From owner-software@net.bio.net Mon Jul 01 23:00:00 1996 Path: biosci!daresbury!lyra.csx.cam.ac.uk!mole.bio.cam.ac.uk!tjrc1 From: tjrc1@mole.bio.cam.ac.uk (Tim Cutts (Zoology)) Newsgroups: bionet.software Subject: Re: What program to open Mac files in Windows PC? Date: 2 Jul 1996 06:39:54 GMT Organization: University of Cambridge Lines: 23 Message-ID: <4rag7q$es8@lyra.csx.cam.ac.uk> References: <4r9s3j$k5k@sjx-ixn4.ix.netcom.com> NNTP-Posting-Host: mole.bio.cam.ac.uk In article <4r9s3j$k5k@sjx-ixn4.ix.netcom.com>, William Howse wrote: >Is there a program out that will let me open Mac files with my Windows >PC? > >I know that Mac has programs out to open Windows files in Mac >computers, like "PC Exchange" and so forth. You have two choices, that I have tried, both of which work. There is a fully-fledged Macintosh emulator, which will also allow you to run a lot of Macintosh software. It's called Executor, and you can get it from ftp.ardi.com. Secondly, if disk copying is all you want, there is a nifty little DOS program around called Mac-ette. Both of these products cost money, but they are quite cheap. Last time I checked, neither program would run under Windows NT, although ARDI may have fixed Executor by now. Regards, From owner-software@net.bio.net Mon Jul 01 23:00:00 1996 Path: biosci!daresbury!lyra.csx.cam.ac.uk!mole.bio.cam.ac.uk!tjrc1 From: tjrc1@mole.bio.cam.ac.uk (Tim Cutts (Zoology)) Newsgroups: bionet.software Subject: Re: Which platform? Date: 2 Jul 1996 06:36:55 GMT Organization: University of Cambridge Lines: 38 Message-ID: <4rag27$es3@lyra.csx.cam.ac.uk> References: <4q918p$4s1@bagan.srce.hr> <4r990d$s65@newstand.syr.edu> NNTP-Posting-Host: mole.bio.cam.ac.uk In article <4r990d$s65@newstand.syr.edu>, wrote: >The problem with running Windows NT, UNIX, and another OS on the same platform is the >harddrive format issue. UNIX and NT use there own special type of format and you need to >partition the drives in order to use them. It can be very hairy to try. Anyone running DOS on a PC should be used to partitioning already. If they have a hard disk >200Mb and they haven't partitioned it already into logical drives they are wasting disk space. On a 300Mb DOS partition, for example, the allocation unit is 8Kb, which means that every file will on average use 4Kb more disk space than it actually needs. If your logical drives are all around 200 Mb in size, that figure is only 2 Kb per file. That's a saving of 2 Mb per thousand files. The MS-DOS filesystem is very inefficient on large partitions. This is one of the advantages of NT, which always allocates 512 bytes at a time, regardless of partition size, so a given file will on average only use 256 bytes more space than it needs. Converting a 300 Mb drive containing 3,000 files from FAT to NTFS will probably gain you about 12 Mb of free hard disk space. >As far as the PPCP Macs running Windows NT, the programs still have to be compiled for that >processor and not many companies are doing that right now. They don't really have an excuse. The MSDN Level II Development Platform was (and maybe still is) shipping with a PowerPC compiler. The same argument is true to an extent of the other non-Intel NT architectures. Once PPCP hits the shops the companies will compile for it. >If you want to run NT and UNIX, if >you can afford it, buy a Digital Alpha computer. You can get a patch to software compiled for the >X86 platforms and they are the fastest processors made : ) I'd love to. I just don't have the money :-) Having said that, there is a disadvantage to non-Intel NT boxes, which is that they cannot run Intel 32-bit Windows programs. 16-bit ones, yes, but not 32-bit, which is something of a limitation, if you can't find a version compiled for your platform. From owner-software@net.bio.net Mon Jul 01 23:00:00 1996 Path: biosci!bcm.tmc.edu!cs.utexas.edu!howland.reston.ans.net!EU.net!Norway.EU.net!nntp.uio.no!nntp-oslo.UNINETT.no!nntp-trd.UNINETT.no!daresbury!is.bbsrc.ac.uk!news.ox.ac.uk!oxpath!rpgrant From: rpgrant@molbiol.ox.ac.uk (Richard P. Grant) Newsgroups: bionet.software Subject: Re: Which platform? Date: 2 Jul 96 09:05:23 GMT Organization: Oxford University Molecular Biology Data Centre Lines: 62 Message-ID: <1996Jul2.090523@molbiol.ox.ac.uk> References: <199606140621.NAA00687@benpc.bionet.nsk.su> <31C56361.7EC4@ibex.ca> <31C87548.7612@bbsrc.ac.uk> <31C977BB.1AA7@ibex.ca> <4r8laj$nc0@nntp1.best.com> NNTP-Posting-Host: ania.path.ox.ac.uk In article <4r8laj$nc0@nntp1.best.com>, jquinn@nntp.best.com (Greg) writes: > > Maybe Canada has real price breaks on Macs, but I doubt it. The big > drawback with the mac is currently the operating system, which simply > doesn't hold a candle to Win95, letalone NT. Not only is the Mac OS Come again? > incapable of true pre-emptive multitasking, but it's handling of virtual The Mac, at the moment does not have pre-emptive multitasking. So what? It's cooperative multitasking (can we say that, boys and girls?) is sufficient for anyone with two hands, two eyes and a single CPU ;-)) I have had a stuffit job going, files copying and been making pasteups in Photoshop all at the same time. Now tell me I want the computer to do something else simultaneously ...... Of course, other programs will be open, but I'm not using them because I only have one keyboard. > memory is terrible (ie. non-existant). If this wasn't bad enough, unless Huh? You've heard of RAM Doubler have you? Stable as houses in my hands. Maybe my two year old 25 MHz LC with 8MB RAM isn't a good example for this argument... (Yes, Apple's VM has had problems, but I doubt you've used a new machine recently) > extremely well set with tons of memory (eg. 32+), they can frequently > crash. Crashes? Well, dodgy beta software and Microsucks crash the machine _in_frequently. I can even run Photoshop over the network on a similar machine at work.... but yes, it goes a lot better on a 8100/110/80MB. > There are extremely good reasons for buying a Mac, principally for > its interface, which a lot of people have grown up with (leastways here in > the US). Also, computer illiterates find them easier to deal with. No one I think computer literates find them easier to deal with too. I don't like fighting a machine before I can work with it. Just because it's intuitive does not mean it's simple. Upgrades? Easy-peasy. Have you tried fitting an ethernet card into a Mac? Flip, wiggle, push. Close. Hey - I know people who use pcs who are scared of Macs because they perceive them as difficult to use. Go figure. > with any experience in this area would suggest that they are cost > effective in terms of computing power or hardware costs. That is simply > not the case. Ahem. Go look in a catalogue somewhere. Compare $$/Mhz, and then realize that the PPC is (on average) ~20% faster than an equivalent MHz CISC chip. Plus, Macs (and clones) come ready to go, and when you buy a Mac outfit you get everything: video cards, sound cards, all part of the price. And I _think_ the new macs have ethernet capability out of the box - although I could be wrong. HTH, Richard (oh, and don't start on reliability/DOA figures....) From owner-software@net.bio.net Mon Jul 01 23:00:00 1996 Path: biosci!rutgers!gatech!newsfeed.internetmci.com!newsxfer2.itd.umich.edu!tank.news.pipex.net!pipex!oleane!jussieu.fr!univ-lyon1.fr!in2p3.fr!swidir.switch.ch!swsbe6.switch.ch!news.unige.ch!news From: LGB computing center Newsgroups: bionet.software Subject: Re: Spatial autocorrelation Date: Tue, 02 Jul 1996 09:32:26 +0200 Organization: Genetics and Biometry Lab Lines: 21 Message-ID: <31D8D08A.6E2F@anthro.unige.ch> References: <4r02p7$416@styx.uwa.edu.au> NNTP-Posting-Host: 129.194.114.133 Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 2.01 (Win95; I) Jane Sampson wrote: > > Does anyone know of any software (preferably Mac) for spatial > autocorrelation analyses? Thanks. Jane Giorgio Bertorelle and Guido Barbujani have written a DOS program called AIDA, that compute autocorrelation coefficient analogues (Geary's c and Moran's I) for DNA sequence data. but I guess it can be used for single locus data as well. The reference is in : Bertorelle, G. and Barbujani, G. Analysis of DNA diversity by spatial autocorrelation. Genetics 140:811-819, 1995. Contact: Giorgio Bertorelle Cheers Laurent From owner-software@net.bio.net Mon Jul 01 23:00:00 1996 Newsgroups: bionet.software Subject: Microsoft Software (all brand new) at LOW Prices! From: dinop.@prostar.com (Dinop ) Path: biosci!rutgers!gatech!newsfeed.internetmci.com!zdc!news3.noc.netcom.net!noc.netcom.net!prostar.com Message-ID: <0023C8BB012A77EC@prostar.com> Date: 29 Jun 96 22:28:33 Organization: Lines: 58 From: dinop Subject: Microsoft Software (all brand new) at LOW Prices! Newsgroups: alt.forsale Message-ID: <01bb67de.212823e0$7ca9d6ce@skyking> X-Newsreader: Microsoft Internet News Lines: 52 Brand new Microsoft Software for Sale at LOW Prices! All software is Full version unless indicated otherwise. First Class Postage costs under $2, including insurance. (Can also ship FedEx or UPS, if desired) If interested, please e-mail me at dinop@prostar.com Microsoft Windows95 (CD) - Upgrade. Retail box. Brand new in unopened package. List price $89.99. Selling for $75. Microsoft Office for Windows95 (CD) - Full version. Excellent productivity package. Includes Excel, Word, PowerPoint, and Schedule+. Brand new in unopened package. List price $449.99. Selling for $165. Microsoft BackOffice Version 1.5 (CD) - Full version. Includes Microsoft Windows NT Server version 3.51 (list price $699.99), MS SQL Server (list price $879.99), MS SNA Server (list price $359.99), MS Systems Management Server (list price $579.99), & MS Mail Server (list price $ 239.99). Includes hundreds of dollars worth of comprehensive network manuals and installation guides on-disk. 2-CD set. Brand new in unopened package. List price $2199.99. Selling for $495. Microsoft Bookshelf 1995 (CD) - Consists of 8 reference books, including American Heritage Dictionary, Roget's Thesaurus, Columbia Encyclopedia, Columbia Dictionary of Quotations, World Almanac, People's Chronology, National Zip Code and Post Office Directory, and a Hammond Atlas. Includes videos, sounds, and a talking dictionary.. Brand new in unopened package. List price 49.99. Selling for $24. Microsoft Bob (CD) - 8 programs that make your computer easier and more fun to use for kids and adults. Includes word processing, address book, calendar, organizer, household manager, checkbook manager, etc. Brand new in unopened package. List price $49.99. Selling for $24. Microsoft Encarta 1996 (CD) - Encyclopedia with video, sounds, pictures, maps, etc. Brand new in unopened package. List price $49.99. Selling for $29. Microsoft Publisher 2.0 (CD) - Great program for making newsletters, banners, business cards, etc. Excellent printed output. Brand new in unopened package. List price $69.99. Selling for $39.. Microsoft Complete Baseball 1995 (CD) - Very comprehensive baseball reference. Sounds, video clips and hundreds of pictures make this a very enjoyable Microsoft Home title. Brand new in unopened package. List price $49.99. Selling for $29. From owner-software@net.bio.net Mon Jul 01 23:00:00 1996 Path: biosci!rutgers!gatech!usenet.eel.ufl.edu!news-res.gsl.net!news.gsl.net!news-stock.gsl.net!news.gsl.net!news.sprintlink.net!news-stk-11.sprintlink.net!southwind.net!NewsWatcher!user From: jnaylor@southwind.net (Jim Naylor) Newsgroups: bionet.software Subject: Re: Which platform? Date: Tue, 02 Jul 1996 01:42:12 -0600 Organization: SouthWind Internet Access, Inc. Lines: 43 Message-ID: References: <199606140621.NAA00687@benpc.bionet.nsk.su> <31C56361.7EC4@ibex.ca> <31C87548.7612@bbsrc.ac.uk> <31C977BB.1AA7@ibex.ca> <4r8laj$nc0@nntp1.best.com> NNTP-Posting-Host: onyx.southwind.net In article <4r8laj$nc0@nntp1.best.com>, jquinn@nntp.best.com (Greg) wrote: > Scott Delinger (Scott.Delinger@ualberta.ca) wrote: > : In article <31C977BB.1AA7@ibex.ca>, Achim Recktenwald wrote: > > : > : >The Mac might be easier to use, but you pay ~2x as much as for the same > : power on an IBM-clone. > > : Absolute rot. I have a Mac on my desk, for $3000 that the equivalent PC > : would cost at least $5000. I think you forgot to put a 3 in the > : denominator of your ~2x (~2x/3). > > Maybe Canada has real price breaks on Macs, but I doubt it. The big > drawback with the mac is currently the operating system, which simply > doesn't hold a candle to Win95, letalone NT. Not only is the Mac OS > incapable of true pre-emptive multitasking, but it's handling of virtual > memory is terrible (ie. non-existant). If this wasn't bad enough, unless > extremely well set with tons of memory (eg. 32+), they can frequently > crash. There are extremely good reasons for buying a Mac, principally for > its interface, which a lot of people have grown up with (leastways here in > the US). Also, computer illiterates find them easier to deal with. No one > with any experience in this area would suggest that they are cost > effective in terms of computing power or hardware costs. That is simply > not the case. I have rarely seen such absolutely ignorant comments! Each and every disadvantage you impute to the Mac is true of Windoze95 instead, with the sole exception of pre-emptive multitasking, which most users wouldn't recognize if it bit them, which it