From owner-software@net.bio.net Thu Oct 01 23:00:00 1992 Path: biosci!MUSICA.MCGILL.CA!CX13 From: CX13@MUSICA.MCGILL.CA ("Yannick@CX13") Newsgroups: bionet.software Subject: good MAC terminal emulator? Message-ID: <02OCT92.12948434.0103.MUSIC@MUSICA.MCGILL.CA> Date: 2 Oct 92 16:59:21 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 13 Hello Netters! Can somebody suggest a good MAC terminal emulator running under DECNET, preferably something small to accomodate our low-grade MAC and which will allow TEKTRONIX graphics? In particular, is there something available in one of the FTP sites? Thanx, Yannick Pouliot Montreal Neurological Institute From owner-software@net.bio.net Thu Oct 01 23:00:00 1992 Path: biosci!agate!spool.mu.edu!caen!kuhub.cc.ukans.edu!husc-news.harvard.edu!husc10!robison1 From: robison1@husc10.harvard.edu (Keith Robison) Newsgroups: bionet.molbio.genbank,bionet.software Subject: Re: NCBI Server Format --> FASTA converter Message-ID: Date: 2 Oct 92 13:29:20 GMT References: Lines: 24 Xref: biosci bionet.molbio.genbank:1048 bionet.software:3383 Nntp-Posting-Host: husc10.harvard.edu robison1@husc10.harvard.edu (Keith Robison) writes: >Does someone already have a program to convert the results of a >NCBI Sequence Server Query into FASTA format? I realize now that I omitted a key qualifier. GenBank queries come back in GenBank format, PIR queries in something that looks like PIR format but with some extra linefeeds separating field labels from data. But the Swiss-Prot returns not only have the extra line-feeds, but use different heading names than the Swiss-Prot distribution (full names rather than abbreviations). I guess the real question is whether these deviations will cause problems for various programs designed to read/convert PIR and Swiss-Prot formats. Keith Robison Harvard University Department of Cellular & Developmental Biology Department of Genetics / HHMI robison@ribo.harvard.edu From owner-software@net.bio.net Thu Oct 01 23:00:00 1992 Path: biosci!agate!ames!haven.umd.edu!darwin.sura.net!wupost!uunet!timbuk.cray.com!equalizer!sdcrsi!network.ucsd.edu!alex!spl From: spl@alex.uucp (Steve Lamont) Newsgroups: bionet.software Subject: Synu [long] (was Re: Microscope Image Processing) Message-ID: <1afc9pINN61r@network.ucsd.edu> Date: 1 Oct 92 17:25:13 GMT References: <199209291614.AA26688@mendel.sis.pasteur.fr> Organization: University of Calif., San Diego/Microscopy and Imaging Resource Lines: 296 NNTP-Posting-Host: alex.ucsd.edu In article <199209291614.AA26688@mendel.sis.pasteur.fr> bloch@pasteur.fr (Laurent Bloch) writes: > After digitization, you can reconstruct the image with a program called >SYNU (SYnthetic UNiverse) from UCSD and the San Diego Supercomputer Center >(costs ~$100 to cover costs) which can handle huge data sets and render >beautiful reconstructions (call David Hessler @ 619 534 7968 or Steve Young >@ 619 534 3539 - unfortunately, it only runs on SGI hardware) Correction: Please don't call David Hessler or Steve Young. Call Dolores Robinson at (619) 534-1392 or send email to me, Steve Lamont, at spl@szechuan.ucsd.edu, if you want to know about Synu. The San Diego Supercomputer Center is no longer involved in distribution of Synu. They'll just forward your requests to us and cause a delay. Since we've had dozens of calls and email queries on this since the quoted article hit the net, indicating that there's considerable interest in Synu, I'm attaching our Synu Frequently Asked Questions file to this message. I apologize for its length but it responds to most of the questions that we've been getting. spl - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - San Diego Microscopy and Imaging Resource Synu Frequently Asked Questions (Last updated September 30, 1992) 0) What is Synu? Synu is a collection of programs for manipulation and visual presentation of scientific data. Synu works with polygon meshes, stacks of contour lines, or three-dimensional volumes from confocal Z-series, tomography, or simulations. 1) What machines does Synu run on? The interactive portion of Synu, SynuView, runs only on Silicon Graphics IRIS machines. The non-interactive portions of Synu are supported on a number of Unix-based machines, from Cray supercomputers to Sun Microsystems workstations to NeXT Cubes. 2) Will Synu run on an IRIS Indigo? Yes, though Indigoes without Elan graphics will be somewhat slower and not produce as good looking images in SynuView, since on the basic Indigo the SGI GL (Graphics Library) is implemented mostly in software and the system only supports eight image bitplanes (256 colors at a time), although it "pretends" to support 24 bitplanes ("true" color). This simulation, called "dithering," will give only an approximation of the true color. If this is confusing, you should contact your Silicon Graphics representative for more information. Noninteractive portions of Synu (SynuRender, SynuConv, and SynuMcube) run just fine. 3) Will Synu run on a Personal IRIS? Yes, but in a somewhat degraded mode. The Personal IRIS does not support alpha planes and, thus, SynuView cannot simulate transparency or translucency. Everything else works okay, though. 4) How about a 4D/70? Yes, it should run there, as well, although it may be pretty slow for non-trivial sized geometries. Other 4D models should run Synu, too. 5) What level of the operating system do I need? Our current development machine is running IRIX 4.0.5. Machines running IRIX 4.0 of any revision should have no problems. If you're running 3.3.2, you should be okay as well, though there are no guarantees. We suggest that you bring your machine up to at least IRIX 4.0.3. We don't have convenient access to earlier versions of IRIX, so it may be hard to debug any specific problems you might have. 6) How much memory do I need? The short answer is: as much as you can afford. The longer and less glib answer is: a good minimum configuration is about 32 megabytes per processor. It really depends upon how big your datasets are and how much else you expect to be going on at the same time. If you're sharing your machine with someone who is doing computational fluid dynamics models, 256 megabytes may not be enough. Seriously, though, somewhere between 32 megabytes and 64 megabytes should be more than adequate for a typical workstation environment where there are only a few relatively small jobs running in the background. Sufficient "real memory" should be available to avoid swapping. Most workstations will support address spaces far in excess of the amount of real memory available on the machine but their performance drastically degrades when they begin to swap to disk. Swap space is disk space and is allocated when the system is originally set up by the vendor or system administrator and is rarely altered once the machine is installed. A good rule of thumb is to allocate between two and three times the amount of real memory for disk swap space. To determine how much space you have allocated for swap space on a Silicon Graphics machine, type the command df -k /debug and you should see something like golgi:/g7/synu> df -k /debug Filesystem Type kbytes use avail %use Mounted on /debug dbg 298396 22788 275608 8% /debug (On IRIX systems, /debug is essentially the swap partition.) Consult your vendor supplied documentation or your local Unix/IRIX guru for more information. If you already have a Silicon Graphics machine and don't know how much memory you have on it, log on, either from the console or from a telnet or rlogin session, and type the command hinv You'll see something that looks like this: golgi:/g7/synu> hinv 1 50 MHZ IP17 Processor FPU: MIPS R4010 Floating Point Chip Revision: 0.0 CPU: MIPS R4000 Processor Chip Revision: 2.2 ... Data cache size: 8 Kbytes Instruction cache size: 8 Kbytes Secondary unified instruction/data cache size: 1 Mbyte Main memory size: 160 Mbytes ... VGX Graphics option installed ... Our machine has 160 Mbytes of memory and has the VGX graphics hardware. Don't worry about data or instruction caches. They're part of the hardware and you can't change them by means other than actually replacing the CPU. You may want to look at third party vendors for memory. You may be able to save a considerable amount of money over the prices Silicon Graphics charges. However this may complicate the issue for you if your machine needs service, since Silicon Graphics may request that your remove any third party memory from the machine before they work on it. Also, since you will probably have to install the memory yourself, you should be sure that you feel comfortable opening up the machine and removing the CPU or memory boards. If this might be a problem, then you should either find someone in your department whom you trust to do this, a third party service vendor, or just buy your memory from Silicon Graphics. 