bionet.neuroscience N2-FIXATION bionet.biology.n2-fixation PARASITOLOGY bionet.parasitology PHOTOSYNTHESIS bionet.photosynthesis PLANT-BIOLOGY bionet.plants POPULATION-BIOLOGY bionet.population-bio PROTEIN-ANALYSIS bionet.molbio.proteins PROTEIN-CRYSTALLOGRAPHY bionet.xtallography PROTISTA bionet.protista RAPD bionet.molbio.rapd SCIENCE-RESOURCES bionet.sci-resources STRUCTURAL-NMR bionet.structural-nmr TROPICAL-BIOLOGY bionet.biology.tropical VIROLOGY bionet.virology WOMEN-IN-BIOLOGY bionet.women-in-bio YEAST bionet.molbio.yeast Listing newsgroups on the comment: line is optional, of course. Thanks again for your cooperation! --------------- please cut here and return portion below --------------- New information or Update to old record (enter N or U): date (DD-MM-YY): first name: middle initial: family name: job title: e-mail address: e-mail network: phone number: FAX number: institution: address1: address2: address3: city: state/province: country: postal code: research interest: research interest: comment: comment: comment: comment: comment: From owner-software@net.bio.net Thu Sep 08 23:00:00 1994 Newsgroups: bionet.molbio.methds-reagnts,bionet.software Path: biosci!agate!howland.reston.ans.net!EU.net!sunic!news.funet.fi!nntp.utu.fi!utu.fi!jarnie From: jarnie@utu.fi (Jarmo Niemi) Subject: Re: TRACTOR, a T-track location program Message-ID: Followup-To: bionet.molbio.methds-reagnts,bionet.software Sender: news@utu.fi (Usenet News admin) Nntp-Posting-Host: polaris.cc.utu.fi Organization: University of Turku, Finland X-Newsreader: TIN [version 1.2 PL2] References: Date: Fri, 9 Sep 1994 08:58:39 GMT Lines: 35 Xref: biosci bionet.molbio.methds-reagnts:18244 bionet.software:9260 I wrote: > The QuickBasic program TRACTOR is used to locate clones in a > known sequence using only one sequencing reaction, a method > generally known as "T-tracking". The program can reduce workload > at the end stage of a sequencing project using the random > subcloning strategy. > A paper discussing the program will be published in Computer > Applications in the Biosciences vol. 10, number 5. Interested > parties are requested to take a look at my WWW page > http://www.utu.fi/~jarnie/ > or contact me at jarnie@utu.fi. > The program is available by anonymous FTP at ftp.funet.fi > as /pub/sci/molbio/msdos/tractor6.zip. Unfortunately, now it no longer is there. File README.CHANGES in /pub/sci/molbio/ says: "The molecular biology directory structure has changed on this server. It has been set up to mirror the popular sites at EMBL and INDIANA. Some of the programmes in the old directories may have disappeared but generally most of the software can still be found in the mirror directories." I'll try to find a new home for the program. Meanwhile, email me. (please tell me whether you can receive binary attachments to emails, or whether I have to send it in uucoded form.) -- Jarmo Niemi,Biochemistry,U.of Turku,jarnie@utu.fi,http://www.utu.fi/~jarnie/ "Honni soit qui mal y pense" -Edward III From owner-software@net.bio.net Thu Sep 08 23:00:00 1994 Path: biosci!EM.AGR.CA!BROUILLETTEP From: BROUILLETTEP@EM.AGR.CA Newsgroups: bionet.software Subject: SUBSCRIPTION Date: 9 Sep 1994 08:53:27 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 2 Sender: daemon@net.bio.net Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net SUBSCRIBE BIO-SOFTWARE Pierre Brouillette From owner-software@net.bio.net Thu Sep 08 23:00:00 1994 Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!gatech!newsxfer.itd.umich.edu!jobone!ukma!ukcc.uky.edu!FJVAND00 From: FJVAND00@ukcc.uky.edu (Frank van de Loo) Newsgroups: bionet.software Subject: Re: Protein Tertiary Structure Modeling Program ? Date: Fri, 09 Sep 94 17:03:18 EDT Organization: The University of Kentucky Lines: 32 Message-ID: <1702CEFE9S86.FJVAND00@ukcc.uky.edu> References: <34klpn$4po@apakabar.cc.columbia.edu> NNTP-Posting-Host: ukcc.uky.edu In article <34klpn$4po@apakabar.cc.columbia.edu> jk32@ciao.cc.columbia.edu (Jose Katz) writes: >Does anyone know if there is a program available which would help in >creating a three-dimensional model of a protein (including secondary >and tertiary structure) given