usually does on the MacOS copy, Windoze95. If your definition of a computer illiterate is someone who wants to get real work done without the machine getting in his face, then sign me up! But I was developing utilities and embedded system software for the original DOS version in 1982 in a proprietary coprocessor-based LAN file server. When Mac II was born, I quickly decided life is too short to mess with MS. As for cost effectiveness, why do you suppose Lockheed Martin Astronautics just purchased three thousand Power Computing Mac clones? And you might as well forget plug and play on Windoze--if you need it, get a Mac; you get more for your money in every way these days. -- Jim Naylor jnaylor@southwind.net Wichita KS From owner-software@net.bio.net Mon Jul 01 23:00:00 1996 Path: biosci!daresbury!nntp-trd.UNINETT.no!oslonett.no!sn.no!Norway.EU.net!EU.net!news-res.gsl.net!news.gsl.net!news.sprintlink.net!news-dc-5.sprintlink.net!news.sprintlink.net!news-dc-9.sprintlink.net!southwind.net!NewsWatcher!user From: jnaylor@southwind.net (Jim Naylor) Newsgroups: bionet.software Subject: Re: Which platform? Date: Tue, 02 Jul 1996 09:36:05 -0600 Organization: SouthWind Internet Access, Inc. Lines: 15 Message-ID: References: <199606140621.NAA00687@benpc.bionet.nsk.su> <4r8laj$nc0@nntp1.best.com> <4rb7pi$g6l@nntp3.u.washington.edu> NNTP-Posting-Host: onyx.southwind.net In article <4rb7pi$g6l@nntp3.u.washington.edu>, joe@evolution.genetics.washington.edu (Joe Felsenstein) wrote: [snip] It's a form of addiction. > Yes, I'm addicted to defending myself when I am blind-sided on a bionet group and called a "computer illiterate" by someone who should know better. My sincere apologies to the rest of the group who don't care--that's just my point--you shouldn't have to. This is my last post on the topic. -- Jim Naylor jnaylor@southwind.net Wichita KS From owner-software@net.bio.net Mon Jul 01 23:00:00 1996 Path: biosci!rutgers!uwm.edu!lll-winken.llnl.gov!enews.sgi.com!decwrl!tribune.usask.ca!rover.ucs.ualberta.ca!news.ucalgary.ca!pc10.mid.ucalgary.ca!user From: sims@acs.ucalgary.ca (Kurt Sims) Newsgroups: bionet.software Subject: Re: A GOOD NEWSREADER Date: Tue, 02 Jul 1996 08:19:30 -0700 Organization: University of Calgary Lines: 26 Message-ID: References: <4r3pjt$dmu@news.xs4all.nl> NNTP-Posting-Host: @pc10.mid.ucalgary.ca In article <4r3pjt$dmu@news.xs4all.nl>, an@christ.pope (pizzaman) wrote: > SEARCHING FOR A GOOD NEWSREADER > > It seems that FREEAGENT (sharewareversion) has a build in > filter that filters out the nonsense messages. > Ofcourse I want to determine myself what's nonsensical > > Who knows more about the Free Agent filtering let the WEB know. > > Thanx, > PIZZAMAN I don't think Free Agent has the filter feature. Their commercial release Agent does have it but you have to pay for it. I'm using one called "News Xpress" now that has a good kill/autoselect feature. All you have to do is select the group or groups that you want to apply the feature to and then type in some keywords. the keywords can be in the subject line. I have "$$" and "Make money" on mine and its amazing how much garbage is filtered out. You can also filter out names in the "from" line so you can delete posts from people you are sick of hearing from. If you want to look at it and a bunch of others you can go to http://www.tucows.com/. They have a lot of mirror sites and I think there is one closer to you so it won't take so long to download. Just click on the newsreader icon to go to that section. They also have links to the homepages of the software so you can check it out directly. From owner-software@net.bio.net Mon Jul 01 23:00:00 1996 Path: biosci!bcm.tmc.edu!cs.utexas.edu!swrinde!newsfeed.internetmci.com!in1.uu.net!news.u.washington.edu!evolution.genetics.washington.edu!joe From: joe@evolution.genetics.washington.edu (Joe Felsenstein) Newsgroups: bionet.software Subject: Re: Which platform? Date: 2 Jul 1996 13:21:54 GMT Organization: University of Washington Genetics Lines: 16 Message-ID: <4rb7pi$g6l@nntp3.u.washington.edu> References: <199606140621.NAA00687@benpc.bionet.nsk.su> <4r8laj$nc0@nntp1.best.com> NNTP-Posting-Host: evolution.genetics.washington.edu Summary: My machine IS better than yours Keywords: Windows, Macintosh, religious wars In article , Andy Law wrote: >This is shaping up for a traditional my-machine-is-better-than-yours >religous war. Since I think we can assume that we are (mostly) intelligent >adults here, can we nip this in the bud right now, or take it off to one >of the advocacy groups where it can die its prolonged and unpleasant death >unnoticed by those who don't really care? You don't understand. These folks are convinced that if they can just make one more comment, the other side will give in, grovel, change over from advocating operating system X to agreeing that those who advocated operating system Y were right all along. It's a form of addiction. -- Joe Felsenstein joe@genetics.washington.edu (IP No. 128.95.12.41) Dept. of Genetics, Univ. of Washington, Box 357360, Seattle, WA 98195-7360 USA From owner-software@net.bio.net Mon Jul 01 23:00:00 1996 Path: biosci!bcm.tmc.edu!cs.utexas.edu!swrinde!howland.reston.ans.net!vixen.cso.uiuc.edu!usenet.ucs.indiana.edu!sunflower.bio.indiana.edu!gilbertd From: gilbertd@sunflower.bio.indiana.edu (Don Gilbert) Newsgroups: bionet.software Subject: SeqPup, biosequence editor & analysis platform, version 0.6 Date: 2 Jul 1996 13:17:47 GMT Organization: Biology, Indiana University - Bloomington Lines: 81 Message-ID: <4rb7hr$6rc@usenet.ucs.indiana.edu> NNTP-Posting-Host: sunflower.bio.indiana.edu SeqPup, version 0.6 development release, June/July 1996 New in this release: Easily use GCG and other command-line software over network Bare-bones autosequencer (ABI,SCF) base calling, editing, assembly Expanded sequence size limits (now can open 1.9MB H.flu genome) Numerous bug fixes and improvements Summary SeqPup is a biological sequence editor and analysis program usable on the common computer systems of Macintosh, MS-Windows and X-Windows. It includes links to network services and external analysis programs. Features include + multiple sequence alignment and single sequence editors - read and write several sequence file formats + easy hand alignment features including colored bases and sliding * Internet sequence analysis services by BOP and email methods - automatic multiple sequence alignment with ClustalW app - automatic gel fragment alignment to contigs with CAP app * automatic base calling from ABI or SCF trace files with autoseq app - phylogenetic analysis of alignments with fastDNAml and LSADT apps - consensus, reverse, complement, degap, and distance/similarity operations - restriction maps + pretty print of alignments and sequences with boxed and shaded regions. - translate dna to/from protein using various codon tables + find strings and ORFs - automatic preference saving - user-definable links to external analysis programs (* new, + updated) NOTICE: This release is still unfinish, and has bugs. It may be useful to you as is, but be warned that it is still prone to problems. SeqPup is being written using DCLAP, a free and portable C++ class application framework. DCLAP is founded on the NCBI Toolkit, especially it's Vibrant user-interface section written primarily by Jonathan Kans. SeqApp/SeqPup was started in 1990 as sequence editor/analysis platform on which analysis programs from other authors could be easily incorporated into a useable interface. You can obtain this release thru anonymous ftp, gopher or http to iubio.bio.indiana.edu, in folder /molbio/seqpup. Versions are available for Macintosh (PowerMac and 68K), MS Windows (Win95, WinNT and Win3), and Unix/XWindows systems including Sun Solaris, SGI Irix, DEC Unix, Linux. The Internet locators to this software are Source code for this software is at . The bopper source for installed a server for SeqPup Internet BOP functions is in this same folder as Comments, bug reports and suggestions for new features (see below) are very welcome and should be sent via e-mail to . June/July 96: version 0.6d release + "bopper" Internet protocol for client/server use of command line programs such as the GCG suite. + autoseq base calling app for reading ABI and SCF sequencer trace file data, plus base/trace editing functions. + Started expanding maximum sequence limit to 2 megabases (from about 30Kb), however most functions beyond viewing will still fail for >30Kb sequences. + Several bug fixes are included for mac, mswin, unix. Added background color in align view, minimum ORF size pref, improved tracking of changed data, improved align editing, save pretty print to PICT or text; fixed child app bugs; fixed mswin edit truncation to 255 bases; editable data tables in selection dialogs -- -- d.gilbert--biocomputing--indiana u--bloomington--gilbertd@bio.indiana.edu From owner-software@net.bio.net Mon Jul 01 23:00:00 1996 Path: biosci!agate!spool.mu.edu!howland.reston.ans.net!swrinde!newsfeed.internetmci.com!news.ac.net!news.cais.net!van-bc!van.istar!ott.istar!istar.net!news.nstn.ca!news.dal.ca!news From: Arlin Stoltzfus Newsgroups: bionet.software Subject: ? tool to remove redundancy from sequence set Date: Tue, 02 Jul 1996 10:10:01 -0300 Organization: Dalhousie University Lines: 15 Message-ID: <31D91FA9.2F76@is.dal.ca> NNTP-Posting-Host: thidwick.biochem.dal.ca Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 2.0 (X11; I; SunOS 5.4 sun4m) Does anyone know of a tool for pruning a set sequences for redundancy? Something that, given a set of sequences (say, in a FASTA archive) and a user-defined value of X, would return a subset of sequences such that no two sequences were more than X% identical. Arlin -- Arlin Stoltzfus Department of Biochemistry Dalhousie University Halifax, Nova Scotia B3H 4H7 CANADA (email) arlin@is.dal.ca (phone) 902-494-3569 (fax) 902-494-1355 From owner-software@net.bio.net Mon Jul 01 23:00:00 1996 Path: biosci!daresbury!is.bbsrc.ac.uk!pc0734.ri.bbsrc.ac.uk!user From: Andy.Law@bbsrc.ac.uk (Andy Law) Newsgroups: bionet.software Subject: Re: Which platform? Date: Tue, 02 Jul 1996 09:24:22 +0100 Organization: Roslin Institute Lines: 10 Message-ID: References: <199606140621.NAA00687@benpc.bionet.nsk.su> <31C56361.7EC4@ibex.ca> <31C87548.7612@bbsrc.ac.uk> <31C977BB.1AA7@ibex.ca> <4r8laj$nc0@nntp1.best.com> NNTP-Posting-Host: pc0734.ri.bbsrc.ac.uk X-Newsreader: Yet Another NewsWatcher 2.1.8 This is shaping up for a traditional my-machine-is-better-than-yours religous war. Since I think we can assume that we are (mostly) intelligent adults here, can we nip this in the bud right now, or take it off to one of the advocacy groups where it can die its prolonged and unpleasant death unnoticed by those who don't really care? Andy Law ------------------ ( Andy.Law@bbsrc.ac.uk ) ( Big Nose in Edinburgh ) From owner-software@net.bio.net Mon Jul 01 23:00:00 1996 Path: biosci!daresbury!lyra.csx.cam.ac.uk!news.ox.ac.uk!oxpath!rpgrant From: rpgrant@molbiol.ox.ac.uk (Richard P. Grant) Newsgroups: bionet.software Subject: Re: Enzyme Kinetic Software for Macs Date: 2 Jul 96 09:14:22 GMT Organization: Oxford University Molecular Biology Data Centre Lines: 21 Message-ID: <1996Jul2.091422@molbiol.ox.ac.uk> References: <31D256C1.472B@dundee.ac.uk> NNTP-Posting-Host: ania.path.ox.ac.uk Don't know if this helps, but have a look at http://www.intergalact.com/g1k/g1k.html In article <31D256C1.472B@dundee.ac.uk>, Dr Douglas J Clarke writes: > I am looking for a good enzyme kinetic software package for the > calculation of Kms, Vmax, Kis etc suitable for a 030, 040 based Mac. > > I don't mind paying up to г100 providing the program is good. > > Does anyone out there no of such a program. > > Thank you in advance for your help. > > Dougie Clarke -- Richard P. Grant MA DPhil rpgrant@molbiol.ox.ac.uk Nuffield Department of Obstetrics and Gynaecology, University of Oxford. http://users.ox.ac.uk/~lady0266 "I'm not repressed anymore" From owner-software@net.bio.net Mon Jul 01 23:00:00 1996 Path: biosci!bcm.tmc.edu!cs.utexas.edu!swrinde!hookup!news.nstn.ca!newsflash.concordia.ca!news.mcgill.ca!cassis.Biol.McGill.CA!JCHO From: JCHO@bio1.lan.mcgill.ca (John Cho) Newsgroups: bionet.software Subject: promoter analysis software Date: Tue, 2 Jul 1996 16:37:21 Organization: McGill University Lines: 8 Message-ID: NNTP-Posting-Host: cassis.biol.mcgill.ca X-Newsreader: Trumpet for Windows [Version 1.0 Rev A] hi. does anyone know of a program that analyses promoter sequences? (hopefully a shareware or web program) much obliged John Cho From owner-software@net.bio.net Mon Jul 01 23:00:00 1996 Path: biosci!rutgers!uwm.edu!newsfeed.internetmci.com!news.ycc.yale.edu!coolcat.med.yale.edu!stenor From: Scott Panzer Newsgroups: bionet.cellbiol,bionet.software,bionet.general,bionet.cellbiol.cytonet,yale.bio.announce Subject: Cytoskeletal Protein Interactions Database Date: 2 Jul 1996 16:41:30 GMT Organization: Yale University School of Medicine Lines: 25 Distribution: world Message-ID: <4rbjfq$bun@news.ycc.yale.edu> NNTP-Posting-Host: coolcat.med.yale.edu Mime-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit X-Newsreader: Nuntius 2.0.4_PPC X-XXMessage-ID: X-XXDate: Tue, 2 Jul 1996 16:50:22 GMT Xref: biosci bionet.cellbiol:5031 bionet.software:15961 bionet.general:22604 bionet.cellbiol.cytonet:590 My apologies if