7) How much disk do I need? See question 4 for the glib answer. Again, this depends upon what you're using the system for. If you're doing large animations on a regular basis, a gigabyte may not be adequate. Synu itself requires about 15 megabytes of disk space. Geometry files may be between a few kilobytes to 10-15 megabytes for something very complicated. Rendered images will vary depending on the resolution you choose. A color 1024x1024 image is about 3 megabytes. Gigabyte disk drives are pretty common and reasonably inexpensive these days. Remember to allow for adequate swap space (see question 4 above). Don't worry, you'll find something to do with "all that space." You may want to look at third party vendors for large capacity disk drives. You may be able to save a considerable amount of money over the prices Silicon Graphics charges. However, as with memory, this may complicate the issue for you if your machine needs service or you are not skilled at hardware installation. If your installation has a large central file server, you may be able to get by with considerably less disk space on your workstation. However, for best performance, you'll probably want at least 720 megabytes of disk on your system for local files, image, etc. Network File System (NFS) performance can be up to 10 times slower than to local disks. Tasks that do a lot of I/O, therefore, can suffer significantly. 8) What else might I want? Synu supports the 6 knob dial box. This may be more convenient to use when rotating or translating objects on the screen when running SynuView. The stereo 3D option is supported by SynuView. You may also wish to have the C programming language and libraries. While the current version of Synu is distributed in executable only form, later versions of Synu are expected to include the Synu programming library. You may also want to write translators from your own favorite data format to Synu format if SynuConv doesn't support them directly. Consult your budget and your Silicon Graphics representative. 9) What do I get when I request Synu? You get a 1/4 inch QIC tape (the standard cartridge tape) with the Synu executables, some example data sets, also on the tape, and a User's Manual with installation instructions and an example of how to convert and use Boulder format contour data with Synu. There are several component parts to the Synu package: SynuConv - this is a file format conversion utility. It "knows" about a number of different popular file formats, as well as, of course, Synu's own geometry and image formats. SynuMcube - this is an implementation of the Marching Cubes surface tiling algorithm. You can use it to generate isosurfaces from volumes from tomography or other sources such as confocal Z-series. It is also used by one of the supplied shell scripts to create tiled surfaces from contours out of the Boulder program. SynuView - this is the interactive portion of Synu. It is used to view Synu surface data. This utility only runs on Silicon Graphics machines. You can alter surface color, trans From owner-software@net.bio.net Thu Oct 01 23:00:00 1992 Path: biosci!JPNAIST.BITNET!RVS22 From: RVS22@JPNAIST.BITNET ("RVS22@JPNAIST ANDREAS,TSUKUBA/JAPA") Newsgroups: bionet.software Subject: (COPY) BIOCOMPUTING & AI AT NLM Message-ID: <9210020251.AA18860@net.bio.net> Date: 2 Oct 92 02:24:00 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 117 DEAR BIOSOFTS, COULD YOU HAVE AN ANSWER TO MY QUESTION BELLOW? THANKS. ANDREAS RVS22@JPNAIS T -------------------------TEXT-OF-FORWARDED-MAIL-------------------------------- Received: (from MAILER@NIHCU for RVS22@JPNAIST via NJE) (UCLA/Mail V1.410 M-SYSMAIL-8594-109); Fri, 02 Oct 92 03:15:39 JST RVS22@JPNAIST, Received: from CU.NIH.GOV by NIHCU (Mailer) id 8586; Thu, 01 Oct 92 11:44:21 EDT Received: from NLM.NIH.GOV by CU.NIH.GOV with TCP; Thu, 1 Oct 92 11:44:05 EDT Received: from work.nlm.nih.gov by nlm.nih.gov (4.1/SMI-4.0) id AA26389; Thu, 1 Oct 92 11:45:20 EDT Received: by work.nlm.nih.gov (920110.SGI/5.6) id AA05651; Thu, 1 Oct 92 11:56:47 -0400 Date: Thu, 1 Oct 92 11:56:47 -0400 From: hunter@NLM.NIH.GOV(Larry Hunter) Message-Id: <9210011556.AA05651@work.nlm.nih.gov> To: RVS22 In-Reply-To: <9210011500.AA06555@csb1.nlm.nih.gov> "RVS22%JPNAIST.BITNET@CU.NIH .GOV" Subject: BIOCOMPUTING & AI AT NLM Date: Thu, 01 Oct 92 19:44 JST To: HUNTER From: "RVS22%JPNAIST ANDREAS,TSUKUBA/JAPA" DEAR DR.HUNTER, PLEASE RESPOND: 1.LIST OF AL AI-TECHNICAL DOCUMENTS FROM THE NLM Such a list is not kept. The closest available document would be the NLM annual report, which contains a bibliography. You may request one by writing to: National Library of Medicine Office of Public Information Building 38, Room 2S10 Bethesda, MD 20894 USA 2.YOUR CURRENT PROJECT AS DIFFERENT FROM THE NCBI DIVISION The Lister Hill Center is the basic research arm of the NLM. I am the director of the Machine Learning Project, which is part of the Computer Science Branch. For more information about the Lister Hill Center and its many research programs, write to Dr. Daniel Masys, Director Lister Hill Center National Library of Medicine Building 38A, Room 7N707 Bethesda, MD 20894 USA 3.SCHEDULLE OF FORTHCOMMING MEETINGS I am involved with two upcoming meetings: 1. The Biotechnology Computing Track of the Hawaii International Conference on System Sciences (HICSS-26). It will be held Jan 5-8, 1993 in Maui, Hawaii, USA. For further information about this meeting, send email to: hicss@uhunix.uhcc.hawaii.edu 2. The first international conference on Intelligent Systems and Molecular Biology. It will be held July 7-9, 1993 at the National Library of Medicine in Bethesda, Maryland, USA. For further information about this meeting, send email to: ismb@nlm.nih.gov 5.DIRECTORY OF AVAILABLE MODELING & SIMULATION SOFTWARE FOR PROTEINS AND DNA I do not maintain or know of any such directory. Well known programs include MIDAS, CHARMM, and QUANTA. There are many others. This is not my area of expertise. You might try looking at the usenet group "bionet.software" 6.MY CURRENT PROJECT HERE IS DEVELOPMENT OF ARTIFICIAL BLOOD VESSELS - THIS IS ASSOCIATED WITH SURFACE COATING BY PRESUMABLY ANTICOAGULANT PROTEINS IN THIS CASE THE HUMAN HISTIDINE RICH GLYCOPROTEIN. PROTEIN PURIFICATION IS AT LEAST FOR ME A NIGHTMARE - THOUGH THIS PROTEIN HAS BEEN ISOLATED 20 YEARS AGO, NO AUTOMATION AND CONVENIENT AVAILABLITY HAS BEEN ACHIEVED. 7.MY IDEA: MODELING & SIMULATION OF THIS LINEAR PROTEIN OF 525 RESIDUES DOCKED ON THE WALL OF AN ATRIFICIAL POLYMER. PARAMETERE SETTING:WALL CONFIG URA TION, BLOOD-WALL INTERFACE MODELLING, BLOOD FLOW IN BRANCHED VESSELS SIMULA TION. This is an interesting problem, and quite computationally challenging. You may also be interested in the DOCK program from UCSF. There is a good article on this: Shoichet BK & Kuntz ID, "Protein docking and complementarity" J Mol Biol 1991 Sep 5;221(1):327-46. Hope this is helpful. Larry Lawrence Hunter, PhD. National Library of Medicine Bldg. 38A, MS-54 Bethesda. MD 20894 (301) 496-9300 (301) 496-0673 (fax) hunter@nlm.nih.gov (internet) From owner-software@net.bio.net Thu Oct 01 23:00:00 1992 Path: biosci!agate!ames!haven.umd.edu!uunet!stanford.edu!leland.Stanford.EDU!moxness From: moxness@leland.Stanford.EDU (Michael Moxness) Newsgroups: bionet.software Subject: quantitative analysis on scanned gels Message-ID: <1992Oct2.001708.7296@leland.Stanford.EDU> Date: 2 Oct 92 00:17:08 GMT Sender: news@leland.Stanford.EDU (Mr News) Organization: DSG, Stanford University, CA 94305, USA Lines: 22 We recently bought a desktop scanner and the Quantiscan program from Biosoft. The scanner works great to get images of protein