the amino acid sequence, type of >tertiary fold (e.g. alpha-beta barrel), and the segments predicted >to be alpha-helices, beta-sheets or turns. The ultimate goal is >to create a pdb file for display, and various types of simulations. > >Thank you very much. > >-- Ferenc Czegledy Hi Ferenc, I asked a similar question recently on bionet.molec-model, so the responses would be a good place for you to start. You can search the bionet archives by gopher to ftp.bio.indiana.edu. Use the search "protein and structure and scratch" since "Protein structure from scratch?" was the subject line of the thread. The bottom line is that it can be done if you have enough good data, the model you achieve may or may not reflect reality, and you'll need considerable computer power to do it - e.g. I am setting up now to use Quanta on a Silicon Graphics workstation, and don't know yet if this will do. In case you're not familiar with the Indiana gopher hole, choose the "Network- News" menu and then enter you search at "Bionet News at IUBio archive" Good Luck! Frank van de Loo USDA/ARS, Lexington KY. From owner-software@net.bio.net Thu Sep 08 23:00:00 1994 Newsgroups: bionet.software Path: biosci!agate!spool.mu.edu!sdd.hp.com!cs.utexas.edu!swrinde!howland.reston.ans.net!EU.net!sunic!trane.uninett.no!daresbury!bioftp.unibas.ch!citi2.fr!jussieu.fr!univ-lyon1.fr!ghost.dsi.unimi.it!genes!oberto From: oberto@genes.icgeb.trieste.it (Jacques Oberto) Subject: DNA bending prediction software Message-ID: <1994Sep9.073429.485@genes.icgeb.trieste.it> Organization: ICGEB Date: Fri, 9 Sep 1994 07:34:29 GMT Lines: 11 Hi All, I am looking for software (PC, Mac, Unix whatever) to predict bends in a given DNA sequence. Any information is welcome. Thanks. Jacques -- Jacques Oberto From owner-software@net.bio.net Thu Sep 08 23:00:00 1994 Path: biosci!CRYSBIO1.BCH.UMONTREAL.CA!nick From: nick@CRYSBIO1.BCH.UMONTREAL.CA ("Nick Blom") Newsgroups: bionet.software Subject: (none) Date: 9 Sep 1994 06:42:48 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 6 Sender: daemon@net.bio.net Distribution: world Message-ID: <9409090941.ZM2288@crysbio1.BCH.UMontreal.CA> NNTP-Posting-Host: net.bio.net unsubscribe bio-soft nick@BCH.UMontreal.CA end From owner-software@net.bio.net Fri Sep 09 23:00:00 1994 Path: biosci!agate!howland.reston.ans.net!news.intercon.com!news1.digex.net!digex.net!not-for-mail From: wbrown@access1.digex.net (William Brown) Newsgroups: bionet.software Subject: Scedule of events for NIH symposium? Date: 9 Sep 1994 21:24:53 -0400 Organization: Express Access Online Communications, Greenbelt, MD USA Lines: 15 Message-ID: <34r1t5$l2p@access1.digex.net> NNTP-Posting-Host: access1.digex.net Does anyone out there have the schedule of events for the upcoming NIH symposium on computers in molecular biology? The symposium is scheduled for the week of the 19th this month. In addition, does anyone have the address of the NIH GOPHER site? Thanks in advance. ------------------------------------------------------------------------------ W. Augustus Brown, Jr. Department of Biochemistry and Molecular Biology College of Medicine Howard University wbrown@access.digex.net Washington, D.C. 71054.3502@compuserve.com ------------------------------------------------------------------------------ From owner-software@net.bio.net Fri Sep 09 23:00:00 1994 Newsgroups: bionet.software Path: biosci!agate!library.ucla.edu!psgrain!charnel.ecst.csuchico.edu!olivea!sgigate.sgi.com!enews.sgi.com!decwrl!netcomsv!netcomsv!genetics.bio-rad.com!rotter From: rotter@genetics.bio-rad.com (Richard Otter 6766) Subject: Re: DNA sequencing from scanned autorads Message-ID: Keywords: DOS/WINDOWS , HP-ScanJet Organization: Genetic Systems Software, Bio-Rad Laboratories, CA, USA References: <33f5rr$2k5@mercury.hgmp.mrc.ac.uk> Date: Sat, 10 Sep 1994 01:13:52 GMT Lines: 14 In article <33f5rr$2k5@mercury.hgmp.mrc.ac.uk> pdezoysa@crc.ac.uk writes: >Does anyone out rhere know of any commercial software or public domain shareware that >will enable me to read DNA sequences from scanned autorads of sequencing gels ? > >Any information will be appreciated. > >Priyal de Zoysa > > You can add the Bio-Rad