you've received more than 1 copy of this post in the past couple of days. "CySPID", and experimental database of cytoskeletal proteins and their interactions and relationships is available for public browsing at: This database is undergoing development and revision, and is being made available as a resource to the cytoskeletal community as well as to solicit feedback so we can improve it. If you're are interested in the cytoskeleton, please have a look. Scott Panzer Yale University ---------------------------------------------------------------- Scott Panzer | Department of Genetics, SHM I-310 stenor@pcnet.com | 333 Cedar Street panzer@seviche.med.yale.edu | New Haven, CT 06510 ---------------------------------------------------------------- Phone: 203-785-2675 Fax: 203-785-6333 Alt Fax: 203-785-7227 WWW URL: http://www.pcnet.com/~stenor/ ---------------------------------------------------------------- From owner-software@net.bio.net Mon Jul 01 23:00:00 1996 Path: biosci!CS.Arizona.EDU!news.Arizona.EDU!hamblin.math.byu.edu!acs2.byu.edu!news.cuny.edu!caen!uwm.edu!cs.utexas.edu!howland.reston.ans.net!ixnews1.ix.netcom.com!ix.netcom.com!ix.netcom.com!news From: wmstudio@ix.netcom.com(William Howse ) Newsgroups: bionet.software Subject: What program to open Mac files in Windows PC? Date: 2 Jul 1996 00:56:19 GMT Organization: Netcom Lines: 13 Message-ID: <4r9s3j$k5k@sjx-ixn4.ix.netcom.com> NNTP-Posting-Host: stl-mo6-17.ix.netcom.com X-NETCOM-Date: Mon Jul 01 5:56:19 PM PDT 1996 Is there a program out that will let me open Mac files with my Windows PC? I know that Mac has programs out to open Windows files in Mac computers, like "PC Exchange" and so forth. And if so is there any places on the Net to download these Programs? Thanks for any help, William wmstudio@ix.netcom.com From owner-software@net.bio.net Mon Jul 01 23:00:00 1996 Path: biosci!bcm.tmc.edu!cs.utexas.edu!swrinde!newsfeed.internetmci.com!tank.news.pipex.net!pipex!oleane!jussieu.fr!rain.fr!news.sprintlink.net!news-dc-9.sprintlink.net!news.2sprint.net!news.iadfw.net!usenet From: aimania@airmail.net (Walter Rothe) Newsgroups: bionet.software Subject: Re: A GOOD NEWSREADER Date: Tue, 02 Jul 1996 20:43:46 GMT Organization: customer of Internet America Lines: 21 Message-ID: <31d989e3.6182349@news.airmail.net> References: <4r3pjt$dmu@news.xs4all.nl> NNTP-Posting-Host: dal23-02.ppp.iadfw.net X-Newsreader: Forte Agent .99e/32.227 an@christ.pope (pizzaman) wrote: >SEARCHING FOR A GOOD NEWSREADER > >It seems that FREEAGENT (sharewareversion) has a build in >filter that filters out the nonsense messages. >Ofcourse I want to determine myself what's nonsensical > > Who knows more about the Free Agent filtering let the WEB know. > >Thanx, >PIZZAMAN > I have their latest shareware version and you are correct in that it allows you to set up select and/or kill expressions. They apply to stuff in the header, not the body, but within that limitation, it allows you to setup about any expression. Forte has their own newsgroup where comments about this should be directed. It is: alt.usenet.offline-reader.forte-agent. Walter Rothe aimania@airmail.net From owner-software@net.bio.net Mon Jul 01 23:00:00 1996 Path: biosci!rutgers!uwm.edu!vixen.cso.uiuc.edu!usenet From: Andrew Dalke Newsgroups: bionet.software Subject: [Announce] NAMD 1.4 released Date: Tue, 02 Jul 1996 15:50:21 -0500 Organization: University of Illinois at Urbana Lines: 75 Message-ID: <31D98B8D.446B@ks.uiuc.edu> NNTP-Posting-Host: juneau.ks.uiuc.edu Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 2.0 (X11; I; IRIX 5.3 IP17) Announcing version 1.4 release of NAMD --------------------------------------- The Theoretical Biophysics group at the University of Illinois and the Beckman Institute would like to announce the availability version 1.4 of the program NAMD, a high-performance molecular mechanics program for simulating large biomolecular systems on parallel and distributed computers. This software is being made available to the molecular modeling community free of charge, and includes commented source code, documentation for users and programmers, and precompiled binaries for HP and SGI workstations. New in this version are various splittings for multiple timestepping, cleaning up of the source and documentation, and various bug fixes. =============== Basic information about NAMD ====================== Obtaining NAMD -------------- A more complete description of NAMD is available on the NAMD WWW home page: http://www.ks.uiuc.edu/Research/namd/ The software itself is available via anonymous ftp in the directory: ftp://ftp.ks.uiuc.edu/pub/mdscope/namd/ (please see the README file in this directory for the latest version info) Email questions to namd@ks.uiuc.edu. Features -------- Efficient full electrostatics: NAMD incorporates the Distributed Parallel Multiple Tree Algorithm (DPMTA) developed by the Scientific Computing Group at Duke University to provide full electrostatic interactions in O(N) time. To further reduce the computational cost, DPMTA is integrated using a multiple timestep integration scheme which computes full electrostatic interactions only periodically during the simulation. Scalable parallelism: To simulate large systems using many processors. Efficient parallel design uses a spatial decomposition scheme coupled with multithreaded, message-driven execution to achieve load balance and overlap of communication with computation. Modifiable: A major design goal of NAMD is to allow researchers to implement new algorithms and techniques easily. To achieve this, the design and implementation of NAMD is fully documented in a Programmer's Guide. To achieve the highest degree of modularity and data abstraction, an object-oriented design is used and NAMD is implemented in C++. Portable: NAMD can run on different parallel machines and message-passing systems. The first two implementations of NAMD use PVM (Parallel Virtual Machine) from Oak Ridge National Laboratories and Charm++ , a message-driven coordination language developed at UIUC. Compatibility with X-PLOR: The input and output files used by NAMD are identical to those used by the program X-PLOR. Thus, simulations can easily be migrated between the packages and the output of NAMD can be analyzed using X-PLOR or any other tool built for these file formats. Standard MD features: Implementation of standard molecular dynamics features such as energy minimization, velocity rescaling, spherical harmonic boundary conditions, harmonic atom restraints, and Langevin dynamics. namd@ks.uiuc.edu July 2, 1996 From owner-software@net.bio.net Tue Jul 02 23:00:00 1996 Message-ID: <31DA7365.41C6@uni-konstanz.de> Date: Wed, 03 Jul 1996 15:19:33 +0200 From: Kay Diederichs Organization: Fakultaet fuer Biologie, Universitaet Konstanz X-Mailer: Mozilla 2.02 (X11; I; IRIX 5.3 IP22) MIME-Version: 1.0 Newsgroups: bionet.software Subject: Re: What program to open Mac files in Windows PC? References: <4r9s3j$k5k@sjx-ixn4.ix.netcom.com> <4rag7q$es8@lyra.csx.cam.ac.uk> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit NNTP-Posting-Host: loop2.biologie.uni-konstanz.de Lines: 8 Path: biosci!rutgers!uwm.edu!cs.utexas.edu!swrinde!tank.news.pipex.net!pipex!oleane!in2p3.fr!swidir.switch.ch!scsing.switch.ch!news.belwue.de!news.uni-konstanz.de! There is also a shareware program called MACSEE (30 days free use for version 2.2 that I used). Locate with Archie! -- Kay Diederichs email: Kay.Diederichs@uni-konstanz.de Tel: +49 7531 88 4049 Fax: 3183 Fakultaet fuer Biologie, Universitaet Konstanz Postfach 5560 (M656), D-78434 Konstanz, Germany From owner-software@net.bio.net Tue Jul 02 23:00:00 1996 Path: biosci!rutgers!uwm.edu!news-res.gsl.net!news.gsl.net!EU.net!Norway.EU.net!nntp.uio.no!nntp-oslo.UNINETT.no!nntp-trd.UNINETT.no!daresbury!lyra.csx.cam.ac.uk!mole.bio.cam.ac.uk!brenner From: brenner@mole.bio.cam.ac.uk (Steven Brenner) Newsgroups: bionet.software Subject: Re: ? tool to remove redundancy from sequence set Date: 3 Jul 1996 13:16:51 GMT Organization: University of Cambridge, England Lines: 29 Message-ID: <4rdrs3$ga@lyra.csx.cam.ac.uk> References: <31D91FA9.2F76@is.dal.ca> NNTP-Posting-Host: mole.bio.cam.ac.uk X-Newsreader: NN version 6.5.0 #3 (NOV) Arlin Stoltzfus writes: >Does anyone know of a tool for pruning a set sequences for >redundancy? Something that, given a set of sequences (say, >in a FASTA archive) and a user-defined value of X, would >return a subset of sequences such that no two sequences >were more than X% identical. There are two subtle issues which are involved here: * There are many, many ways of producing such a set. You could try to produce the largest such set, the smallest such set, the best (depending upon some quality measure) set. Which one you want depends upon your ultimate use of the data. * If the percent identity not very large (e.g., maybe 50%), identity is a very poor measure of propinquity. You'd do far better using either smith-waterman score or (better yet) a statistical measure. I have code which could be for producing some such sets. Steve Brenner -- Steven E. Brenner | S.E.Brenner@bioc.cam.ac.uk MRC Laboratory of Molecular Biology | Hills Road | Office: +44 1223 248011 Cambridge CB2 2QH, UK | Fax: +44 1223 213556 From owner-software@net.bio.net Tue Jul 02 23:00:00 1996 Path: biosci!agate!spool.mu.edu!newshub.tc.umn.edu!fu-berlin.de!news.belwue.de!News.Uni-Marburg.DE!news.th-darmstadt.de!uni-erlangen.de!lrz-muenchen.de!news From: Klaus Salger Newsgroups: bionet.software Subject: Re: promoter analysis software Date: Wed, 03 Jul 1996 01:43:08 +0200 Organization: Zoologisches Institut der Uni Muenchen Lines: 33 Distribution: world Message-ID: <31D9B40C.15FB@zi.biologie.uni-muenchen.de> References: NNTP-Posting-Host: wap4.zi.biologie.uni-muenchen.de Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 2.0 (X11; I; AIX 2) John Cho wrote: > > hi. > > does anyone know of a program that analyses promoter sequences? (hopefully a > shareware or web program) > > much obliged > > John Cho John, you could try the following web sites: http://www.genome.ad.jp/SIT/TFSEARCH.html http://transfac.gbf-braunschweig.de/TRANSFAC/browse/index.html http://ch.nus.sg/gcg/sigscan/signal.html http://ch.nus.sg/bio/proscan/proscan.html http://dot.imgen.bcm.tmc.edu:9331/gene-finder/gf.html Cheers Klaus -- Klaus Salger phone : +49 (0)89 5902 -502 Zoologisches Institut FAX : -450 AG MacWilliams e-mail: salger@zi.biologie.uni-muenchen.de Luisenstr. 14 80333 Muenchen Germany BioLinks: http://www.zi.biologie.uni-muenchen.de/~salger/salger.html From owner-software@net.bio.net Tue Jul 02 23:00:00 1996 Path: biosci!daresbury!nntp-trd.UNINETT.no!online.no!Norway.EU.net!EU.net!usenet2.news.uk.psi.net!uknet!usenet1.news.uk.psi.net!uknet!uknet!lyra.csx.cam.ac.uk!news.ox.ac.uk!news From: Geoff Barton Newsgroups: bionet.software Subject: Re: ? tool to remove redundancy from sequence set Date: Wed, 03 Jul 1996 16:07:39 +0100 Organization: Laboratory of Molecular Biophysics Lines: 43 Message-ID: <31DA8CBB.167E@bioch.ox.ac.uk> References: <31D91FA9.2F76@is.dal.ca> <4rdrs3$ga@lyra.csx.cam.ac.uk> NNTP-Posting-Host: weevil.biop.ox.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 2.0 (X11; I; IRIX 5.3 IP22) To: Steven Brenner Steven Brenner wrote: > > Arlin Stoltzfus writes: > >Does anyone know of a tool for pruning a set sequences for > >redundancy? Something that, given a set of sequences (say, > >in a FASTA archive) and a user-defined value of X, would > >return a subset of sequences such that no two sequences > >were more than X% identical. > > There are two subtle issues which are involved here: > > * There are many, many ways of producing such a set. You could try to > produce the largest such set, the smallest such set, the best > (depending upon some quality measure) set. Which one you want depends > upon your ultimate use of the data. > > * If the percent identity not very large (e.g., maybe 50%), identity > is a very poor measure of propinquity. You'd do far better using > either smith-waterman score or (better yet) a statistical measure. > As Steve points out, this is not a straightforward problem to solve. In addition to the complications that Steve mentions, you need to worry about the lengths of your proteins. Two sequences may share a common domain or module, but otherwise be different. If you use a simple cutoff, you will be throwing away non-redundant information. A solution to this is to require pairs to have N% of residues in common as well as being X% similar. However, if you do this, you will still have some redundancy in the final set. If you need a non-redundant set for statistical analysis, then you could mask out the common part from one of each pair. If you need non-redundancy to speed a database search, then redundancy of this type would probably not be a problem. Geoff. -- Geoffrey J. Barton, Laboratory of Molecular Biophysics, University of Oxford, Rex Richards Building, South Parks Road, Oxford OX1 3QU, U.K. mailto:gjb@bioch.ox.ac.uk, Tel: +44 1865 275368, Fax: +44 1865 510454, ftp://geoff.biop.ox.ac.uk, http://geoff.biop.ox.ac.uk From owner-software@net.bio.net Tue Jul 02 23:00:00 1996 Path: biosci!bcm.tmc.edu!pendragon!news.msfc.nasa.gov!newsfeed.internetmci.com!news.ac.net!news.cais.net!nntp.primenet.com!news1.best.com!nntp1.best.com!jquinn From: jquinn@nntp.best.com (Greg) Newsgroups: bionet.software