gels and autoradiograms, but Quantiscan is the worst piece of software that I have ever seen. We have had major problems with the peak picking and integration. We are going to return the software but would like to find another software package that can serve our purposes. We need to quantitate bands from the image in both dimensions, output gel lane plot profiles, and some sort of peak picking would be a nice luxury, not to mention gaussian fits. I have downloaded Image and it seems to be a very nice program, but it is limited in the size of images it can handle. I was wondering if there is anything else out there that will be even better. Am I being too greedy? Ideally, it would run on a DOS 386 machine but either a Mac or Sparc station version would be OK also. And of course the cheaper the better. Sorry if this has been discussed recently, but I just started reading this newsgroup. If you could direct me to a faq file, I would be grateful. Mike Moxness moxness@bogart.stanford.edu PS The Artiscan scanner with slidescan kit has worked out well for us and it only cost about $1800. From owner-software@net.bio.net Thu Oct 01 23:00:00 1992 Path: biosci!agate!spool.mu.edu!darwin.sura.net!haven.umd.edu!mimsy!lhc!ray!dab From: dab@ray.nlm.nih.gov (Dennis Benson) Newsgroups: bionet.molbio.genbank,bionet.software Subject: Re: NCBI Server Format --> FASTA converter Message-ID: <1992Oct2.220656.6313@nlm.nih.gov> Date: 2 Oct 92 22:06:56 GMT References: Sender: news@nlm.nih.gov Organization: National Library of Medicine Lines: 46 Xref: biosci bionet.molbio.genbank:1050 bionet.software:3388 X-Newsreader: Tin 1.1 PL4 robison1@husc10.harvard.edu (Keith Robison) writes: : : >Does someone already have a program to convert the results of a : >NCBI Sequence Server Query into FASTA format? : : : I realize now that I omitted a key qualifier. GenBank queries : come back in GenBank format, PIR queries in something that looks : like PIR format but with some extra linefeeds separating field : labels from data. But the Swiss-Prot returns not only have the : extra line-feeds, but use different heading names than the : Swiss-Prot distribution (full names rather than abbreviations). : I guess the real question is whether these deviations will cause : problems for various programs designed to read/convert PIR and : Swiss-Prot formats. : : : : Keith Robison : Harvard University : Department of Cellular & Developmental Biology : Department of Genetics / HHMI : : robison@ribo.harvard.edu Keith -- You've pointed out something I want to fix over the next couple weeks. The only reason the PIR, Swiss-Prot, (and EMBL) come out looking a little unfamiliar is that you are seeing the entries as formatted for IRX text retrieval. GenBank entries have been passed through a filter to turn them back into flat-file style records. I just need to write the filters for the other databases. So please, if you can be patient a little longer, don't write converters for the present output. I also wonder whether as an interim solution, a FASTA type output option would take care of some of your needs, ie, do you need all of a PIR record in PIR format or is your principal need to get an identifier line and the sequence itself. It would be easy to have a field in the mail message 'FASTA yes' or just 'FASTA' and have the program return just the FASTA-formatted sequence for any of the databases. Regards, Dennis Benson NCBI From owner-software@net.bio.net Thu Oct 01 23:00:00 1992 Path: biosci!agate!spool.mu.edu!sdd.hp.com!usc!zaphod.mps.ohio-state.edu!darwin.sura.net!haven.umd.edu!wam.umd.edu!desai From: desai@wam.umd.edu (hey what's up) Newsgroups: bionet.software,bionet.molbio.methds-reagnts Subject: software to analyse evolutionary tree for nucleotide and aa.. Message-ID: <1992Oct2.152411.19884@wam.umd.edu> Date: 2 Oct 92 15:24:11 GMT Sender: usenet@wam.umd.edu (USENET News system) Distribution: na Organization: University of Maryland, College Park Lines: 16 Xref: biosci bionet.software:3384 bionet.molbio.methds-reagnts:3075 Nntp-Posting-Host: rac2.wam.umd.edu HI Net fellows: Friend of mine who does not have access to net like to know the availability of a program (software) to analyse the evolutionary tree for nucleotide and amino acid sequence determination by Maximum- parsimony analysis with PAUP software. He is interested to know from where he can get this program, is it on any ftp sites or is it commercially available? thanks in advance. Dinakar From owner-software@net.bio.net Thu Oct 01 23:00:00 1992 Path: biosci!daresbury!news From: ROUCHDA@VAX1.COMPUTER-CENTRE.BIRMINGHAM.AC.UK (Duncan Rouch) Newsgroups: bionet.software Subject: RE: Improving Biocomputing Facilities Message-ID: <1992Oct2.191001.5747@gserv1.dl.ac.uk> Date: 2 Oct 92 18:26:00 GMT Sender: list-admin@daresbury.ac.uk Distribution: bionet Lines: 107 Original-To: BIO-SOFT@UK.AC.DARESBURY Hi Netters, I agree with Keith Elliston that comparing to what other's have is a top argument for getting better computing facilities, but I draw attention to an essential factor missing in most discussions about facilities: the quality of service. Quality is defined and built in practice by management principles. Wazzat? Just so we know what we are talking about, good management IS -identifying problems, their solutions, and ensuring they are solved. It's an ongoing process, attempting to deal with new problems in the most efficient manner as they arrive. A computing facility usually lets other people use it apart from the people who run the computers, so it offers a SERVICE. Maybe that's obvious, but some people haven't thought through what that really means. You have to ask and answer questions like: How do you offer a good computing service? How do you tell how good the service is? How well does it help biologists with their research? Going back to Keith's goal, to get better computing facilities, it is then essential to look at how effective other facilities are, so you can point your finger and say "Geez, look how well their research is going with that kinda service, we need that quality". Getting bigger and better computers and more staff doesn't mean a lot if the service doesn't deliver what's needed. As I've said, offering an effective service is a management problem. You need to apply professional management skills to help deal with it, to define what you need, get the resources you need, get it running, and keep it running, and get the service updated to keep up with what the biologists need. And all that in the most efficient way. Of course their are constraints, like the budget, so you aim for a defined level of service that you can deal with. Power for Change in Joining Forces: If biologists need more from the computing service than it can give, then it's time for computing management and the biologists using the service to get together to go for more. Getting in 'Da Management': Decent sized facilities of course do have some kind of management structure, but not all are as effective as they might be. Academic institutions are normally not too hot on management, especially time-based management which is important for a multi-task environnment like a computer service. So we can learn from our business friends who know all about it. You might even consider head-hunting a manager or two from an appropriate part of the commercial sector, as some have done, to improve effectiveness at a site. However, moving commercial practices into the academic environment without adapting them for the new environment could be a bad move. The academic world has different priorities to the business world, for a start, academia relies on having time for creative analytical thought, that has no place in all, or almost all, parts of a major business. Overcoming Resistance: An initial stumbling block to bringing in management, as well as support bods and equipment, could well be at the decision making level. Few senior staff members at many biology institutions or departments are computer literate, beyond typing a letter on a PC. It can be difficult to persuade decision makers of the importance of something they don't understand, so educate them! Existing support bod(s) at a small facility might simply be managing themselves. In an upgrade they might