Gene Reader to the list... From owner-software@net.bio.net Fri Sep 09 23:00:00 1994 Path: biosci!agate!howland.reston.ans.net!news.intercon.com!news.iac.net!news.iac.net!not-for-mail From: gwaddell@iac.net (George Waddell) Newsgroups: bionet.software Subject: ECG analysis software Date: 9 Sep 1994 23:46:12 -0400 Organization: Internet Access Cincinnati 513-887-8877 Lines: 6 Message-ID: <34ra64$joi@great-miami.iac.net> NNTP-Posting-Host: great-miami.iac.net X-Newsreader: TIN [version 1.2 PL2] Hello, I am looking for software that will do analysis of electrocardiograms. Is something like this available on the net for ftp? George From owner-software@net.bio.net Fri Sep 09 23:00:00 1994 Path: biosci!IRCM.UMontreal.CA!JOHANNE From: JOHANNE@IRCM.UMontreal.CA Newsgroups: bionet.software Subject: repetititves sequences Date: 10 Sep 1994 07:40:07 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 22 Sender: daemon@net.bio.net Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net Good morning I am looking for a databases of repetitives sequences like Alu family from eukaryotes. I looked in the previous articles of Usenet group and I found two alternatives: 1- send a sequence to Pythia but this test a sequence against repetitive sequences for human only 2- make a small databank from Embl and Genbank with all the sequences containing "repeat" in the definition. This can mix things... Those answers date from a relatively long time. May be new ressources are now available. It would help us a lot if something would be available. Thank you ___________________________________________________________________________ Johanne Duhaime tel (514)987-5556 Institut de recherches cliniques de Montreal fax (514)987-5644 DuhaimJ@ircm.umontreal.ca ___________________________________________________________________________ From owner-software@net.bio.net Sat Sep 10 23:00:00 1994 Path: biosci!agate!howland.reston.ans.net!news.cac.psu.edu!usenet From: jtn2@genesis.ait.psu.edu (Jason Newman) Newsgroups: bionet.software Subject: MacPlasmap Date: 11 Sep 1994 18:23:15 GMT Organization: Penn State University, Center for Academic Computing Lines: 10 Message-ID: <34vhuj$bpa@hearst.cac.psu.edu> NNTP-Posting-Host: ppp85.cac.psu.edu X-Posted-From: InterNews 1.0.2@ppp85.cac.psu.edu X-Authenticated: jtn2 on POP host genesis.ait.psu.edu Is there a newer version of MacPlasmap (newer than ver 1.82) out there on the net somewhere? Ver 1.82 doesn't seem to like system 7.1 all that well, plus there is no support for color. Are there any other plasmid drawing software programs out there for the Mac? Sure, I know there is MacDNAsis, but I think that program costs over $800 dollars. Thanks in advace for any info. Jason Newman jtn2@email.psu.edu From owner-software@net.bio.net Sun Sep 11 23:00:00 1994 Path: biosci!agate!howland.reston.ans.net!europa.eng.gtefsd.com!newsxfer.itd.umich.edu!zip.eecs.umich.edu!panix!ddsw1!redstone.interpath.net!news.sprintlink.net!indirect.com!slip237.indirect.com!raphael From: raphael@indirect.com (Raphael Carter) Newsgroups: bionet.software Subject: Simulation of the spread of a gene through a population Date: Sun, 11 Sep 1994 22:27:26 Organization: Excluded Middle Incorporate Lines: 13 Distribution: world Message-ID: NNTP-Posting-Host: slip237.indirect.com X-Newsreader: Trumpet for Windows [Version 1.0 Rev A] Does anyone know of an MS-DOS program to track the spread of a gene through a (human) population? I'd prefer something that comes with source code, since my purposes would almost certainly require some modification. In fact, what would be most useful is an algorithm and/or a library of appropriate code snips. Thanks for any help you can provide. -- ===== Raphael Carter | raphael@indirect.com | pre-operative Minnesotan ===== ===== For Darmok Dictionary, Sonnets on Science, and PGP key, use URL: ===== home ================== Reading: Anne Somerset, ELIZABETH I ===================== From owner-software@net.bio.net Sun Sep 11 23:00:00 1994 Newsgroups: bionet.software Path: biosci!agate!howland.reston.ans.net!pipex!uknet!festival!leeds.ac.uk!news From: bmb5meb@biovax.leeds.ac.uk Subject: Consensus pattern searching Message-ID: <1994Sep12.100417.9727@leeds.ac.uk> Sender: news@leeds.ac.uk Reply-To: bmb5meb@biovax.leeds.ac.uk Organization: The University of Leeds, UK Date: Mon, 12 Sep 1994 11:04:16 +0100 (BST) Lines: 13 I am looking for a program that will run on a DEC Vax running VAX/VMS v5.5-2 or a DEC Alpha running OpenVMS AXP v1.5 which will allow me to scan a protein database with consensus patterns. Preferably the program should allow patterns with flexible gaps, etc., and needs to be able to handle a database which contains ~85,000 sequences. Please post or e-mail any suggestions; any help will be greatly appreciated. Mike. Michael Beck (Leeds University Rifle Coach) : Juggle 'til you drop Protein Database Group, University of Leeds : : To all masochists, try doing e-mail : bmb5meb@biovax.leeds.ac.uk : the Mills' Mess when drunk. From owner-software@net.bio.net Sun Sep 11 23:00:00 1994 Newsgroups: bionet.software Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!swrinde!dptspd!news From: jks@giskard.utmem.edu (Jack Spitznagel) Subject: Primer analysis software Reply-To: jks@giskard.utmem.edu (Jack Spitznagel) Organization: Rancho Malario Distribution: bionet software Date: Mon, 12 Sep 1994 19:59:01 GMT Message-ID: Summary: PD software available for? X-Newsreader: IBM NewsReader/2 v1.02 Keywords: PubDom Primer PC Mac Unix? Sender: news@dptspd.sat.datapoint.com (dptspd News Administrator) Lines: 13 I've been trying to trick Archie into finding PC, Mac, or Unix based public domain or shareware dna/rna primer analysis software. I am less converned about graphics than I am about results. TIA for any pointer or suggestions to find executables or source code! ********************************************************************* * John Spitznagel, DDS, PhD * Sancho Panza Institute * * Internet: jks@giskard.utmem.edu * for Advanced Studies * * AMPRNet: kd4iz@kd4iz.ampr.org * Department of Bogometrics * * CIS: 76044,476 * * * Tel: (901) 448-6441 * (C) JKS, 1993 * ********************************************************************* From owner-software@net.bio.net Sun Sep 11 23:00:00 1994 Path: biosci!agate!overload.lbl.gov!bks From: bks@s27w007.pswfs.gov (Bradley K. Sherman) Newsgroups: bionet.software Subject: Re: how to find an Email address Date: 12 Sep 1994 19:06:35 GMT Organization: Dendrome, A Genome Database for Forest Trees Lines: 21 Distribution: bionet Message-ID: <3528rr$88n@overload.lbl.gov> References: <351u50$k2q@mserv1.dl.ac.uk> NNTP-Posting-Host: s27w007.pswfs.gov In article <351u50$k2q@mserv1.dl.ac.uk> kulmburg@sun1.ukl.uni-freiburg.de (Peter Kulmburg) writes: > >I have a problem common to several of my internet friends: I know somebody >has an email address and I know a little bit of where he or she is. I get asked this question a lot, and there are some tricks of the trade, but the best answer is this: Send email to someone who knows the person better than you do, asking them for the address. The telephone is appropriate technology as well, but email decreases transcription errors. --bks -- Bradley K. Sherman Computer Scientist Dendrome Project 510-559-6437 FAX: -6440 Institute of Forest Genetics bks@s27w007.pswfs.gov P.O. Box 245, Berkeley, CA 94701 http://s27w007.pswfs.gov/People/bks.html From owner-software@net.bio.net Sun Sep 11 23:00:00 1994 Path: biosci!agate!howland.reston.ans.net!usc!nic-nac.CSU.net!charnel.ecst.csuchico.edu!xmission!u.cc.utah.edu!mac64_46.med.utah.edu!tom_doak From: Tom Doak Newsgroups: bionet.software Subject: Re: Consensus pattern searching Date: 12 Sep 1994 15:53:18 GMT Organization: CVMBiology, UofUtah Lines: 31 Distribution: world Message-ID: <351the$6tj@u.cc.utah.edu> References: <1994Sep12.100417.9727@leeds.ac.uk> NNTP-Posting-Host: mac64_46.med.utah.edu X-Newsreader: Nuntius Version 1.2 X-XXMessage-ID: X-XXDate: Mon, 12 Sep 1994 09:55:32 GMT In article <1994Sep12.100417.9727@leeds.ac.uk> , bmb5meb@biovax.leeds.ac.uk writes: >I am looking for a program that will run on a DEC Vax running VAX/VMS v5.5-2 >or a DEC Alpha running OpenVMS AXP v1.5 which will allow me to scan a protein >database with consensus patterns. Preferably the program should allow >patterns with flexible