Subject: Re: Which platform? Date: 3 Jul 1996 14:15:15 GMT Organization: Best Internet Communications Lines: 48 Message-ID: <4rdv9j$bb8@nntp1.best.com> References: <199606140621.NAA00687@benpc.bionet.nsk.su> <31C56361.7EC4@ibex.ca> <31C87548.7612@bbsrc.ac.uk> <31C977BB.1AA7@ibex.ca> <4r8laj$nc0@nntp1.best.com> NNTP-Posting-Host: shellx.best.com X-Newsreader: TIN [version 1.2 PL2] Jim Naylor (jnaylor@southwind.net) wrote: : In article <4r8laj$nc0@nntp1.best.com>, jquinn@nntp.best.com (Greg) wrote: : > Maybe Canada has real price breaks on Macs, but I doubt it. The big : > drawback with the mac is currently the operating system, which simply : > doesn't hold a candle to Win95, letalone NT. Not only is the Mac OS : > incapable of true pre-emptive multitasking, but it's handling of virtual : > memory is terrible (ie. non-existant). If this wasn't bad enough, unless : > extremely well set with tons of memory (eg. 32+), they can frequently : > crash. There are extremely good reasons for buying a Mac, principally for : > its interface, which a lot of people have grown up with (leastways here in : > the US). Also, computer illiterates find them easier to deal with. No one : > with any experience in this area would suggest that they are cost : > effective in terms of computing power or hardware costs. That is simply : > not the case. : I have rarely seen such absolutely ignorant comments! Each and every : disadvantage you impute to the Mac is true of Windoze95 instead, with the : sole exception of pre-emptive multitasking, which most users wouldn't MacOS does not handle virtual memory, without the use of a third party product (RAM DOUBLER), and even with this product installed, 'out of memory' errors can frequently present themselves when using system intensive progs. : recognize if it bit them, which it usually does on the MacOS copy, : Windoze95. If your definition of a computer illiterate is someone who : wants to get real work done without the machine getting in his face, then : sign me up! But I was developing utilities and embedded system software : for the original DOS version in 1982 in a proprietary coprocessor-based : LAN file server. When Mac II was born, I quickly decided life is too short : to mess with MS. As for cost effectiveness, why do you suppose Lockheed : Martin Astronautics just purchased three thousand Power Computing Mac : clones? Since Apple are going belly-up, you can look forward to seeing more headline-grabbing amazing breaks from them. This was a high-profile contract which they desperately needed. These three thousand power Macs they have just ordered should make excellent dumb terminals into their mini computers. : And you might as well forget plug and play on Windoze-- Eh? Plug and Play works just great on '95. : you get more for your money in every way these days. From owner-software@net.bio.net Tue Jul 02 23:00:00 1996 Path: biosci!bcm.tmc.edu!pendragon!news.msfc.nasa.gov!newsfeed.internetmci.com!news.ac.net!news.cais.net!nntp.primenet.com!news1.best.com!nntp1.best.com!jquinn From: jquinn@nntp.best.com (Greg) Newsgroups: bionet.software Subject: Re: Which platform? Date: 3 Jul 1996 14:17:57 GMT Organization: Best Internet Communications Lines: 15 Message-ID: <4rdvel$bb8@nntp1.best.com> References: <199606140621.NAA00687@benpc.bionet.nsk.su> <4r8laj$nc0@nntp1.best.com> <4rb7pi$g6l@nntp3.u.washington.edu> NNTP-Posting-Host: shellx.best.com X-Newsreader: TIN [version 1.2 PL2] Joe Felsenstein (joe@evolution.genetics.washington.edu) wrote: : In article , : Andy Law wrote: : >This is shaping up for a traditional my-machine-is-better-than-yours : >religous war. Since I think we can assume that we are (mostly) intelligent : >adults here, can we nip this in the bud right now, or take it off to one : >of the advocacy groups where it can die its prolonged and unpleasant death : >unnoticed by those who don't really care? : You don't understand. These folks are convinced that if they can just make one : more comment, the other side will give in, grovel, change over from : advocating operating system X to agreeing that those who advocated operating : system Y were right all along. It's a form of addiction. Joe has hit the nail on the head. From owner-software@net.bio.net Tue Jul 02 23:00:00 1996 Path: biosci!rutgers!uwm.edu!newsspool.doit.wisc.edu!news.doit.wisc.edu!ebv.oncology.wisc.edu!aiyar From: aiyar@ebv.oncology.wisc.edu (Ashok Aiyar) Newsgroups: bionet.software Subject: Re: Which platform? Date: 3 Jul 1996 15:53:21 GMT Organization: Sugden Lab, McArdle Laboratory for Cancer Research, UW-Madison Lines: 25 Message-ID: References: <199606140621.NAA00687@benpc.bionet.nsk.su> <31C56361.7EC4@ibex.ca> <31C87548.7612@bbsrc.ac.uk> <31C977BB.1AA7@ibex.ca> <4r8laj$nc0@nntp1.best.com> <4rdv9j$bb8@nntp1.best.com> Reply-To: aiyar@ebv.oncology.wisc.edu NNTP-Posting-Host: ebv.oncology.wisc.edu X-Newsreader: slrn (0.8.8.2 (Sat May 25 08:04:18 CDT 1996) UNIX) On 3 Jul 1996 14:15:15 GMT, Greg wrote: >MacOS does not handle virtual memory, Surely this is something you *believe* and not something you *know*. I *know* that every version of MacOS that I have used from 7.1 up has supported virtual memory, without adding any external products. >without the use of a third party product (RAM DOUBLER), And .... RamDoubler does not create or use virtual memory in the usual sense of the term. I don't particularly care for any of Apple's or Microsoft's operating systems; this thread however is not served by any of us relaying incorrect information. Ashok -- Ashok Aiyar, Ph.D. aiyar@ebv.oncology.wisc.edu Department of Oncology University of Wisconsin-Madison "If people are good only because they fear punishment, and hope for reward, then we are a sorry lot indeed." -- Albert Einstein From owner-software@net.bio.net Tue Jul 02 23:00:00 1996 Path: biosci!rutgers!netnews.upenn.edu!taurus.fccc.edu!rr_hardy From: rr_hardy@fccc.edu (Richard R. Hardy) Newsgroups: bionet.software Subject: Re: Which platform? Date: Wed, 03 Jul 1996 11:51:45 -0400 Organization: I.C.R., Fox Chase Cancer Center Lines: 17 Message-ID: References: <199606140621.NAA00687@benpc.bionet.nsk.su> <31C56361.7EC4@ibex.ca> <31C87548.7612@bbsrc.ac.uk> <31C977BB.1AA7@ibex.ca> <4r8laj$nc0@nntp1.best.com> <4rdv9j$bb8@nntp1.best.com> NNTP-Posting-Host: mighty.facs.fccc.edu Mime-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit X-Newsreader: Yet Another NewsWatcher 2.2.0b13 In article <4rdv9j$bb8@nntp1.best.com>, jquinn@nntp.best.com (Greg) wrote: >Since Apple are going belly-up, you can look forward to seeing more >headline-grabbing amazing breaks from them. This was a high-profile >contract which they desperately needed. These three thousand power Macs >they have just ordered should make excellent dumb terminals into their >mini computers. Please! I sincerely doubt that anyone is listening to this thread, just shouting their prejudices. As has been mentioned, it's hard to discuss religion (OS preference) in a rational fashion. Can we all return to our work (whether on Wintels or Macs) now? ___________________________________________________________ Richard R. Hardy Member, Inst. for Cancer Research Fox Chase Cancer Center Tel: (215) 728-2463 7701 Burholme Ave. FAX: (215) 728-2412 Philadelphia, PA 19111 E-MAIL: RR_HARDY@fccc.edu From owner-software@net.bio.net Tue Jul 02 23:00:00 1996 Path: biosci!bcm.tmc.edu!pendragon!news.msfc.nasa.gov!newsfeed.internetmci.com!news2.cais.net!news.cais.net!nntp.primenet.com!news1.best.com!nntp1.best.com!jquinn From: jquinn@nntp.best.com (Greg) Newsgroups: bionet.software Subject: Re: promoter analysis software Date: 3 Jul 1996 15:58:15 GMT Organization: Best Internet Communications Lines: 11 Message-ID: <4re5an$d2s@nntp1.best.com> References: NNTP-Posting-Host: shellx.best.com X-Newsreader: TIN [version 1.2 PL2] John Cho (JCHO@bio1.lan.mcgill.ca) wrote: : hi. : does anyone know of a program that analyses promoter sequences? (hopefully a : shareware or web program) I believe that a program called Grail and X-Grail can do this, but it's been some time since I last used them, so I can't stake my life on that. Both of these are UNIX progs. Sorry, can't remember the location (I think that it's a '.gov' site), but a lycos or Altavista web search should locate them. From owner-software@net.bio.net Tue Jul 02 23:00:00 1996 Path: biosci!bcm.tmc.edu!pendragon!news.msfc.nasa.gov!elroy.jpl.nasa.gov!usc!usc!not-for-mail From: pcorley@hsc.usc.edu (Pamela M. Corley) Newsgroups: bionet.software Subject: Restriction map Date: 3 Jul 1996 13:17:02 -0700 Organization: University of Southern California, Los Angeles, CA Lines: 30 Sender: pcorley@hsc.usc.edu Message-ID: <4rekfu$fgv@hsc.usc.edu> NNTP-Posting-Host: hsc.usc.edu Keywords: restriction enzymes enzyme map maps endonuclease A student would like to locate restriction map software that he could use via the WWW or Internet. He brought a map that had been generated for him through IG and would like a WWW site with software that would display the map in a similar format. (He stated that he did not like the format that is available through GCG). The map through IG looked like the following segment: RsaI NlaIII Csp6I Bs1I Bs1I BsiYI BsiYI AfaI ||| ....tacgggaactgctaca.... ...TYR... He said he wanted to find *free* software that would answer the question "Can I use any restriction enzymes on the sequence?" Thanks for your assistance. Please email me directly. Pamela M. Corley, Information Specialist Internet: pcorley@hsc.usc.edu USC Norris Medical Library (213) 342-1483 2003 Zonal Avenue (213) 221-1235 (fax) Los Angeles, CA 90033-4582 From owner-software@net.bio.net Tue Jul 02 23:00:00 1996 Path: biosci!rutgers!uwm.edu!spool.mu.edu!sgigate.sgi.com!news1.best.com!nntp1.best.com!jquinn From: jquinn@nntp.best.com (Greg) Newsgroups: bionet.software Subject: Re: Which platform? Date: 3 Jul 1996 19:16:20 GMT Organization: Best Internet Communications Lines: 26 Message-ID: <4regu4$hft@nntp1.best.com> References: <199606140621.NAA00687@benpc.bionet.nsk.su> <31C56361.7EC4@ibex.ca> <31C87548.7612@bbsrc.ac.uk> <31C977BB.1AA7@ibex.ca> <4r8laj$nc0@nntp1.best.com> <4rdv9j$bb8@nntp1.best.com> NNTP-Posting-Host: shellx.best.com X-Newsreader: TIN [version 1.2 PL2] Ashok Aiyar (aiyar@ebv.oncology.wisc.edu) wrote: : On 3 Jul 1996 14:15:15 GMT, Greg wrote: : >MacOS does not handle virtual memory, : Surely this is something you *believe* and not something you *know*. : I *know* that every version of MacOS that I have used from 7.1 up : has supported virtual memory, without adding any external products. : >without the use of a third party product (RAM DOUBLER), : And .... RamDoubler does not create or use virtual memory in the : usual sense of the term. : I don't particularly care for any of Apple's or Microsoft's operating : systems; this thread however is not served by any of us relaying : incorrect information. Quite right, too. Clearly an error on my part based on my lack of Mac OS familiarity. Duly retracted and hopefully an end to this thread. A timely reminder to me that it's not a good idea to write about matters that I am not 100% familiar with, since it's both misleading and unhelpful. Point taken. I stick by my general thrust of argument however that the Mac does not handle virtal memory as well as '95 and that the Mac OS is less stable using a range of different softwares. From owner-software@net.bio.net Wed Jul 03 23:00:00 1996 Path: biosci!daresbury!nntp-trd.UNINETT.no!oslonett.no!sn.no!Norway.EU.net!EU.net!howland.reston.ans.net!newsfeed.internetmci.com!netnews.nwnet.net!news.u.washington.edu!roach From: roach@u.washington.edu (Jared Roach) Newsgroups: bionet.software Subject: Re: A self contained C++ (or c) sequence alignement function Date: 4 Jul 1996 08:19:08 GMT Organization: University of Washington, Seattle Lines: 175 Message-ID: <4rfups$5np@nntp3.u.washington.edu> References: <4qn4te$59b@sjx-ixn5.ix.netcom.com> NNTP-Posting-Host: saul2.u.washington.edu NNTP-Posting-User: roach This isn't quite what was wanted, but it comes *very* close and should be easily hackable. I apologize for its slovenly adherence to basic programming elegance, but hey (!) it works. It is C code for the Macintosh, and furthermore it is written as an XFCN for HyperCard; I've included the whole code, but the dynamic alignmetn bit is easy to pick out. Now, this code does *not* save the alignment - it just saves the score and the endpoint on each sequence. If you want the alignment, it costs RAM, but it shouldn't be too difficult to hack this code to get it. I just might do it myself. // DynaCLip XFCN by Jared Roach й June 1996 // This program does dynamic local alignment of two sequences and saves the endpoint of the alignment // The intention is to use this for endclipping vector from the 5' end of sequence reads // The core C code was hacked from code by David Gordon to whom I owe a great debt // Max Robinson was instrumental in explaining basic (yeah right) C syntax to me // The XFCN shell was downloaded form the Web and is й 1992 Mark Hanrek //*********************************************************** **************************** // Hanrek XCMD Shell 1.2 // // й1992 Mark Hanrek & The Information Workshop. All Rights Reserved. // // Note: Do all your programming between the bold black lines below. // Put additional functions you create into the "Support Functions" // section