not initially go for the idea of a professional manager, as they like their independence. Also, because they are working flat out they could well think they're doing an effective job. However, they may also complain that the department doesn't take their requests for more equipment and people seriously. This is a prime situation for calling in 'da management'. The hard working support bod may not take kindly to instruction from above, but it's a two-way street. A manager can set priorities on the many different tasks involved in support, to maximize efficient use of the support person's time. And it is part of their job to argue for and help get the necessary equipment and extra staff. Manager are placed closer in the heirarchy to the decision makers, so they are in a better position to influence the decisions, naturally. Conclusion: Go for quality service, get in 'da management'. The role of management and other factors in getting better biocomputing facilities is discussed by me and the other guys in the SEQNET User Documentation crew, U.K., in a previous posting on bio-soft, "Improving Front-line User-Support: Proposals for Greater Efficiency in Computational Molecular Biology." This has now appeared in BINARY, (1992)4:129-132. Duncan Rouch Birmingham University, U.K. Disclaimer: I am not nor have been a manager in this life, or any previous one. From owner-software@net.bio.net Thu Oct 01 23:00:00 1992 Path: biosci!CSHL.ORG!theiss From: theiss@CSHL.ORG (Bobbie Peters in Grace) Newsgroups: bionet.software Subject: auto-mail program for BLAST? Message-ID: <9210022032.AA28843@phage.cshl.org> Date: 2 Oct 92 20:32:19 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 24 We have a program here that sends parameters & sequences to the old FASTA e-mail address in the correct format. It would ask the user questions - What is the name of the sequence, what databank do you want to search against, are these parameters OK, etc. Then it mailed the info to the old fasta bio.net address. I seem to remember that someone else offered the same type of program ages ago for FASTA. Rather than us re-writing the fasta program, has anyone written an auto mail program for BLAST? Along the same lines, is there a list of programs like BLAST, SeqApp, etc that are available via e-mail? This doesn't seem to be a question that Archie would easily answer. thanks for your help Bobbie Peters User Liaison v v v v v v v v v v v v v v v v v v v v v v v v v v v v v v v v v v Cold Spring Harbor Laboratory Voice: (516) 367-8390 Box 100 Fax: (516) 367-9576 1 Bungtown Road Internet: Cold Spring Harbor, NY 11724-2213, USA (or theiss@...) ^ ^ ^ ^ ^ ^ ^ ^ ^ ^ ^ ^ ^ ^ ^ ^ ^ ^ ^ ^ ^ ^ ^ ^ ^ ^ ^ ^ ^ ^ ^ ^ ^ ^ From owner-software@net.bio.net Fri Oct 02 23:00:00 1992 Path: biosci!DARTMOUTH.EDU!Keith.A.Johnson From: Keith.A.Johnson@DARTMOUTH.EDU Newsgroups: bionet.software Subject: blaze Message-ID: <1596036@blitzen.Dartmouth.EDU> Date: 2 Oct 92 00:57:59 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 8 I haven't been paying strict attention to some of the more recent postings on the database search programs and the ftp names now in use. I was wondering if there is a site available for BLAZE searches as there is for the BLAST searches? I have had a bad experience with a BLAST search and received more believable information from the BLAZE algorithm. Thanks Keith Johnson From owner-software@net.bio.net Fri Oct 02 23:00:00 1992 Path: biosci!agate!dog.ee.lbl.gov!ucbvax!pasteur.fr!bloch From: bloch@pasteur.fr (Laurent Bloch) Newsgroups: bionet.software Subject: Microscope image processing (summary) Message-ID: <199210032106.AA18766@mendel.sis.pasteur.fr> Date: 3 Oct 92 21:09:20 GMT Sender: daemon@ucbvax.BERKELEY.EDU Lines: 513 X-Unparsable-Date: Sat, 3 Oct 92 23:06:36 MET DST Here is a summary of the answers I have received so far on a image processing program for quantitative fluorescence microscopy : ========================================================================== ========================================================================== ========================================================================== >From knosp@sarah.iaf.uiowa : Vaytek, Inc. offers a line of products that run on pcs, mac II's, HP workstations, and Silicon Graphics workstations. They can be reached at 515-472-2227 (Fairfield, IA). Their microtome software performs deconvolution and other useful microscopy operations. Their volume rendering software, Voxblast, operates on SGI, HP, Dec, IBM, Sun workstations and they also have a version which operates on PC's and Mac II's. Voxblast allows several 3d quantitative operations in addition to an array of display and data manipulation techniques. Vaytek has demos of their software they can send you. boyd Boyd Knosp 319-335-6715 University of Iowa knosp@tessa.iaf.uiowa.edu Image Analysis 77 EMRB Iowa City, IA 52242 ========================================================================== >From hauch@cheme.washington.edu : You will undoubtedly want to contact the Inovision Corp. Inovision CorporationJ PO Box 12539 2810 Meridian Parkway Ste 100 Research Triangle Park NC 27709-2539J USA Doug Benson, President David Fine sales rep Image analysis software for sun. ISee, RatiotoolJ 919-361-4609J 919-361-5876 FaxJ ========================================================================== >From mangalam@salk-sc2.sdsc.edu : Regarding your request for information regarding the capture and processing of video images from a microscope at 1000X1000X12-16 bits, for an application running on a *nix workstation. >The application should meet these requirements >(or at least part of them) : > >- deliver a good and fast video display of the image(s)* (see below) >- standard operations on images (+, x, -, convoluation,* > noise reduction, linear or non linear LUTs)*(with the free NCSA PALedit) >- counting cells* >- numbering nuclei as objects (contours, areas, ...)* (I think) >- integrating the signal within these objects* >- define masks and apply them to other images* >- show the data in statistical format (histograms, > correlations, ...) or export it in a format compatible with > standard statistics processing applications (Macintosh > or MS/DOS Excel,Cricket Graph, or Unix based applications,..)* > > > >OPTIONALLY > >- print the images to a thermal/laser printer * >- drive the microscope stage (z axis, or even 3 axes) >- perform 3-D reconstruction and display from a user > defined angle. *(sort of) There are number of answers, none of which (of course) answers all your requirements. Surprisingly, many of them can be met by Wayne Rasband's (free) NIH Image running on a Mac. It can perform all the points marked by a * above, including direct support for at least 2 video frame grabbers. The major limitation is that it was not built to handle the _huge_ image files that you mention and it has the unfortunate limitation that it will only handle 8bits of color/greyscale. If you can reduce the amount of data, or you are willing to write the modifications to his routines (Pascal source code is freely available)), then you could save a great deal of money. (If you were to re-write the source code you could also link in the routines to use a very fast coprocessor like the Tuplex i860 for the graphic convolutions/transformations.) The first thing to do is to download the documentation and the program to see if it is worth the effort. Image is available from alw.nih.gov in /pub/image. If you absolutely demand the size of files you state, only a _very_ fast workstation will be able to handle them in a 'real-timely' manner, an SGI Indigo R4000/Elan at minimum and up. SGI recently released it's Reality Engine - 8 i860 superscalar processors dedicated to graphics processing at (only!) $60,000 academic on top of whatever VME box you put it in (AMAZING machine!) The SGI recently released a set of video manipulation tools for the Indigo - it requires a $2500 board (that only fits into the R3000 based Indigo because of the size of the R4000 board) but some software tools are included in the system software. I rather doubt that this board will handle 1Kx1Kx16 bit video capture, though - ask SGI about it. At any rate, to do the analysis, you will have to use some additional