gaps, etc., and needs to be able to handle a database >which contains ~85,000 sequences. Please post or e-mail any suggestions; any >help will be greatly appreciated. > >Mike. > I probably can't be of any direct help to you, we use the comercial GCG package, which we like a lot, and which allows you to search with various patterns, such as a consensus. But I wanted to point out that if you have a family of proteins aligned, you are throwing out a lot of information by using the consensus, unless the conservation is very high. Better, IMO, is to use profile technology (Gribskov, et al In Methods in Enzymology, 183;146-159 (1989)), which takes into account far more of the allowed variation in a family alignment than can be accounted for in the consensus of the alignment. GCG has an implementation of the Profile set of programs. Tom Doak SaltLakeCity, Utah tom_doak@hlthsci.med.utah.edu From owner-software@net.bio.net Sun Sep 11 23:00:00 1994 Path: biosci!daresbury!not-for-mail From: kulmburg@sun1.ukl.uni-freiburg.de (Peter Kulmburg) Newsgroups: bionet.software Subject: how to find an Email address Date: 12 Sep 1994 17:03:44 +0100 Lines: 19 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <351u50$k2q@mserv1.dl.ac.uk> X-Sender: kulmburg@skl1.ukl.uni-freiburg.de Original-To: bio-software@dl.ac.uk Dear collegues, I have a problem common to several of my internet friends: I know somebody has an email address and I know a little bit of where he or she is. Is there a possibility to check that out with Mosaic (is there an URL out with a serchable catalog, accepting names or institute's names?). It should be something like "archie for email addresses". To give you an exemple: I am looking for Dr. E.(M?) CANTIN at the "City of Hope" in Duarte, California. How am I to proceed with Mosaic? Thank you very much for your help! Sincerely yours Peter Peter KULMBURG (193.196.226.110 MacName: ktl110.ukl.uni-freiburg.de) home: Tel./Fax:+49 761 808439 work: Tel.:+49 761 270/7195 Fax:/7177 From owner-software@net.bio.net Sun Sep 11 23:00:00 1994 Path: biosci!agate!howland.reston.ans.net!EU.net!sunic!trane.uninett.no!daresbury!not-for-mail From: J R Beeching Newsgroups: bionet.software Subject: RFLP / RAPD band profile database Date: 12 Sep 1994 13:44:34 +0100 Lines: 22 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <351ifi$7as@mserv1.dl.ac.uk> MIME-Version: 1.0 Original-To: BIO-SOFTWARE Dear All, I am looking for some software, preferably public domain, which can be used to store and compare RFLP and/or RAPD band profile data. Ideally it should be able to accept cumulative date from different probes or primers. It should also have the capability to be interrogated in order to determine whether or not a pattern from a new organism is already in the database. If there is much interest and many replies I will post a compilation. Thank you for your help. John ------------------------------------------------------------------- | John Beeching E-mail: J.R.Beeching@bath.ac.uk | | Biology & Biochemistry | | University of Bath | | Bath BA2 7AY Phone: +44 (0)225 826826 ext 5193| | U.K. Fax: +44 (0)225 826779 | ------------------------------------------------------------------- From owner-software@net.bio.net Sun Sep 11 23:00:00 1994 Path: biosci!NATURE.BERKELEY.EDU!bosborne From: bosborne@NATURE.BERKELEY.EDU (Brian Osborne) Newsgroups: bionet.software Subject: chromap program? Date: 12 Sep 1994 15:02:13 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 19 Sender: daemon@net.bio.net Distribution: world Message-ID: <199409122202.PAA03712@nature.Berkeley.EDU> NNTP-Posting-Host: net.bio.net To the Group, I am looking for a program called "chromap" that draws maps of chromosomes from a set of coordinates. Unfortunately I don't know what platform it runs on and archie can't find it on the Net either. Does anyone know where it can be found? Thank you for your attention to this matter, Brian Osborne Plant Gene Expression Center 800 Buchanan Street Albany, CA USA 94710 TEL 510-559-5919 FAX 510-559-5718 bosborne@nature.berkeley.edu From owner-software@net.bio.net Sun Sep 11 23:00:00 1994 Path: biosci!agate!overload.lbl.gov!ames!enews.sgi.com!decwrl!lll-winken.llnl.gov!osi-east2.es.net!oracle.pnl.gov!netnews.nwnet.net!news.u.washington.edu!evolution.genetics.washington.edu!joe From: joe@evolution.genetics.washington.edu (Joe Felsenstein) Newsgroups: bionet.software Subject: Re: Simulation of the spread of a gene through a population Date: 12 Sep 1994 06:23:44 GMT Organization: University of Washington, Seattle Lines: 24 Distribution: world Message-ID: <350s5g$b6i@news.u.washington.edu> References: NNTP-Posting-Host: evolution.genetics.washington.edu Summary: SIMUL8 might do it. Keywords: Population genetic simulation, spread of a gene In article , Raphael Carter wrote: >Does anyone know of an MS-DOS program to track the spread of a gene through a >(human) population? > >I'd prefer something that comes with source code, since my purposes would >almost certainly require some modification. In fact, what would be most >useful is an algorithm and/or a library of appropriate code snips. I have a program, SIMUL8, that I use for teaching that simulates the change of gene frequency of an allele in a set of human populations, with the user able to set population size, fitnesses, mutation, and migration rates. Versions for various systems (DOS, Mac, and Unix/X) are available in C source code and executables by ftp in directory pub/popgen on my workstation: evolution.genetics.washington.edu (128.95.12.41). It depends in part on whether by "spread" Carter meant change of frequency in a single population (which could be a human population) or whether he meant spread through a geographically structured population. In the former case my program will be more useable than in the latter. ----- Joe Felsenstein, Dept. of Genetics, Univ. of Washington, Seattle, WA 98195 Internet: joe@genetics.washington.edu (IP No. 128.95.12.41) From owner-software@net.bio.net Sun Sep 11 23:00:00 1994 Path: biosci!daresbury!trane.uninett.no!nac.no!eunet.no!nuug!EU.net!uunet!newsflash.concordia.ca!canopus.cc.umanitoba.ca!bova!frist From: frist@cc.umanitoba.ca (Brian Fristensky) Newsgroups: bionet.software Subject: Re: repetititves sequences Date: 12 Sep 1994 22:06:06 GMT Organization: The Univeristy of Manitoba. Lines: 34 Distribution: world Message-ID: <352jcf$b2d@canopus.cc.umanitoba.ca> References: Reply-To: frist@ccu.umanitoba.ca NNTP-Posting-Host: bova.cc.umanitoba.ca In article BBE05D8A901FE00467@vxircm.IRCM.UMontreal.CA, JOHANNE@IRCM.UMontreal.CA () writes: > I am looking for a databases of repetitives sequences like Alu family > from eukaryotes. I looked in the previous articles of Usenet group and > I found two alternatives: deleted > 2- make a small databank from Embl and Genbank with all the sequences > containing "repeat" in the definition. This can mix things... > ___________________________________________________________________________ > Johanne Duhaime tel (514)987-5556 > Institut de recherches cliniques de Montreal fax (514)987-5644 > DuhaimJ@ircm.umontreal.ca > ___________________________________________________________________________ The FEATURES program from XYLEM can extract any features that are annotated in GenBank entries. In your case, you might run the program, extracting any features with feature keys such as repeat_unit {extracts just the repeat unit itself} repeat_region {extracts the entire region containing repeats} Only parts of each sequence that are annotated as repeats will be extracted. The XYLEM programs run under Unix and can be obtained by anonyous FTP to directory 'psgendb' at ftp.cc.umanitoba.ca =============================================================================== Brian Fristensky | Department of Plant Science | A question is like a knife that slices University of Manitoba | through the stage backdrop and gives us Winnipeg, MB R3T 2N2 CANADA | a look at what lies hidden behind. frist@cc.umanitoba.ca | Office phone: 204-474-6085 | Milan Kundera, THE UNBEARABLE LIGHTNESS FAX: 204-261-5732 | OF BEING =============================================================================== From owner-software@net.bio.net Mon Sep 12 23:00:00 1994 Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!gatech!newsxfer.itd.umich.edu!nntp.cs.ubc.ca!unixg.u