below that. Put function prototypes into ExampleXFCN.h. // /************************************************************ ******* Includes ********/ #include #include #include #include "StandardFunctions.h" /************************************************************ ******* Main Entry ******/ pascal void main( XCmdPtr paramPtr ) // No need to ever change any of this... { RememberA0(); SetUpA4(); InitializeReturnInfo( paramPtr ); ExternalHandler( paramPtr ); RestoreA4(); } //еееееееееееееееееееееееееееееееееееееееееееееееееееееееееее еееееееееееееееееееееееее // // DynaClipXFCN HyperTalk Syntax: // // put 5 into gappenalty // put 2 into matchscore // put 1 into mismatchpenalty // // // put cd fld "Vector" into vector // put cd fld "Left-Clipped-Sequence" into seq // put the number of chars of vector into vectorlength // put the number of chars of seq into seqlength // if max (vectorlength,seqlength)>1499 then abort script // // put DynaClipXFCN( seqlength, vectorlength, seq, vector, gappenalty, matchscore, mismatchpenalty ) into cd fld "output" // // #include "DynaClipXFCN.h" #define MAX( arg1, arg2 ) (( (arg1) > (arg2) ) ? (arg1) : (arg2)) void ExternalHandler( XCmdPtr paramPtr ) { short nGap; short nMatch; short nMismatch; short i; short nBestScore = 0; short nBestDown = 0; short nBestAcross = 0; short nScoreDiagonallyAbove; short nToBeScoreDiagonallyAbove; short nScoreByDiagonal; short nAcross; short nDown; char pSeqDown[1500]; char pSeqAcross[1500]; short nSeqDownLength; short nSeqAcrossLength; short pnBestDown; short pnBestAcross; short pnBestScore; short nScore[1500]; for (i=0; i < 1500; ++i) nScore[i] = 0; ParamToShort( 0, &nSeqDownLength ); // the first parameter is "nSeqDownLength" ParamToShort( 1, &nSeqAcrossLength ); // the second parameter is "nSeqAcrossLength" ParamToCString( 2, pSeqDown ); // the third parameter is the "pSeqDown" string ParamToCString( 3, pSeqAcross ); // the third parameter is the "pSeqAcross" string ParamToShort( 4, &nGap ); ParamToShort( 5, &nMatch ); ParamToShort( 6, &nMismatch ); for( nDown = 1; nDown <= nSeqDownLength; ++nDown ) { nToBeScoreDiagonallyAbove = nScore[0]; /* case of first column */ nScore[0] = nScore[0] - nGap; /* now handle case of other columns */ for( nAcross = 1; nAcross <= nSeqAcrossLength; ++nAcross ) { nScoreDiagonallyAbove = nToBeScoreDiagonallyAbove; nToBeScoreDiagonallyAbove = nScore[nAcross]; if ( pSeqAcross[nAcross-1] == pSeqDown[nDown-1] ) nScoreByDiagonal = nScoreDiagonallyAbove + nMatch; else nScoreByDiagonal = nScoreDiagonallyAbove - nMismatch; nScore[nAcross] = MAX( 0 , MAX( nScore[nAcross] - nGap, MAX( nScore[nAcross - 1] - nGap, nScoreByDiagonal))); if (nScore[nAcross] > nBestScore ) { nBestScore = nScore[nAcross]; nBestAcross = nAcross; nBestDown = nDown; } } } AppendReturnInfo( kResult, "|i nBestScore \r", nBestScore ); AppendReturnInfo( kResult, "|i nBestAcross \r", nBestAcross ); AppendReturnInfo( kResult, "|i nBestDown \r", nBestDown ); } From owner-software@net.bio.net Wed Jul 03 23:00:00 1996 Path: biosci!rutgers!uwm.edu!cs.utexas.edu!howland.reston.ans.net!EU.net!Norway.EU.net!nntp.uio.no!news.cais.net!news.structured.net!empnet.com!cjoyce.dublclick.com!user From: FredS@broadcastsoft.com (sales) Newsgroups: bionet.software Subject: Newton Software Date: Wed, 03 Jul 1996 16:18:58 -0700 Organization: BroadCast Software Corp. Lines: 11 Message-ID: NNTP-Posting-Host: cjoyce.dublclick.com Try this great Newton product: Equate is a powerful spreadsheet that provides many of the features of a desktop spreadsheet in a package small enough to run on the Newton. It offers notepad-like data entry, spreadsheets of any size and import/export to Excel using the optional "Equate Connect" software. To find out more about this great product. http://www.unboxed.com http://www.1stopsoft.com. From owner-software@net.bio.net Wed Jul 03 23:00:00 1996 Path: biosci!rutgers!uwm.edu!vixen.cso.uiuc.edu!newsfeed.internetmci.com!in2.uu.net!ott.istar!istar.net!news.nstn.ca!news.dal.ca!news From: Arlin Stoltzfus Newsgroups: bionet.software Subject: Re: ? tool to remove redundancy from sequence set Date: Wed, 03 Jul 1996 21:13:37 -0300 Organization: Dalhousie University Lines: 36 Message-ID: <31DB0CB1.2AF2@is.dal.ca> References: <31D91FA9.2F76@is.dal.ca> <4rdrs3$ga@lyra.csx.cam.ac.uk> <31DA8CBB.167E@bioch.ox.ac.uk> NNTP-Posting-Host: thidwick.biochem.dal.ca Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 2.0 (X11; I; SunOS 5.4 sun4m) Geoff Barton wrote: > Steven Brenner wrote: > > There are two subtle issues which are involved here: ... > As Steve points out, this is not a straightforward problem to solve. [subtle and complicated issues deleted] These considerations are valid, in principle, but don't apply to my problem. I'm just looking at 1000's of splice junction sequences with the intention of analyzing informational signals, and I don't want the results to be biased by large sets of nearly identical sequences (e.g., human antibody genes). All of the sequence fragments are the exactly the same length, there are no gaps, and a simple measurement of nucleotide identity is sufficient to quantify the relationship between any two sequences (unless I want to take into account base composition). One possible solution is the CLEANUP program (brought to my attention by Sabino Liuni, one of the developers): Grillo, et al. 1996, CABIOS 12(1):1, CLEANUP: a fast computer program for removing redundancies from nucleotide sequence databases. which is dependent on GCG and NCBI libraries (I don't have the GCG libraries, yet, but I'm working on it). Arlin -- Arlin Stoltzfus Department of Biochemistry Dalhousie University Halifax, Nova Scotia B3H 4H7 CANADA (email) arlin@is.dal.ca (phone) 902-494-3569 (fax) 902-494-1355 From owner-software@net.bio.net Wed Jul 03 23:00:00 1996 Path: biosci!CS.Arizona.EDU!news.Arizona.EDU!hamblin.math.byu.edu!acs2.byu.edu!news.cuny.edu!caen!newsxfer2.itd.umich.edu!tank.news.pipex.net!pipex!usenet2.news.uk.psi.net!uknet!usenet1.news.uk.psi.net!uknet!uknet!lyra.csx.cam.ac.uk!mole.bio.cam.ac.uk!tjrc1 From: tjrc1@mole.bio.cam.ac.uk (Tim Cutts (Zoology)) Newsgroups: bionet.software Subject: Re: Ques: how to print postscript files? (Win3.1 based) Date: 4 Jul 1996 15:59:31 GMT Organization: University of Cambridge Lines: 18 Message-ID: <4rgpp3$5br@lyra.csx.cam.ac.uk> References: <4rgob3$f78@news.orst.edu> NNTP-Posting-Host: mole.bio.cam.ac.uk In article <4rgob3$f78@news.orst.edu>, Don Chen wrote: >I would like to print out partial trees from the Ribosomal Database >Project. The options are postscript, newkirk and text. The text >files are funky and I would like a "pretty" tree. We have a >Windows-based system with a HP Inkjet printer. Is there a way to >print postscript files with this set up? And what are Newkirk files? You can print PostScript files on any graphics-capable printer using the free interpreter GhostScript. You should be able to find this on most large ftp sites. It has a friendlier front-end called GhostView. Be warned that it doesn't necessarily do a good job, particularly with text at large point sizes, although if you have something like Adobe Type Manager you can make GhostScript use the real Adobe fonts from that, which removes the problem. For your purposes it shouldn't matter at all. Tim. From owner-software@net.bio.net Wed Jul 03 23:00:00 1996 Path: biosci!CS.Arizona.EDU!news.Arizona.EDU!hamblin.math.byu.edu!acs2.byu.edu!news.cuny.edu!caen!uwm.edu!cs.utexas.edu!howland.reston.ans.net!vixen.cso.uiuc.edu!news.uoregon.edu!newsfeed.orst.edu!news.orst.edu!news From: chend@ucs.orst.edu (Don Chen) Newsgroups: bionet.software Subject: Ques: how to print postscript files? (Win3.1 based) Date: Thu, 04 Jul 1996 15:36:19 GMT Organization: Oregon State University Lines: 12 Message-ID: <4rgob3$f78@news.orst.edu> NNTP-Posting-Host: slip22.ucs.orst.edu X-Newsreader: Forte Free Agent 1.0.82 I would like to print out partial trees from the Ribosomal Database Project. The options are postscript, newkirk and text. The text files are funky and I would like a "pretty" tree. We have a Windows-based system with a HP Inkjet printer. Is there a way to print postscript files with this set up? And what are Newkirk files? Thanks for your help. Don From owner-software@net.bio.net Wed Jul 03 23:00:00 1996 Path: biosci!bcm.tmc.edu!cs.utexas.edu!howland.reston.ans.net!EU.net!usenet2.news.uk.psi.net!uknet!usenet1.news.uk.psi.net!uknet!uknet!lyra.csx.cam.ac.uk!sunsite.doc.ic.ac.uk!warwick!news.nott.ac.uk!wpbfd.biochem.nottingham.ac.uk!user From: mbxfd@unix.ccc.nottingham.ac.uk (Fergus Doherty) Newsgroups: bionet.software Subject: Directory of Molbiol/Biochem software for the Mac? Followup-To: bionet.software Date: 4 Jul 1996 12:30:44 GMT Organization: Nottingham University, UK. Lines: 22 Distribution: world Message-ID: NNTP-Posting-Host: wpbfd.biochem.nottingham.ac.uk I have volunteered to compile a directory of biochemistry/molecular biology software available for the Mac. Commercial and PD. This is for Apple in the UK, and for an academic Mac managers group (Mac Supporters), but I aim to make it available on the WWW. This is a daunting task. Does anyone know if there is an up to date directory of this kind already available, so mabe I don't have to bother? Would you help me? I would like info on all sorts of Mac software relevant to these disciplines (sequence analysis, molecular modelling, enzyme kinetics, CAL, data aquisition etc.) If you can supply info on software *especially if you use it* and can provide some views on its usefulness (ie. a review), e-mail me at the address below. Fergus Doherty, dept. Biochemistry, University Medical School, Queen's Medical Centre, Nottingham NG7 2UH Tel: (0)115 970 9366 FAX (0)115 942 2225 Internet: Fergus.Doherty@nottingham.ac.uk From owner-software@net.bio.net Wed Jul 03 23:00:00 1996 Path: biosci!bcm.tmc.edu!cs.utexas.edu!howland.reston.ans.net!vixen.cso.uiuc.edu!usenet.ucs.indiana.edu!gnat.bio.indiana.edu!user From: tjyin@bio.indiana.edu (Tongjia Yin) Newsgroups: bionet.software Subject: Re: Restriction map Date: Thu, 04 Jul 1996 07:31:20 -0500 Organization: Indiana University Lines: 38 Message-ID: References: <4rekfu$fgv@hsc.usc.edu> NNTP-Posting-Host: gnat.bio.indiana.edu Try this one. You will get a better output format (need a browser with frame capacity). http://www.bio.indiana.edu/~tjyin/WebGene/RE.html Tongjia In article <4rekfu$fgv@hsc.usc.edu>, pcorley@hsc.usc.edu (Pamela M. Corley) wrote: > A student would like to locate restriction map software that he could use > via the WWW or Internet. He brought a map that had been generated for him > through IG and would like a WWW site with software that would display the > map in a similar format. (He stated that he did not like the format that > is available through GCG). > > The map through IG looked like the following segment: > > RsaI > NlaIII > Csp6I > Bs1I > Bs1I > BsiYI > BsiYI > AfaI > ||| > ....tacgggaactgctaca.... > ...TYR... > > He said he wanted to find *free* software that would answer the question > "Can I use any restriction enzymes on the sequence?" > > Thanks for your assistance. Please email me directly. > > Pamela M. Corley, Information Specialist Internet: pcorley@hsc.usc.edu > USC Norris Medical Library (213) 342-1483 > 2003 Zonal Avenue (213) 221-1235 (fax) > Los Angeles, CA 90033-4582 From owner-software@net.bio.net Wed Jul 03 23:00:00 1996 Path: biosci!daresbury!nntp-trd.UNINETT.no!online.no!Norway.EU.net!EU.net!main.Germany.EU.net!Frankfurt.Germany.EU.net!howland.reston.ans.net!newsfeed.internetmci.com!sgigate.sgi.com!esiee.fr!jussieu.fr!univ-lyon1.fr!in2p3.fr!swidir.switch.ch!scsing.switch.ch!news.belwue.de!fu-berlin.de!cs.tu-berlin.de!uni-erlangen.de!lrz-muenchen.de!news From: Klaus Salger Newsgroups: bionet.software Subject: Re: Restriction map Date: Thu, 04 Jul 1996 01:28:09 +0200 Organization: Zoologisches Institut der Uni Muenchen Lines: 26 Distribution: world Message-ID: <31DB0209.2781@zi.biologie.uni-muenchen.de> References: <4rekfu$fgv@hsc.usc.edu> NNTP-Posting-Host: wap4.zi.biologie.uni-muenchen.de Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 2.0 (X11; I; AIX 2) Pamela M. Corley wrote: > > A student would like to locate restriction map software that he could > use via the WWW or Internet. He could try Webcutter at http://www.ccsi.com/firstmarket/firstmarket/cutter/ or the server of Brookhaven National Laboratory at http://genome1.bio.bnl.gov/bbq.html Cheers Klaus -- Klaus Salger phone : +49 (0)89 5902 -502 Zoologisches Institut FAX : -450 AG MacWilliams e-mail: salger@zi.biologie.uni-muenchen.de Luisenstr. 