software. After digitization, you can reconstruct the image with a program called SYNU (SYnthetic UNiverse) from UCSD and the San Diego Supercomputer Center (costs ~$100 to cover costs) which can handle huge data sets and render beautiful reconstructions (call David Hessler @ 619 534 7968 or Steve Young @ 619 534 3539 - unfortunately, it only runs on SGI hardware) There is also a horrendously expensive (~$20,000), but quite capable 3D volume rendering/analysis package called VoxelView (Vital Images; phone: 515-472-7726 Ext 118, fax: 515-472-1661, email: userserv@vitalimages.com) which can do some of the other kinds of image analysis that you require (also requires SGI hardware). Summary - try NIH Image first, rewriting that code that you need to, then use SYNU if you need it for better reconstruction. Std Disclaimers Apply... Cheers, Harry Harry Mangalam Vox:(619) 453-4100, x250 Dept of Biocomputing Fax:(619) 552-1546 The Salk Institute mangalam@salk-sc2.sdsc.edu 10010 N Torrey Pines Rd mangalam@salk-sgi.sdsc.edu La Jolla CA 92037 mangalam@salk.bitnet ========================================================================== From: s.budd@imperial.ac.uk : I would suggest you look at the KHOROS software. I enclose a short description. RRegards sinclair Budd KHOROS 1.0 (Patch Level 4) RELEASE ANNOUNCEMENT INTRODUCTION Khoros is an integrated software development environ- ment for information processing and visualization, based on X11R4. Khoros components include a visual programming language, code generators for extending the visual language and adding new application packages to the system, an interactive user interface editor, an interactive image display package, an extensive library of image processing, numerical analysis and signal processing routines, and 2D/3D plotting packages. X Windows Applications Animate - Interactive Image Sequence Display Tool Cantata - Extensible Visual Programming Language Concert - A system for distributed X user interfaces (groupware) Editimage - Interactive Image Display & Manipulation Program Xprism2 and Xprism3 - Comprehensive 2D and 3D Plotting Packages Viewimage - A basic interactive program for surface rendering Warpimage - An interactive program for registering and warping images Data Processing Algorithms Khoros contains over 260 programs, in the following categories: arithmetic, classification, color conversion, data conversion, file format conversion, feature extraction, frequency filtering, matrix algebra (LINPACK and EISPACK), spatial filtering, morphology filtering, geometric manipula- tion, histogram manipulation, statistics, signal generation, linear operations, segmentation, spectral estimation, sub- region, and transforms. Khoros supports the following file formats: TIFF, pbm, BIG, DEM, DLG, ELAS, FITS, MATLAB, Sun raster, TGA, and xbm. User Interface Tools Preview - Graphical User Interface Display Tool Composer - Interactive Graphical User Interface Editor Conductor - Code Generation Tool for a Graphical User Interface Ghostwriter - Code Generation Tool for a Command Line User Interface Source Configuration & Management - Tools to install and maintain a distributed source tree. KHOROS DISTRIBUTION METHODS 1) Anonymous FTP Khoros is available via anonymous ftp from pprg.eece.unm.edu (129.24.24.10). Use your e-mail address as the password (for example, ralph@whizbang.wmu.edu). Once you have logged in, cd to the "pub/khoros/release" directory and get the ascii file install.ftp. This file will give you complete instructions on how to get Khoros and install it on your system. To get this file, execute the following commands or steps: a. Use ftp to connect to pprg.eece.unm.edu. % ftp pprg.eece.unm.edu -or- % ftp 129.24.24.10 b. Use "anonymous" or "ftp" as the user name. Name (pprg.eece.unm.edu:login): anonymous -or- Name (pprg.eece.unm.edu:): ftp c. Use your e-mail address as the password; please carefully use a valid e-mail address, as this ver- From owner-software@net.bio.net Fri Oct 02 23:00:00 1992 Path: biosci!agate!ames!haven.umd.edu!uunet!seas.gwu.edu!merlot.gwu.edu!danj From: danj@chablis.gwu.edu (Dan Jacobson ) Newsgroups: bionet.software Subject: Re: Paup Message-ID: <1992Oct2.213308.6870@seas.gwu.edu> Date: 2 Oct 92 21:33:08 GMT Sender: news@seas.gwu.edu Organization: George Washington University, Washington, D.C. Lines: 29 Originator: danj@merlot.gwu.edu A question was asked about the availibility of the PUAP phylogeny package. Paup is commercial, though the last I heard a great price ~$50 (US). As such it is not (*should not*) be on any ftp server. You might want to contact the author of Puap: David L. Swofford Phone: (217)244-6959 Illinois Natural History Survey FAX: (217)333-4949 607 E. Peabody Drive BITNET: DAVESWOF@UIUCVMD Champaign, Illinois 61820 USA Internet: swofford@uxh.cso.uiuc.edu If you're doing phylogeny you might want to take a look at PHYLIP by Joe Felsenstein. Phylip is also a suite of programs for phylogeny but is free, at a ftp site near you and comes with LOTS of documentation. Best of luck, Dan Jacobson danj@chablis.gwu.edu NOTE: My email address has changed to danj@chablis.gwu.edu, I am no longer danj@welchgate.welch.jhu.edu. From owner-software@net.bio.net Fri Oct 02 23:00:00 1992 Path: biosci!uwm.edu!rpi!think.com!yale.edu!spool.mu.edu!hri.com!noc.near.net!news.cs.brandeis.edu!news From: ahouse@hydra.rose.brandeis.edu Newsgroups: bionet.software Subject: GCG7 to Paup translation? Keywords: GCG, Paup, file translation Message-ID: <1992Oct3.205816.14831@news.cs.brandeis.edu> Date: 3 Oct 92 20:58:16 GMT Sender: news@news.cs.brandeis.edu (USENET News System) Organization: Brandeis University Lines: 27 I need to find a program that will take me from the multiple sequence alignments that I can get out of GCG 7's pileup program to the format required by Paup on the Mac. Do you all do this by hand? Do you have a good/better multiple sequence alignment tool on the Mac? Any info would be very helpful, - jeremy ::::::::::::: Jeremy John Ahouse Center for Complex Systems and Biology Dept Brandeis University Waltham, MA 02254-9110 (617) 736-4954 email: ahouse@hydra.rose.brandeis.edu -- ::::::::::::::::::::::::::::::: Jeremy Ahouse Center for Complex Systems From owner-software@net.bio.net Fri Oct 02 23:00:00 1992 Path: biosci!agate!ames!haven.umd.edu!darwin.sura.net!jvnc.net!nuscc!bchtantw From: bchtantw@nuscc.nus.sg (Dr Tan Tin Wee) Newsgroups: bionet.software Subject: Prophet integrated sw - comments? Message-ID: <1992Oct3.124935.740@nuscc.nus.sg> Date: 3 Oct 92 12:49:35 GMT Organization: National University of Singapore Lines: 30 Dear Bionetters, I have recently come across the software package Prophet. From the initial description, it seems like a nicely integrated package that stretches across many biological subdisciplines including molbio, stats, graphics display etc. It claims to be easily maintained and expanded to incorporate new software. Our problem has been that our users have to use a diverse range of software, often on different platforms DOS, Mac and Unix, in order to achieve their goal. This package sounds very promising. Has anyone had experience with this?i Any comments on this software will be much appreciated, as we are considering purchase as the licence is $150! any catch? Of course, we will have to get Suns and Sparcstations to our users, who currently are running 286 and 386s! - tall order that.. Thanks in advance. Tin-Wee. bchtantw@nuscc.nus.sg Dept of Biochemistry, Natl Univ of Singapore -- Tin-Wee TAN / INTERNET: bchtantw@nuscc.nus.sg Dept of Biochemistry / BITNET: BCHTANTW@NUSVM National University of Singapore / Tel: (65)-772-3678 Singapore 0511 / Fax: (65)-779-1453 From owner-software@net.bio.net Fri Oct 02 23:00:00 1992 Path: biosci!ucselx!sol.ctr.columbia.edu!destroyer!gatech!concert!rutgers!att-out!pacbell.com!iggy.GW.Vitalink.COM!psinntp!psinntp!alsys1!aecom.yu.edu! From: @aecom.yu.edu Newsgroups: bionet.software Subject: gel analysis software Summary: need a good package for analyzing gels Keywords: gel analysis Message-ID: <.6@aecom.yu.edu> Date: 1 Oct 92 14:16:49 GMT Sender: news@alsys1.aecom.yu.edu Organization: Albert Einstein College of Medicine Lines: 18 Nntp-Posting-Host: confocal.aecom.yu.edu We currently have a