14 80333 Muenchen Germany BioLinks: http://www.zi.biologie.uni-muenchen.de/~salger/salger.html From owner-software@net.bio.net Wed Jul 03 23:00:00 1996 Path: biosci!CS.Arizona.EDU!news.Arizona.EDU!hamblin.math.byu.edu!acs2.byu.edu!news.cuny.edu!caen!spool.mu.edu!uwm.edu!cs.utexas.edu!swrinde!newsfeed.internetmci.com!in2.uu.net!EU.net!usenet2.news.uk.psi.net!uknet!usenet1.news.uk.psi.net!uknet!uknet!lyra.csx.cam.ac.uk!hgmp.mrc.ac.uk!sanger.ac.uk!pmr From: pmr@sanger.ac.uk (Peter Rice) Newsgroups: bionet.software Subject: Re: Restriction map Date: 04 Jul 1996 16:31:25 GMT Organization: The Sanger Centre Lines: 20 Message-ID: References: <4rekfu$fgv@hsc.usc.edu> NNTP-Posting-Host: unst.sanger.ac.uk In-reply-to: tjyin@bio.indiana.edu's message of Thu, 04 Jul 1996 07:31:20 -0500 In article <4rekfu$fgv@hsc.usc.edu>, pcorley@hsc.usc.edu (Pamela M. Corley) wrote: > A student would like to locate restriction map software that he could use > via the WWW or Internet. He brought a map that had been generated for him > through IG and would like a WWW site with software that would display the > map in a similar format. (He stated that he did not like the format that > is available through GCG). One of the changes due in GCG 9.0 is to write the enzyme names horizontally, so your student will probably be happy with GCG's output in the near future. -- ------------------------------------------------------------------------ Peter Rice | Informatics Division, E-mail: pmr@sanger.ac.uk | The Sanger Centre, Tel: (44) 1223 494967 | Wellcome Trust Genome Campus, Fax: (44) 1223 494919 | Hinxton, Cambs, CB10 1SA, URL: http://www.sanger.ac.uk/~pmr/ | England From owner-software@net.bio.net Thu Jul 04 23:00:00 1996 Path: biosci!bcm.tmc.edu!cs.utexas.edu!chi-news.cic.net!ddsw1!news.mcs.net!van-bc!unixg.ubc.ca!xiangl From: xiangl@unixg.ubc.ca (Xiang Li) Newsgroups: bionet.software Subject: Help: Software on PC served as a sequence data centre. Date: 5 Jul 1996 18:44:54 GMT Organization: University of British Columbia, Vancouver, B.C., Canada Lines: 15 Message-ID: <4rjnr6$g1m@nntp.ucs.ubc.ca> NNTP-Posting-Host: interchg.ubc.ca X-Newsreader: TIN [version 1.2 PL2] Hello, I am looking for some softwares for PC which can be used to collect DNA and/or protein sequence data for search. Any suggestions will be appreciated. Have a nice weekend. Xiang -- Xiang Li, PhD West-East Centre for Microbial Diversity University of British Columbia BC, Canada From owner-software@net.bio.net Thu Jul 04 23:00:00 1996 Path: biosci!rutgers!uwm.edu!cs.utexas.edu!news.sprintlink.net!news-stk-200.sprintlink.net!news.sprintlink.net!news-pen-14.sprintlink.net!tank.news.pipex.net!pipex!oleane!jussieu.fr!univ-lyon1.fr!news From: Laurent Duret Newsgroups: bionet.software Subject: GenBank/EMBL format conversion Date: 5 Jul 1996 14:54:04 GMT Organization: Universite Claude Bernard - Lyon 1 Lines: 31 Message-ID: <4rjaac$e4o@tempo.univ-lyon1.fr> Reply-To: ld41429@ggr.co.uk NNTP-Posting-Host: acnuc.univ-lyon1.fr Dear colleagues, I am looking for a program that can convert an EMBL entry to the GenBank format. I don't want to convert only the sequence (I know that the "readseq" program does this) but I also want to convert annotations (sequence features, bibliography, etc...). I know that EMBL and GenBank exchange their data. So I imagine that such a program already exists, but I didn't find any such tool on the NCBI or EBI FTP servers. Could you please tell me if it is possible to get such a program ? Thank you very much for your help. ________________________________________________________________________________ Laurent Duret Phone : +41.22.706.9914 GIMB Chemin des Aulx 14 FAX : +41.22.794.6965 CH-1228 Plan-les-Ouates e-mail : ld41429@ggr.co.uk Switzerland ======================== ________________________________________________________________________________ From owner-software@net.bio.net Thu Jul 04 23:00:00 1996 Path: biosci!CS.Arizona.EDU!news.Arizona.EDU!hamblin.math.byu.edu!acs2.byu.edu!news.cuny.edu!caen!uwm.edu!cs.utexas.edu!howland.reston.ans.net!Germany.EU.net!zib-berlin.de!fu-berlin.de!news.belwue.de!news.uni-hohenheim.de!rs4704.ansc1.uni-hohenheim.de!root From: root@rs4704.ansc1.uni-hohenheim.de () Newsgroups: bionet.software Subject: Looking for NAG and VOSTORG Date: 5 Jul 1996 13:19:27 GMT Organization: CC University of Hohenheim (not responsible for contents) Lines: 8 Distribution: world Message-ID: <4rj4ov$cgu@power5.rz.uni-hohenheim.de> NNTP-Posting-Host: rs4704.ansc1.uni-hohenheim.de Does someone know who is distributing NAG and VOSTORG ? Are these programms available via ftp ? ---------------------------------------------------------------------------- Irina Griesinger Phone +49 0711-459-3008 University of Hohenheim Fax +49 0711-459-3101 Email griesing@uni-hohenheim.de From owner-software@net.bio.net Thu Jul 04 23:00:00 1996 Path: biosci!biosci!not-for-mail From: claus@iesd.auc.dk (Claus S. Jensen) Newsgroups: bionet.software,bionet.molbio.gene-linkage Subject: Linkage analysis in large pedigrees Date: 4 Jul 1996 22:52:16 -0700 Organization: CS at Aalborg University Lines: 37 Sender: daemon@net.bio.net Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net Xref: biosci bionet.software:15989 bionet.molbio.gene-linkage:1107 I hereby announce the availability of the first alpha version (0.1) of 'block', a program for performing pedigree and linkage analysis in large and complex pedigrees. The program 'block' implements a method called blocking Gibbs sampling. The method is based on the Markov chain Monte Carlo method, Gibbs sampling, but combines this stochastic method with exact local computations to get a method that can successfully handle very large and complex (e.g., inbred) pedigrees (thousands of individuals) with an arbitrary number of alleles. The method allows the user to test the presence of linkage between two genes. As this is the first public version of the program, there is bound to be errors and other kinds of problems. All these should of course be reported to me. For more information, contact me, or download the program from : ftp.iesd.auc.dk/pub/packages/block/ The program is available for the architectures : Linux ELF and a.out, Sparc Solaris and SunOS, FreeBSD, IRIX 64, and MS-DOS. There is also a hopepage associated with the program at http://www.iesd.auc.dk/~claus/block.html Greetings, Claus Skaanning Jensen -- Claus Skaanning Jensen, Ph.D.-student at Aalborg University, Denmark claus@iesd.auc.dk, http://www.iesd.auc.dk/~claus From owner-software@net.bio.net Thu Jul 04 23:00:00 1996 Path: biosci!biosci!not-for-mail From: knight@cs.ucdavis.edu (James Knight) Newsgroups: bionet.software,bionet.software.gcg Subject: ANNOUNCE: SEQIO, version 1.2 is now available Date: 4 Jul 1996 22:45:32 -0700 Organization: University of California, Davis Lines: 124 Sender: daemon@net.bio.net Distribution: world Message-ID: <4r7b0g$g35@mark.ucdavis.edu> NNTP-Posting-Host: net.bio.net Xref: biosci bionet.software:15988 bionet.software.gcg:1867 This message is to announce the release of version 1.2 of the SEQIO package. The package is freely available to anyone for commercial or non-commercial use, and can be ftp'ed from the following FTP site: ftp://ftp.cs.ucdavis.edu/pub/strings/seqio.tar.gz It is a gzip'ed, tar file (356K compressed) containing the package code and documentation files. I've also set up a web site for the package at http://wwwcsif.cs.ucdavis.edu/~knight/seqio.html Also, see the description below for more information about the package. Major changes from version 1.1: * Added the GCG, MSF and BLAST program output formats. (including the ability to convert between non-GCG and GCG forms of GenBank, PIR, EMBL, Swiss-Prot, FASTA, NBRF and IG/Stanford formats without losing any header information) * Added the ability to index database entries based on any (or all) identifiers given in the entry. Including the new NID and PID numbers. * Added the ability to handle database identifiers (with wildcards) and randomly access the specified entries. * Added a "single entry access specification" mode for regular files, so that you can extract, say, just the third entry in a file, or the entry whose identifier is "sp:104k_thepa". * Added a number of example programs to show how to use the package. * The file conversion program (fmtseq) now can do "big alignments" of BLAST output, and can do conversions between GCG and non-GCG forms of sequence entries without losing any header information. For those of you who were at ISMB'96 and to whom I promised that both this package and my new database search algorithm would be available last weekend, the database search algorithm isn't ready yet. (I still haven't gotten the hang of the difference between estimates for "down the hallway" software, i.e. software written for the folks down the hallway, and real product quality software.) However, it will be ready soon. Certainly, by the time my post-doc runs out at the end of July. For those of you who weren't at ISMB (or who I didn't tell about my database search algorithm), I've developed an alternative to FASTA and BLAST that should produce Smith-Waterman quality alignments, i.e. the same alignments you'd get if you ran the full-blown Smith-Waterman search, but with the speed of FASTA and BLASTP. (It will probably take me until the next version of this program to get to BLASTN speeds.) Which reminds me. My post-doc here at UC Davis ends at the end of July, and so I'm looking for a job (either an industry, algorithm/software-development position or a postdoc working with biologists). If you have such a position or know about such a position (that hasn't been widely advertised on the newsgroups or on the WWW, because I've seen those), please let me know. I would appreciate it. Jim ************************* ************************* SEQIO: A C/C++ Package for Reading and Writing Sequences The SEQIO package is a C/C++ package (or library) which makes reading and writing sequences and biological databases as easy as reading and writing files, while at the same time supporting I/O in the following file formats: Raw/Plain, GenBank, PIR (CODATA), EMBL, Swiss-Prot, FASTA, NBRF, IG/Stanford, ASN.1 text files, GCG, MSF, PHYLIP, Clustalw, and output from the FASTA and BLAST suites of programs supporting completely configurable databases, using the new BIOSEQ standard for describing databases, like this one for GenBank: # # The GenBank Flat-File Database # >GenBank,gb: /databases/genbank >Name: GenBank >IdPrefix: gb >Index: gbindex >Format: gbfast >Alphabet: DNA # # GenBank files as found at ftp site ncbi.nlm.nih.gov in /genbank. # gbbct.seq, gbest?.seq, gbinv.seq, gbmam.seq, gbpat.seq, gbphg.seq gbpln.seq, gbpri.seq, gbrna.seq, gbrod.seq, gbsts.seq, gbsyn.seq gbuna.seq, gbvrl.seq, gbvrt.seq daily-nc/nc????.flat, daily:(daily-nc/nc????.flat) and supporting the transparent specification (as far as the program is concerned) of single entries of databases, like "gb:humhb*" for all of the human beta globin GenBank entries, and of single entries of any files, like "myseqs@3,4" or "myseqs@gb:humhba1" to specify either the third or fourth entry of file "myseqs" or the entry in "myseqs" whose identifier is the GenBank HUMHBA1 locus. Also, the database entries can be specified using the database specific identifiers (i.e., GenBank locus numbers, PIR entry names, ...) or using the cross-database accession, NID or PID numbers. Or all three, if you want. In addition, the distribution comes with a reimplementation and extension of Don Gilbert's readseq program (called fmtseq). In addition to a much better user interface, this program also has the ability to perform "no loss" conversions between the non-GCG and GCG forms of GenBank, PIR, EMBL, Swiss-Prot, FASTA, NBRF and IG/Stanford entries, and the ability to take the output from one of the FASTA and BLAST alignments and construct a "big alignment" by lining up all of the pairwise alignments into a multiple alignment. There's some other stuff too, but really, don't you think that's enough? From owner-software@net.bio.net Thu Jul 04 23:00:00 1996 Path: biosci!SEQNET.DL.AC.UK!mbpzh From: mbpzh@SEQNET.DL.AC.UK (l) Newsgroups: bionet.software Subject: Plasmid Drawing for Windows Date: 5 Jul 1996 02:04:12 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 7 Sender: daemon@net.bio.net Distribution: world Message-ID: <31DCD94B.41C6@seqnet.dl.ac.uk> NNTP-Posting-Host: net.bio.net Hi there Does anyone know of a source for Windows software (not too expensive) for drawing publication quality plasmid diagrams ? If possible it would be nice to be able to draw a map without needing sequence info and be able to export the maps into other software. Thanks phil From owner-software@net.bio.net Thu Jul 04 23:00:00 1996 Path: biosci!rutgers!uwm.edu!newsfeed.internetmci.com!in2.uu.net!psinntp!psinntp!usenet2.news.uk.psi.net!uknet!usenet1.news.uk.psi.net!uknet!uknet!lyra.csx.cam.ac.uk!mole.bio.cam.ac.uk!tjrc1 From: tjrc1@mole.bio.cam.ac.uk (Tim Cutts (Zoology)) Newsgroups: bionet.software Subject: Bouncing of posts by mailing list Date: 5 Jul 1996 07:08:43 GMT Organization: University of Cambridge Lines: 19 Message-ID: <4rif1r$9qf@lyra.csx.cam.ac.uk> NNTP-Posting-Host: mole.bio.cam.ac.uk I don't suppose it's just me this happens to, but every single thing I post to bionet.software gets bounced back to me by mail. It seems that a user on a gated mailing list no longer exists, and rather than the bounced message going to the list administrator (which is where it should go) it goes to the original poster, who can't do anything about it. Who runs the gated mailing list? For a start their setup may well be broken, and secondly it would be wonderful if they could do something about this particular user (okanes@uni.edu, I think). Furthermore, I *think* the list is operated by wugate.wustl.edu, but I'm not sure. Hopefully someone reading this will know the correct person to ask. Tim. From owner-software@net.bio.net Thu Jul 04 23:00:00 1996 Path: biosci!biosci!not-for-mail From: bloch@pasteur.fr (Laurent Bloch) Newsgroups: bionet.general,bionet.software Subject: Course in