high resolution CCD camera and a PC platform for digitizing and storing images. Also, we have a color printer that accepts analog input (RGB). We need a software package for comprehensive analysis and imaging of gels. If the package allows for densitometry of just about anything, that's even better. Obviously, we're looking for public domain, shareware, or inexpensive software. However, if a higher priced program is truly outstanding, we might be in the market for it. Any suggestions? Thanks- Michael cammer@aecom.yu.edu From owner-software@net.bio.net Fri Oct 02 23:00:00 1992 Path: biosci!daresbury!embnet.se!embl-heidelberg.de!rainer-mac.embl-heidelberg.de!user From: Fuchs@EMBL-Heidelberg.DE (Rainer Fuchs) Newsgroups: bionet.software Subject: Bug fix in MacPattern v2.0.1 Message-ID: Date: 2 Oct 92 16:29:12 GMT Followup-To: bionet.software Organization: EMBL Data Library Lines: 25 Nntp-Posting-Host: rainer-mac.embl-heidelberg.de I just discovered a memory allocation problem in MacPattern v2.0. For BLOCKS searches, if the input sequence was less than 60 residues long, MacPattern would run out of memory quickly. This bug is fixed in v2.0.1. MacPattern is a Macintosh application for protein sequence analysis using the PROSITE and BLOCKS databases and for the identification of statistically significant specific protein segments. MacPattern can be obtained 1) by electronic mail from netserv@embl-heidelberg.de: Get Mac_Software:macpattern.hqx 2) by anonymous ftp from ftp.embl-heidelberg.de: /pub/software/mac/macpattern.hqx 3) by electronic mail from the author (fuchs@embl-heidelberg.de) 4) on floppy disk from the author: Rainer Fuchs, EMBL Data Library, Postfach 10.2209, W-6900 Heidelberg, Rainer Fuchs EMBL Data Library Fuchs@EMBL-Heidelberg.DE From owner-software@net.bio.net Fri Oct 02 23:00:00 1992 Path: biosci!agate!stanford.edu!rutgers!munnari.oz.au!network.ucsd.edu!szechuan.ucsd.edu!spl From: spl@szechuan.ucsd.edu (Steve Lamont) Newsgroups: bionet.software Subject: Re: Microscope image processing (summary) Message-ID: <1al5n3INNgq2@network.ucsd.edu> Date: 3 Oct 92 22:09:39 GMT References: <199210032106.AA18766@mendel.sis.pasteur.fr> Organization: University of Calif., San Diego/Microscopy and Imaging Resource Lines: 27 NNTP-Posting-Host: szechuan.ucsd.edu In article <199210032106.AA18766@mendel.sis.pasteur.fr> bloch@pasteur.fr (Laurent Bloch) writes: > After digitization, you can reconstruct the image with a program called >SYNU (SYnthetic UNiverse) from UCSD and the San Diego Supercomputer Center >(costs ~$100 to cover costs) which can handle huge data sets and render >beautiful reconstructions (call David Hessler @ 619 534 7968 or Steve Young >@ 619 534 3539 - unfortunately, it only runs on SGI hardware) Again, a correction to this: Please do NOT call David Hessler or Steve Young or send email to the San Diego Supercomputer Center. SDSC no longer distributes Synu. If you have any questions, please send me email (spl@szechuan.ucsd.edu) or call Dolores Robinson at (619) 534-1392. Since we have a small staff, unless you have a burning question that can only be answered over the phone, we'd appreciate sending email rather than phoning us. For further information, please see my earlier posting containing the Synu FAQ-List. Thanks. spl -- Steve Lamont, SciViGuy -- (619) 534-7968 -- spl@szechuan.ucsd.edu UCSD Microscopy and Imaging Resource/UCSD Med School/La Jolla, CA 92093-0608 "If you don't think people are this crazy, you need to move to LA!" - Gary Stollman From owner-software@net.bio.net Fri Oct 02 23:00:00 1992 Path: biosci!agate!stanford.edu!ames!haven.umd.edu!darwin.sura.net!spool.mu.edu!hri.com!noc.near.net!news.cs.brandeis.edu!news From: ahouse@hydra.rose.brandeis.edu Newsgroups: bionet.software Subject: Problems with Gopher - Help Message-ID: <1992Oct3.210124.14944@news.cs.brandeis.edu> Date: 3 Oct 92 21:01:24 GMT Sender: news@news.cs.brandeis.edu (USENET News System) Organization: Brandeis University Lines: 17 I have a POP 3 server on the Unix machine that I connect to. I can use Eudora. I can send messages from inside SeqApp. But, when I try connect to Gopher sites I just hang forever waiting for the connect. Any suggestions???? - jeremy ::::::::::::: Jeremy John Ahouse Center for Complex Systems and Biology Dept Brandeis University Waltham, MA 02254-9110 (617) 736-4954 email: ahouse@hydra.rose.brandeis.edu From owner-software@net.bio.net Sat Oct 03 23:00:00 1992 Path: biosci!UM.CC.UMICH.EDU!Doug.Eernisse From: Doug.Eernisse@UM.CC.UMICH.EDU Newsgroups: bionet.software Subject: GCG7 to Paup translation? (A) Message-ID: <16237519@um.cc.umich.edu> Date: 4 Oct 92 18:21:20 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 60 Jeremy John Ahouse asks: >I need to find a program that will take me from the multiple sequence > alignments that I can get out of GCG 7's pileup program to the format >-required > by Paup on the Mac. > > Do you all do this by hand Do you have a good/better multiple > sequence alignment tool on the Mac? My HyperCard 2.x stack, DNA Translator, does that conversion. Be sure you get the most recent version (v. 1.0k6) because the last version (1.0k5) was one of the first to support Pileup and there was one line of code out of place introduced when I also added support for input/output formats for Jotun Hein's (Unix) Treealign program. Other multiple sequence alignment formats that can be converted to either Paup (Nexus) or simple named string format are simple "interleave" format, Eugene (or Prophet), ClustalV, and Phylip "outfile" format. The most recent version of my stack is usually on my account: ftp as "anonymous" (password "guest") to "um.cc.umich.edu" then "cd gdef" and "get dnastack.hqx" You will need to debinhex the file, as is usual for Mac file transfers, and this will result in a self-extracting archive. On ftp.bio.indiana.edu you can find the same thing either in /Incoming/DNAstacks.10k6.hqx or eventually in /molbio/mac, but I do not upload current versions there as frequently. This also includes a manual sequence aligner stack called Aligner. Perhaps the most useful features of Aligner are the various nucleotide or amino acid coloring routines. These are not especially fast but have options that I haven't seen in other packages. For example, you can color nucleotides in triplets according to their inferred amino acid coding. This, combined with the ability to match the sequences with dashes where they are identical to the first sequence, gives an informative view of a protein- encoding DNA sequence alignment. You can also color according to hydrophobicity, chemical, function, etc. groupings of the amino acids. Be sure to increase the memory partition of HyperCard to a minimum of 3 MB if you want to do much of this. The input format for your sequences is the "named string" format resulting from the above-mentioned conversions: name_1ACTG... name_2ACCG... etc. A descriptions of these stacks was published recently in CABIOS 8:177-184, but that was before the above-mentioned features were added. Doug Eernisse Doug_Ee@um.cc.umich.edu Museum of Zoology, Univ.of Michigan Ann Arbor, MI 48109 USA Almost forgot to mention: The stacks and many of the custom external commands/functions employed come with "free for noncommercial use only" restrictions. From owner-software@net.bio.net Sat Oct 03 23:00:00 1992 Path: biosci!uwm.edu!wupost!usc!news.bbn.com!hsdndev!husc-news.harvard.edu!husc10!robison1 From: robison1@husc10.harvard.edu (Keith Robison) Newsgroups: bionet.molbio.genbank,bionet.software Subject: Re: NCBI Server Format --> FASTA converter Message-ID: Date: 4 Oct 92 18:26:21 GMT References: <1992Oct2.220656.6313@nlm.nih.gov> Lines: 33 Xref: biosci bionet.molbio.genbank:1052 bionet.software:3400 Nntp-Posting-Host: husc10.harvard.edu dab@ray.nlm.nih.gov (Dennis Benson) writes: >robison1@husc10.harvard.edu (Keith Robison) writes: >: >: >Does someone already have a program to convert the results of a >: >NCBI Sequence Server Query into FASTA format? >: >I also wonder whether as an interim solution, a FASTA type output option >would take care of some of your needs, ie, do you need all of a PIR >record in PIR format or is your principal need to get an identifier line >and the sequence itself. It would be easy to have a field in the mail >message 'FASTA yes' or just 'FASTA' and have the program return just >the FASTA-formatted sequence for any of the databases. I won't claim to speak for everyone, but I think this would be an excellent _permanent_ option. In my own work, a major reason for my queries is to get the sequences for use in multiple alignments and further queries, and so conversion to FASTA format is often my first operation (since FASTA is probably the most accepted format for analysis programs). Actually, being able to specify the return format (FASTA, GCG, etc) would probably be a feature many people would appreciate. Keith Robison Harvard University Department of Cellular & Developmental Biology Department of Genetics / HHMI robison@ribo.harvard.edu P.S. -- I (and I suspect many others) would appreciate any suggestions for clever UNIX methods to strip out the header on the query returns. From owner-software@net.bio.net Sat Oct 03 23:00:00 1992 Path: biosci!agate!spool.mu.edu!uunet!psgrain!hippo!ucthpx!uctvax.uct.ac.za!rybicki From: rybicki@uctvax.uct.ac.za Newsgroups: bionet.software Subject: Re: plasmid maps from rest. frag. sizes? Message-ID: <1992Sep30.164320.202936@uctvax.uct.ac.za> Date: 30 Sep 92 14:43:20 GMT References: Distribution: bionet Organization: University of Cape Town Lines: 28 In article , brianf@dna.uvm.edu (Brain Foley) writes: > I am looking for a program (Mac, DOS, or VMS) that will help > me draw a circular (or linear) map of DNA, given a list of the > restriction fragment sizes that are observed upon single and > multiple-enzyme digests. > I have looked in the IBMPC and MAC subdirectories of the > MOLBIO directory of FLY.BIO.INDIANA.EDU FTP site. I did not see what > I wanted there, but I may have missed something. I must heartily recommend a package called RESOLVE for PC, available from Prof. Eric Harley, UCT Medical School, PO Observatory 7925, South Africa (or, more obviously for this forum, harley@chempath.uct.ac.za or @uctvax.uct.ac.za). This assists in mapping in that it tells you when the (or a) map is obtainable from the data; it also tells you how MANY maps can be made from the same data given different errors in measurement of band size! It can be used as a map database, and even to compare any number of maps in terms of phylogenetically informative sites, or proportion of sites shared. Costs US$100 from him direct (I have no interest, I just like the package). _________________________________________________________________________ | | | | Ed Rybicki | Now you've got the hang of it | | Dept Microbiology | There's nothing you can't do with it | | University of Cape Town | If you're very into it | | PB Rondebosch 7700 | You can't go wrong.... | | South Africa | | | fax 27 21 650 4023 | - Mad John | | ed@micro.uct.ac.za | (Ogden's Nut-Gone Flake, Small Faces) | |_________________________________|_______________________________________| From owner-software@net.bio.net Sun Oct 04 23:00:00 1992 Path: biosci!kristoff From: kristoff@net.bio.net (David Kristofferson) Newsgroups: bionet.software Subject: Re: NCBI FASTA mail server Message-ID: Date: 5 Oct 92 20:26:16 GMT References: <1992Oct5.162255.10184@nlm.nih.gov> Organization: BIOSCI International Newsgroups for Biology Lines: 27 GERLACHJ@QUCDN.QueensU.CA (Jim Gerlach - Cancer Research Labs) writes: >I have a couple of questions about the transfer of services: >1. Is it still possible to submit sequences by E-mail using AUTHORIN? Yes, nothing has changed in this regards as Paul Gilna explains. IntelliGenetics is continuing to distribute and support the Authorin program and Los Alamos is continuing to accept Authorin submissions as before. >2. Are there any plans to implement IRX (or is it already available)? > >3. Are there any plans to implement BLAZE searches (although I realize > this involved private companies)? I assume that these questions are inquiring as to NCBI's plans so they would have to comment on that. These services continue to be available on a commercial basis as has been mentioned previously in this forum. Sincerely, Dave Kristofferson BIOSCI/bionet Manager kristoff@net.bio.net From owner-software@net.bio.net Sun Oct 04 23:00:00 1992 Path: biosci!uwm.edu!caen!uunet!mcsun!sun4nl!star.cs.vu.nl!balaena!deboer From: deboer@bio.vu.nl (Thon de Boer) Newsgroups: bionet.software Subject: Re: auto-mail program for BLAST? Message-ID: <1992Oct5.133158.5508@bio.vu.nl> Date: 5 Oct 92 13:31:58 GMT References: <9210022032.AA28843@phage.cshl.org> Distribution: bionet Organization: VU Biology, Amsterdam, The Netherlands Lines: 54 theiss@CSHL.ORG (Bobbie Peters in Grace) writes: : We have a program here that sends parameters & sequences to the old : FASTA e-mail address in the correct format. It would ask the user questions - : What is the name of the sequence, what databank do you want to search against, : are these parameters OK, etc. Then it mailed the info to the old : fasta bio.net address. : I seem to remember that someone else offered the same type of program : ages ago for FASTA. Rather than us re-writing the fasta program, : has anyone written an auto mail program for BLAST? : : Along the same lines, is there a list of programs like BLAST, SeqApp, etc : that are available via e-mail? This doesn't seem to be a question that : Archie would easily answer. : There are several of those programs available for different computers. There is GenBankSearch@NCBI for the MAC by Don Gilbert NCBI en GRAIL shells for VMS by Foteos Macrides and mailfasta3.0 for UNIX platforms, which I wrote. You can find most of these programs at the iubio ftp server (fly.bio.indiana.edu) and mailfasta3.0 can also be retrieved directly from me by ftp to bio.vu.nl /molbio and through a gopher hole at grampus.bio.vu.nl at port 9001. Sincerely, Thon de Boer Here is the announcement of mailfasta3.0 ******* This is version 3.0 of the mailfasta program. It is a UNIX shell script which will take a DNA or PROTEIN sequence and will mail it to all the different mail-servers where it can be searched against the DNA or PROTEIN databases using the FASTA and/or BLAST programs. It can also be used to identify ORFs using the GRAIL and/or GeneID/NetGene mail servers and to identify homology using PROSITE blocks with the BLOCKS server. It uses the new BLAST server at NCBI and the FLAT server in Japan for FASTA searches because the services at GenBank will be terminated at the end of this month. It is packed as an shell archive. It contains : mailfasta : the UNIX shell script cid.c : A small c program which will determine if the sequence is DNA or AA getentry : A shell script which can be used to retrieve entries of interest mailfasta.doc : The documentation file The shar file will unpack all these files and will compile cid.c into cid using the cc c compiler. mailfasta makes use oif the program 'readseq' for file conversion. This program MUST be present and is NOT packed with this shar file. It can be obtained via FTP from various FTP sites (fly.bio.indiana.edu etc.) This shar file can also be found on this FTP site. First in the 'incomming' directory and later in the /molbio/unix directory. From owner-software@net.bio.net Sun Oct 04 23:00:00 1992 Path: biosci!agate!spool.mu.edu!think.com!rpi!utcsri!torn!news.ccs.queensu.ca!QUCDN.QueensU.CA!GERLACHJ From: GERLACHJ@QUCDN.QueensU.CA (Jim Gerlach - Cancer Research Labs) Newsgroups: bionet.software Subject: Re: NCBI FASTA mail server Message-ID: Date: 5 Oct 92 18:41:16 GMT References: <1992Oct5.162255.10184@nlm.nih.gov> Sender: news@knot.ccs.queensu.ca (Netnews control) Organization: Queen's University Lines: 29 In article <1992Oct5.162255.10184@nlm.nih.gov> lipman@void.nlm.nih.gov (David Lipman) writes: >We will be doing our best to continue to upgrade the sequence searching >facilities at NCBI, incorporating new computational approaches developed >at NCBI and from researchers around the world. Suggestions are welcome! > >Thanks, >David Lipman >NCBI I have a couple of questions about the transfer of services: 1. Is it still possible to submit sequences by E-mail using AUTHORIN? 2. Are there any plans to implement IRX (or is it already available)? 