Informatics at Pasteur Institute Date: 5 Jul 1996 00:30:05 -0700 Organization: Institut Pasteur, Paris, France Lines: 82 Sender: daemon@net.bio.net Distribution: world Message-ID: <4ridut$nlj@montespan.pasteur.fr> NNTP-Posting-Host: net.bio.net Xref: biosci bionet.general:22639 bionet.software:15991 Course in informatics offered at the Pasteur Institute. ====================================================== In the series of courses offered at the Pasteur Institute, a course will be offered in informatics in biology. The next session will take place from January to April 1997. The course description is attached. Registration is mandatory via the committee of courses. Call the secretary of Information and Education of the Pasteur Institute at +33 (1) 45 68 81 40 or via E-mail at algo@pasteur.fr for further information. The working language of the course is French. Tuition costs: a nominal fee, approximately 2 500 French Francs (500 US Dollars). Course Description ================== Informatics in biology ---------------------- The objective of this course is to give to the researchers and future researchers in biology, an initial exposure to informatics. Entry in the course is reserved to those with a degree in biology or an equivalent discipline. With more and more tools available to the biologist, it has become important that the biologist acquire the ability to judge for themselves the usefulness of a new software by the algorithms it employs. The accent is put on the fundamental aspect of this discipline. Two applications in biology will be studied, the analysis of sequences and molecular modeling. The theoretic aspects of informatics will be introduced: programming languages, programing, logic, and also in the technical domain of the system, the network, and computer architecture. Programming is taught according to the functional paradigm (Scheme), but other styles of programming, such as algorithmic and object oriented, will be introduced. The goal of an excellent level of theory will not hurt the acquisition of practical knowledge which will be directly usable in the labratory. The course will consist of lectures and practical sessions. Algorithms and programming lecture 69h Algorithms and programming practical (with Scheme) 52h Theory of Programming languages 9h Object-oriented programming (with SmallTalk) 12h Procedural programming (with Fortran) 6h The programming language C and systems programming 12h Introduction to Unix and X practical 17h History of informatics lecture 6h Perspectives of informatics lecture 10h Algorithms for Biology Algorithms 45h Examples (Sequence analysis & molecular modeling) practical 27h Installation (gcc) 10h Machine architecture and System planning 10h Logic 10h Networks 12h ==================================================================== Total 307h Course Instructors Laurent Bloch William Saurin Frederic Chauveau Harald Wertz Catherine Letondal Daniel Azuelos Eric Gressier Thierry Rose Louis Jones Guy Vaysseix Francoise Balmas Christophe Wolfhugel Stephane Bortzmeyer From owner-software@net.bio.net Thu Jul 04 23:00:00 1996 Path: biosci!biosci!not-for-mail From: Scott Panzer Newsgroups: bionet.cellbiol,bionet.software,bionet.general,bionet.cellbiol.cytonet,yale.bio.announce Subject: Cytoskeletal Protein Interactions Database Date: 4 Jul 1996 23:25:45 -0700 Organization: Yale University School of Medicine Lines: 24 Sender: daemon@net.bio.net Distribution: world Message-ID: <4r9icj$lba@news.ycc.yale.edu> NNTP-Posting-Host: net.bio.net Xref: biosci bionet.cellbiol:5049 bionet.software:15990 bionet.general:22635 bionet.cellbiol.cytonet:595 "CySPID", and experimental database of cytoskeletal proteins and their interactions and relationships is available for public browsing at: This database is undergoing development and revision, and is being made available as a resource to the cytoskeletal community as well as to solicit feedback so we can improve it. If you're are interested in the cytoskeleton, please have a look. Scott Panzer Yale University ---------------------------------------------------------------- Scott Panzer | Department of Genetics, SHM I-310 stenor@pcnet.com | 333 Cedar Street panzer@seviche.med.yale.edu | New Haven, CT 06510 ---------------------------------------------------------------- Phone: 203-785-2675 Fax: 203-785-6333 Alt Fax: 203-785-7227 WWW URL: http://www.pcnet.com/~stenor/ ---------------------------------------------------------------- From owner-software@net.bio.net Thu Jul 04 23:00:00 1996 Path: biosci!rutgers!uwm.edu!news-res.gsl.net!news.gsl.net!ix.netcom.com!netcom.net.uk!sunsite.doc.ic.ac.uk!charlie.lif.icnet.uk!m.mitchell From: m.mitchell@icrf.icnet.uk (Mike Mitchell) Newsgroups: bionet.software Subject: Re: Directory of Molbiol/Biochem software for the Mac? Date: Fri, 05 Jul 1996 09:29:02 +0000 Organization: Imperial Cancer Resaerch Fund Lines: 31 Distribution: world Message-ID: References: NNTP-Posting-Host: morpheus.lif.icnet.uk X-Newsreader: Yet Another NewsWatcher 2.2.0b7 In article , mbxfd@unix.ccc.nottingham.ac.uk (Fergus Doherty) wrote: > I have volunteered to compile a directory of biochemistry/molecular biology > software available for the Mac. Commercial and PD. This is for Apple in > the UK, and for an academic Mac managers group (Mac Supporters), but I aim > to make it available on the WWW. This is a daunting task. Does anyone > know if there is an up to date directory of this kind already available, so > mabe I don't have to bother? > > Would you help me? I would like info on all sorts of Mac software relevant > to these disciplines (sequence analysis, molecular modelling, enzyme > kinetics, CAL, data aquisition etc.) If you can supply info on software > *especially if you use it* and can provide some views on its usefulness > (ie. a review), e-mail me at the address below. There are several good archives of good PD Mac biological applications. ftp://ftp.ebi.ac.uk/pub/software/mac ftp://ftp.bio.indiana.edu/biology/mac ftp://ftp.bio.indiana.edu/chemistry/mac ftp://ftp.bio.indiana.edu/molbio/mac ftp://ftp.bio.indiana.edu/science/mac -- Michael Mitchell "Smoke me a kipper, User Support I'll be back for breakfast." Molecular Biology Software Ace Rimmer, Test Pilot +44 (0)171 269 3115 BBC-TV Red Dwarf ENFJ http://www.biu.icnet.uk/~mike From owner-software@net.bio.net Thu Jul 04 23:00:00 1996 Path: biosci!daresbury!bioftp.unibas.ch!infobiogen.fr!jussieu.fr!esiee.fr!sgigate.sgi.com!news.msfc.nasa.gov!newsfeed.internetmci.com!netnews.nwnet.net!news.u.washington.edu!microb3.biostat.washington.edu!user From: gosink@u.washington.edu (John Gosink) Newsgroups: bionet.software Subject: BlueBasic - an amino acid colored font Date: Thu, 04 Jul 1996 16:12:48 -0800 Organization: University of Washington Lines: 15 Message-ID: NNTP-Posting-Host: microb3.biostat.washington.edu Hi, I've just made a font for use with multiple sequence alignments of amino acids. It's currently made for the Macintosh operating system. You use it just like any other font. It's based on the Courier font, but each of the letters are color coded as a mnemonic for the chemical nature or charge of the amino acid. I'm going to be very busy for the next month or two, so I won't have much time to adjust it, but if you'd like to give it a try, please go to: http://weber.u.washington.edu/~gosink/BlueBasic/AAFont.html I'll be able to answer questions and take comments, but probably not as promptly as usual (a little thing called a dissertation came up :-) -John From owner-software@net.bio.net Thu Jul 04 23:00:00 1996 Path: biosci!CS.Arizona.EDU!news.Arizona.EDU!hamblin.math.byu.edu!acs2.byu.edu!news.cuny.edu!caen!uwm.edu!cs.utexas.edu!howland.reston.ans.net!surfnet.nl!ruu.nl!news From: I.nijman@vetmic.dgk.ruu.nl (I.Nijman) Newsgroups: bionet.software Subject: PC version of PAUP with bootstrapping available????? Date: 4 Jul 1996 11:22:54 GMT Organization: RUU Lines: 22 Message-ID: <4rg9ie$fvu@newshost.cc.ruu.nl> Reply-To: I.Nijman@vetmic.dgk.ruu.nl NNTP-Posting-Host: bac023.vetmic.dgk.ruu.nl X-Newsreader: WinVN 0.92.6+ Hello, Does anybody know if (and were) there is a version of PAUP, the phylogenetic package available for DOS compatibles? I know it's there for Apple MAc's Any information greately appreciated!! Thanks, Ies Nijman I.J. Nijman Institute of Infectious Diseases and Immunology Department of Bacteriology, Faculty of Veterinary Medicine Yalelaan 1 3585 CL Utrecht The Netherlands Private: Phone: (31) (0) 30 2 53 39 43 (31)(0)35 6 24 79 32 Fax : (31) (0) 30 2 54 07 84 Prins Bernhardstraat 35 Email: I.Nijman@vetmic.dgk.ruu.nl 1211 GJ Hilversum The Netherlands From owner-software@net.bio.net Thu Jul 04 23:00:00 1996 Path: biosci!rutgers!uwm.edu!news.cse.psu.edu!news.math.psu.edu!news.cac.psu.edu!juncol.juniata.edu!hoquerx4 From: hoquerx4@juncol.juniata.edu Newsgroups: bionet.software Subject: FREE JavaScript Message-ID: <1996Jul4.200610.2283@juncol.juniata.edu> Date: 4 Jul 96 20:06:10 -0500 Organization: Juniata College, Huntingdon PA Lines: 6 Would you like to create great looking homepages without knowing howto program? Come check out http://rhoque.com/book to findout how you can use preprogrammed JavaScript to make your homepages look more interactivethan ever. Put sound, movie and WOW your friends! I am working on a book on JavaScript. Come check outparts of the book in my homepage. The code is FREE! So what are you waiting for... From owner-software@net.bio.net Thu Jul 04 23:00:00 1996 Path: biosci!CS.Arizona.EDU!news.Arizona.EDU!hamblin.math.byu.edu!acs2.byu.edu!news.cuny.edu!news.sprintlink.net!news-stk-200.sprintlink.net!news.sprintlink.net!news-pen-14.sprintlink.net!news.ultranet.com!homer.alpha.net!uwm.edu!cs.utexas.edu!howland.reston.ans.net!newsxfer.itd.umich.edu!news2.acs.oakland.edu!cwis-20.wayne.edu!cmb.biosci.wayne.edu!dwomble From: dwomble@cmb.biosci.wayne.edu (David Womble) Newsgroups: bionet.software Subject: Re: Ques: how to print postscript files? (Win3.1 based) Date: 4 Jul 1996 23:21:56 GMT Organization: Wayne State University Lines: 25 Message-ID: <4rhjmk$i7t@cwis-20.wayne.edu> References: <4rgob3$f78@news.orst.edu> <4rgpp3$5br@lyra.csx.cam.ac.uk> Reply-To: dwomble@cmb.biosci.wayne.edu NNTP-Posting-Host: cmb.biosci.wayne.edu X-Newsreader: TIN [version 1.2 PL2] Tim Cutts (Zoology) (tjrc1@mole.bio.cam.ac.uk) wrote: : In article <4rgob3$f78@news.orst.edu>, Don Chen wrote: : >files are funky and I would like a "pretty" tree. We have a : >Windows-based system with a HP Inkjet printer. Is there a way to : >print postscript files with this set up? And what are Newkirk files? : You can print PostScript files on any graphics-capable printer using : the free interpreter GhostScript. You should be able to find this on : most large ftp sites. It has a friendlier front-end called GhostView. [snips above] Yes, GhostScript etc. do work, but they are bulky, slow, and not easy to deal with for most people. My suggestion is to just get a PostScript printer (some of the higher end HP Inkjets are). Your department only needs to buy one and put it on the network, so easy with Win95 or WFWG 3.11. Works well with Macs, too, if you have a few extra dollars for a JetDirect (for HP) or other ethernet card for the printer. If you have a UNIX or other type of higher end network, that works great for both also, but usually requires an administrator type person to set it up for you. -- David D. Womble Phone: 313-577-2374 Center for Molecular Medicine and Fax: 313-577-6200 Genetics, Wayne State University E-mail: dwomble@cmb.biosci.wayne.edu 5047 Gullen Mall, Detroit, MI 48202 http://cmmg.biosci.wayne.edu/ From owner-software@net.bio.net Fri Jul 05 23:00:00 1996 Newsgroups: bionet.software Path: biosci!daresbury!nntp-trd.UNINETT.no!online.no!Norway.EU.net!EU.net!usenet2.news.uk.psi.net!uknet!usenet1.news.uk.psi.net!uknet!tank.news.pipex.net!pipex!usenet.eel.ufl.edu!news-res.gsl.net!news.gsl.net!hunter.premier.net!newsfeed.internetmci.com!newsxfer2.itd.umich.edu!agate!hpg30a.csc.cuhk.hk!news.cuhk.edu.hk!hkpu01.hkp.hk!polyu.edu.hk!rcsleung From: rcsleung@polyu.edu.hk (Samy Nonsense) Subject: [Q] Cybex 6000 data format Message-ID: Lines: 13 Sender: usenet@hkpu01.polyu.edu.hk (Usenet Account) Nntp-Posting-Host: 158.132.98.237 Organization: Hong Kong Polytechnic University X-Newsreader: Trumpet for Windows [Version 1.0 Rev B final beta #4] Date: Sat, 6 Jul 1996 00:50:22 GMT I am doing an isokinetic exercise study using Cybex 6000. In my mind, Cybex is a usefull isokinetic system and performed many research. For research purpose, data analysis is an important part of a project. However, I have a difficulty to analysis an torque data of each cycle . Cybex 6000 have not provided a report format which satisfy my requirment and cannot print or export a data to ASCII format. Also, this system is not allow synchronise with other system, ex. EMG system. Now I only know that Cybex saved the data file as binary form. If I know the binary format of data file, I could export the data. Could anyone have experience to solve the above problem or have a binary format of data file? Please send me a email. Thank you for your attention From owner-software@net.bio.net Fri Jul 05 23:00:00 1996 Path: biosci!rutgers!sgigate.sgi.com!news.msfc.nasa.gov!newsfeed.internetmci.com!in1.uu.net!fu-berlin.de!news.belwue.de!news.uni-ulm.de!rz.uni-karlsruhe.de!news.uni-kl.de!sun.rhrk.uni-kl.de!nenno From: nenno@rhrk.uni-kl.de (Mario Nenno [Bio.]) Newsgroups: bionet.software Subject: RE: program for CGH analysis Date: 6 Jul 1996 16:23:41 GMT Organization: Universitaet Kaiserslautern Lines: 8 Message-ID: <4rm3ud$mgh@sun.rhrk.uni-kl.de> NNTP-Posting-Host: aix4.rhrk.uni-kl.de X-Newsreader: NN version 6.5.0 #7 (NOV) I am looking for a CGH(comparative genomic hybridization) analysis program. Most software is highly expensive, but maybe somebody knows of cheap ones. The prefered hardware is SGI or MAC. Every hint and comment is wellcome! Mario Nenno, nenno@rhrk.uni-kl.de From owner-software@net.bio.net Fri Jul 05 23:00:00 1996 Path: biosci!daresbury!daresbury!not-for-mail From: "James O. McInerney PhD" Newsgroups: bionet.software Subject: Re: Ques: how to print postscript files? (Win3.1 based) Date: 5 Jul 1996 09:16:54 +0100 Organization: Porifera Section, The Natural History Museum Lines: 78 Sender: lpddist@mserv1.dl.ac.uk Message-ID: <4rij1m$dkl@mserv1.dl.ac.uk> References: <9674173448.~INN-YSAa00210.bionet-news@dl.ac.uk> Reply-To: j.mcinerney@nhm.ac.uk MIME-Version: 1.0 Original-To: bio-software@dl.ac.uk Don Chen wrote: > > I would like to print out partial trees from the Ribosomal Database > Project. The options are postscript, newkirk and text. The text > files are funky and I would like a "pretty" tree. We have a > Windows-based system with a HP Inkjet printer. Is there a way to > print postscript files with this set up? And what are Newkirk files? > > Thanks for your help. > > Don Don, I think you have gotten many answers concerning the postscript stuff. Your question about 'Newkirk' tree formats (actually it's 'Newick' format apparently named after a restaurant or bar in New Hampshire). Very simply...suppose two sequences/taxa/molecules/whatever are the most closely related in your dataset, then you can represent this fact thus: (A,B) \/ say also that their closest relative is sequence C, then we might have a Newick tree like this: ((A,B),C) \/ / \ / \/ and finally, taxa D and E are each other's closest relatives..sooooo (((A,B),C),(D,E)) \/ / \/ \ / / \/ / \ / \ / | The exact details of this 'standard' have yet to be standardised, so there are many flavours implemented in different programs (with branch lengths, comments, bootstrap support etc.). There are programs that transfer this information into nice pretty trees. The PHYLIP package has drawing programs: http://evolution.genetics.washington.edu/ (I think?!) Rod page in Glasgow has produced Treeview (Mac, Windows) http://taxonomy.zoology.gla.ac.uk/software.html#Tree viewing Don Gilbert in Indiana has produced TreeDraw Deck (I think the kudos goes to him, although I think also the program is based on PHYLIP code???) ftp://iubio.bio.indiana.edu/ Happy treedrawing, james -- --- Dr. James O. McInerney Ph.D. Phone/Voicemail: +44 171 938 9247 Senior Scientific Officer, email:j.mcinerney@nhm.ac.uk The Natural History Museum, Cromwell Road, London SW7 5BD UK --- From owner-software@net.bio.net Fri Jul 05 23:00:00 1996 Path: biosci!rutgers!uwm.edu!cs.utexas.edu!howland.reston.ans.net!vixen.cso.uiuc.edu!news.eecs.uic.edu!news.cc.uic.edu!usenet From: David Newsgroups: bionet.software Subject: Current situation for EditBase ? Date: Sat, 06 Jul 1996 09:56:42 -0500 Organization: UIC Lines: 13 Message-ID: <31DE7EAA.7988@uic.edu> NNTP-Posting-Host: slip2-03.dialin.uic.edu Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 2.01 (Win95; I) Hi! I have a program called EditBase. This program is very nice and useful for DNA cloning and stuff like that. It is developed by Purdue Reserach Fundation & USDA/ARS. The version I have is 0.74. Anyone happen to know the current situation for this program? I tried to e-mail the author of this program in Perdue but never got any response. Good luck in research. Chii-Shen Yang Dept. Physiology & Biophysics U. of Ill. at Chicago cyang3@uic.edu From owner-software@net.bio.net Fri Jul 05 23:00:00 1996 Path: biosci!rutgers!uwm.edu!cs.utexas.edu!howland.reston.ans.net!newsfeed.internetmci.com!newsxfer2.itd.umich.edu!news.eecs.umich.edu!newshub.tc.umn.edu!fu-berlin.de!news.belwue.de!news.uni-stuttgart.de!news.ruhr-uni-bochum.de!usenet From: Markus Piotrowski Newsgroups: bionet.software Subject: Re: What program to open Mac files in Windows PC? Date: Sat, 06 Jul 1996 16:26:16 -0300 Organization: Dep of Plant Phys, Ruhr-Universit=?iso-8859-1?Q?=E4t Bochum, Germany?= Lines: 19 Message-ID: <31DEBDD8.6267@rz.ruhr-uni-bochum.de> References: <4r9s3j$k5k@sjx-ixn4.ix.netcom.com> NNTP-Posting-Host: r3-87.pfp.ruhr-uni-bochum.de Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 2.01 (Win16; I) William Howse wrote: > > Is there a program out that will let me open Mac files with my Windows > PC? Dear William, there's a shareware program from Paul E. Thomson, called TransMac, that allows you to read Mac-formatted Disk on your Windows-PC. Don't know where and if to download, but here are some adresses: Acute Systems PO Box 37 Algonquin IL 60102 Paul E. Thomson Internet:70461.2542@compuserve.com Hope that will help, Markus From owner-software@net.bio.net Sat Jul 06 23:00:00 1996 Newsgroups: bionet.software Path: biosci!rutgers!uwm.edu!cs.utexas.edu!swrinde!elroy.jpl.nasa.gov!news.msfc.nasa.gov!newsfeed.internetmci.com!in2.uu.net!hearst.acc.Virginia.EDU!murdoch!usenet From: wrp@alpha0.bioch.virginia.edu (William R. Pearson) Subject: Re: FASTA version 3.0t (threaded) available In-Reply-To: wrp@alpha0.bioch.virginia.edu's message of Sat, 25 May 1996 18:44:49 GMT X-Nntp-Posting-Host: alpha0.bioch.virginia.edu Message-ID: Sender: wrp@alpha0.bioch.Virginia.EDU Organization: University of Virginia X-Newsreader: Gnus v5.1 References: Date: Sat, 6 Jul 1996 19:53:38 GMT Lines: 15 A revised version of FASTA3.0 - fasta30t4.shar.Z is available from ftp.virginia.edu in pub/fasta. This version hopefully finally fixes the problems that people were having with fasta-formatted DNA database searches. It also provides some corrections to the fastx program. In addition, thanks to Joachim Theilhaber at IBM, it is now possible to run the threaded version in parallel on SMP multiprocesssor IBM RS/6000's like the J30. See Makefile.ibm. Bill Pearson From owner-software@net.bio.net Sat Jul 06 23:00:00 1996 Path: biosci!rutgers!uwm.edu!vixen.cso.uiuc.edu!newsfeed.internetmci.com!in2.uu.net!news.abs.net!cs.umd.edu!info.usuhs.mil!usenet From: Mika Salminen Newsgroups: bionet.software Subject: Bootscanning for recombination Date: Sat, 06 Jul 1996 15:02:27 -0500 Organization: Henry M. Jackson Foundation Lines: 944 Message-ID: <31DEC653.10A1@pasteur.hjf.org> Reply-To: msalminen@pasteur.hjf.org NNTP-Posting-Host: 131.158.31.254 Mime-Version: 1.0 Content-Type: multipart/mixed; boundary="------------38861FD42F61" X-Mailer: Mozilla 3.0b5 (Macintosh; I; PPC) This is a multi-part message in MIME format. --------------38861FD42F61 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Announcement: The software package for performing "Bootscanning" is now available from our website at http://hivgenome.hjf.org/ "Bootscanning" is a method for detecting recombination in viral sequences. We have only applied it to HIV-1, but it should work for any genes that contain sufficient phylo- genetic signal. You will need GDE and Phylip to run the package, and at the current time, we only provide SUN executables. However, the source-code is also included, so anyone who would care to compile on another system capable of running GDE and Phylip is free to do so. Below is an excerpt from some of the documentation: Bootscanning Package v. 1.0beta1 Principal Idea and Approach: Mika Salminen, msalminen@hiv.hjf.org Design and programming: Wayne Cobb, wcobb@reed.hjf.org (c) 1994-1996: Mika Salminen, Wayne Cobb, Henry M. Jackson Foundation Description: Bootscanning is a method for anaysis of viral recombination. It can be used to compare an unknown, suspected recombinant sequence, to a set of predefined potential parental sequences. It should be independent of organism, but we have only used it for HIV-1 and suspect that it only works for sufficiently variable genes. In the case of HIV-1 there are predefined genetic subtypes which have been called A-H in analyses based on the envelope and gag genes, with the notable exception that the E-subtype does not exist in gag. Viruses with E-subtype envelopes group with the A-type viruses in gag. Bootscanning relies on the alignment of a suspected recombinant sequence with a set of potential parental reference sequences (groups of sequences from the differnt subtypes, or consensus sequences created from sets of reference sequences). After optimal alignment, the alignment is broken into sequential, overlapping segments (or windows) which are fed to a program for phylogenetic analysis (any of the sequence programs of Phylip could be used, we have included menus for three methods). Bootstrapped phylogenetic trees are built for each segment and finally the bootstrap value for placing the unknown with each of the reference sequences/sequence groups is tabulated and plotted along the genome. The assumption is that the unknown will always reach high bootstrap values with it's parental subtypes in windows covering areas of that subtype in the unknown. When a recombination breakpoint is reached, the bootsrap value for one parent+the unknown will go down, and the bootsrap value for the second parent+ the unknown should go up. Therefore we should find the breakpoint in the intersection of the plotted bootscanning lines. Reference alignments of non-recombinant gag and env genes and subtype-reference sequences are included in the package. However, be aware that the B and D-subtypes are sometimes difficult to separate in gag and that the A-subtype in some regions separates to at least 2 subclusters. Therefore we have included consensus sequences A1 and A2 in the cocnsensus alignments. The package contains the following components: Menufile for GDE: "GDEmenus.Bootscan" Insert the menus in this file into your ".GDEmenus"-file. Shell-scripts (place all in /GDE/bin/): "mlbootscan.sh" Performs Maximum Likelihood Bootscanning analysis using SEQBOOT, DNADIST, FITCH and CONSENSE "njbootscan.sh" Performs Neighbor Joining Bootscanning analysis using SEQBOOT, DNADIST, NEIGHBOR and CONSENSE "parsboot.sh" Performs Neighbor Joining Bootscanning analysis using SEQBOOT, DBNAPARS and CONSENSE "analyze.sh" Shell script to run the program analyze. "genchop.sh" Shell script to run the program chop Executables (place all in /GDE/bin/): readseq Fixed sequence format converter. "PhyloMask" Creates masks to exclude gaps (menu available in GDEmenus.Bootscan). "chop" Breaks up masked alignment into individual segments which are created as sequentially numbered input files to the Phylip programs in a subdirectory of your home directory. Each window is numbered at the midpoint of the segment in the alignment. For each segmnet a corresponding outfile and treefile is created which will contain the bootstrap values and the consensus trees. The programs 'analyze' and 'report' are used to extract and tabulate the bootstrap values of specified groups of sequences (taxa or clades). Plotting the tables using the alignment as the x-axis and the bootrap value as the y-axis can be used to identify recombination points. "analyze" Extracts bootstrap values from outfiles. Use analyze.sh to run "report" Collects bootstrap values in tab-delimited table. Attached to this file is also an example of a bootscan-plot of an A/D-recombinant virus. We hope that you will be able to use the method to produce some useful data, and would certainly be happy to hear comments and critique about the package and certainly also bug-reports. We would especially be delighted to here from anyone who has managed to successfully install the package. We also acknowledge that the package is crude and simple, we have not put a lot of effort into getting it very elegant, but it works for us, and we hope that it will for other people, too. We have tried to remove any bugs that have crept up during development, but there will certainly be more. Anyone using the package will do it on their own risk, we take no responsibility for any loss of data or hardware that may result from the use of the package (hopefully there will be none!). Finally, some acknowledgements and disclaimers: This work was supported in part by cooperative agreement N. DAMD17-93-V-3004, between the United States Army Medical Research and Materiel Command and the Henry M. jackson Foundation for the Advancement of Military Medicine, and by grant No. 19191 from the Finnish Academy of Science (Mika Salminen). The views and opinions expressed herein are those of the authors and do not purport to reflect the official policy or position of the US Army or of the Department of Defense. Please refer to the following publications if using the package: Mika O. Salminen, Jean K. Carr, Donald S. Burke and Francine E. McCutchan. (1995). Identification of Breakpoints in Intergenotypic Recombinants of HIV-1 by Bootscanning. AIDS Research and Human Retroviruses, 11, 1423-25. Smith S, Overbeek R, Woese CR, Gilbert W and Gillevet P. (1994) The Genetic Data Environment: An expandable GUI for Multiple Sequence Analysis. Comp Appl Biol Sci, 10, 671-675. Felsenstein, J. (1991). 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