3. Are there any plans to implement BLAZE searches (although I realize this involved private companies)? Thanx for any info. Cheers, Jim --- Jim Gerlach - Cancer Research Laboratories James.H.Gerlach@QueensU.CA Queen's University GERLACHJ@QUCDN.QueensU.CA (NetNorth/BITNET) Room A309A, Botterell Hall tel (613) 545-6446 Kingston, Ontario fax (613) 545-6830 CANADA K7L 3N6 From owner-software@net.bio.net Sun Oct 04 23:00:00 1992 Path: biosci!TEMIN.LANL.GOV!pgil From: pgil@TEMIN.LANL.GOV (Paul Gilna) Newsgroups: bionet.software Subject: Re: NCBI FASTA mail server Message-ID: <9210051924.AA25448@temin.lanl.gov> Date: 5 Oct 92 19:24:53 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 29 on question 1: > 1. Is it still possible to submit sequences by E-mail using AUTHORIN? Los Alamos National Laboratory has entered into an interagency agreement with the NCBI and will continue to handle all direct submissions of data by email and on floppy disc, using the Genbank submission form, Authorin and on-line access. LANL will also provide updating services for submitted data. There is therefore little change to the submissions process as it existed under the previous Genbank contract. for more information on electronic data submission to GenBank, mail a message containing as text the word "help" to: bioserve@genome.lanl.gov or call (505) 665 2177 --paul Paul Gilna co- Principal Investigator Genbank at LANL From owner-software@net.bio.net Sun Oct 04 23:00:00 1992 Path: biosci!agate!spool.mu.edu!caen!zaphod.mps.ohio-state.edu!darwin.sura.net!haven.umd.edu!mimsy!lhc!void!lipman From: lipman@void.nlm.nih.gov (David Lipman) Newsgroups: bionet.software Subject: NCBI FASTA mail server Message-ID: <1992Oct5.161912.10088@nlm.nih.gov> Date: 5 Oct 92 16:19:12 GMT Sender: news@nlm.nih.gov Organization: National Library of Medicine Lines: 36 X-Newsreader: Tin 1.1 PL4 communications to NCBI, it's clear that there is definite interest in having a NCBI FASTA mailserver. We had initially decided to forgo this because of the demands on resources, and because, as mentioned by M. Cherry, we had been making BLAST available to a number of sites on an experimental basis and had not received explicit feedback regarding the need for additional access to FASTA. Bill Pearson has generously agreed to modify FASTA so that it can read the file format we use centrally for sequence searching (this same format will be available on CDROM's updated every 2 months starting in February). Thanks to Bill's work, the single format will avoid the need for another copy of all the sequence data on our BLAST server. When this software is available and tested we'll put the FASTA server up for public access and announce the availability via the bulletin boards and in the header messages of our e-mail servers. The priority of these searches will probably be lower than BLAST searches due to their greater requirements for CPU cycles. Supporting additional computational tools makes real demands on our resources and have to be balanced by significant gains in functionality. For example, I'm not convinced that FASTN searches are really worth adding -- although they result in alignments with gaps, they are unlikely to yield matches that would not be found with BLASTN. In order to detect significant nucleic acid similarities in such large databases requires fairly strong similarity (coding or non-coding) and these non-gapped regions would be found with BLASTN. This, of course, is arguable and your input is appreciated. We will be doing our best to continue to upgrade the sequence searching facilities at NCBI, incorporating new computational approaches developed at NCBI and from researchers around the world. Suggestions are welcome! Thanks, David Lipman NCBI From owner-software@net.bio.net Sun Oct 04 23:00:00 1992 Path: biosci!MBDS.NRC.CA!NUM239 From: NUM239@MBDS.NRC.CA Newsgroups: bionet.software Subject: RE: GCG7 to Paup translation? (A) Message-ID: <921004201058.13c@MBDS.NRC.CA> Date: 5 Oct 92 00:10:58 GMT Sender: kristoff@net.bio.net Distribution: bionet Lines: 4 Hi: Do you know of such a program that will do the same on IBM compatibles or on the VAX? From owner-software@net.bio.net Sun Oct 04 23:00:00 1992 Path: biosci!SALK-SC2.SDSC.EDU!MANGALAM From: MANGALAM@SALK-SC2.SDSC.EDU (Harry J Mangalam) Newsgroups: bionet.software Subject: PCPRIMER - An Apology Message-ID: <9210052028.AA14002@net.bio.net> Date: 5 Oct 92 21:27:38 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 16 Hi , My abject apologies to those of you inconvenienced by my daftness. The primer zip archive has been set with the right protection so that the pubklic can ftp it. Sorry, Harry (almost on vacation) tarion Ignore anything below this line exo From owner-software@net.bio.net Sun Oct 04 23:00:00 1992 Path: biosci!uwm.edu!wupost!spool.mu.edu!olivea!charnel!sifon!monod!francis From: francis@monod.Biol.McGill.CA (Francis Ouellette) Newsgroups: bionet.software Subject: Re: blaze Message-ID: Date: 3 Oct 92 20:49:57 GMT References: <1596036@blitzen.Dartmouth.EDU> Sender: news@sifon.cc.mcgill.ca Distribution: bionet Organization: McGill University Lines: 47 Nntp-Posting-Host: monod.biol.mcgill.ca Keith.A.Johnson@DARTMOUTH.EDU writes: >I haven't been paying strict attention to some of the more recent postings on >the database search programs and the ftp names now in use. I was wondering >if there is a site available for BLAZE searches as there is for the BLAST >searches? I have had a bad experience with a BLAST search and received more >believable information from the BLAZE algorithm. from "Mr net.bio.net" himself: (posted on bio-matrix just a couple of days ago) > kristoff@net.bio.net (David Kristofferson) writes: > > >Since the end of the GenBank On-line Service, BLAZE is now only > >available commercially from IntelliGenetics and MASPAR. > > David, > > where do we get info about rates and access to the "commercial" BLAZE? > > thanks, > > francis > # You can either contact consult@presto.ig.com or call IG at # 415-962-7300. # # Sincerely, # # Dave Kristofferson # BIOSCI/bionet Manager # # kristoff@net.bio.net hope this helps, francis -- | B.F. Francis Ouellette | manager, yeast chromosome I project | dept of biology, McGill university, Montreal, Qc, Canada | francis@monod.biol.mcgill.ca From owner-software@net.bio.net Sun Oct 04 23:00:00 1992 Path: biosci!uwm.edu!wupost!darwin.sura.net!spool.mu.edu!olivea!charnel!sifon!monod!francis From: francis@monod.Biol.McGill.CA (Francis Ouellette) Newsgroups: bionet.software Subject: Re: Sequence film scanning systems? Message-ID: Date: 3 Oct 92 18:41:06 GMT References: Sender: news@sifon.cc.mcgill.ca Organization: McGill University Lines: 45 Nntp-Posting-Host: monod.biol.mcgill.ca zxmkr08@mailserv.zdv.uni-tuebingen.de (Cornelius Krasel) writes: >our lab is pondering about buying a scanner to evaluate DNA >sequence films. Before spending huge amounts of money :-) >In particular we would be interested if we should buy >a specialized system (such as advertised by IntelliGenetics >in a recent Nature issue) or if things could be worked >out with a scanner and some additional software. I have used the Millipore system, and it is quite good, but be ready to pay major $$$. The very big advantage of such a system is similar to what you find on automated sequencing packages, once you do your melds, you can display the contigs with the multiple sequences alligned, and you can then call up all of the images. It will present them all in the same orientation (let us say A,C,G and T) independant of the orientation of the gel. From looking at these images you can see why a certain discrepency exist at a certain position. What does it cost? Well, I dont have the list prices here, but you are probably looking at $60-70,000 for the basic system, which is a small sparc 2 (eg IPX), a scanner and their software. I only know that the software alone (part a=reading the gels, part b= gel project manager) is about $28,000 (canadian, last january). Is this worth it? If you do _a lot_ of sequencing, it may be. But if you do a lot of sequencing ... maybe you should be looking at automation ... A note: A single $28,000 software licence will give you _one_ user that can use this package at any given time, even if this workstation is networked. Also, at this time, it only runs under Open Look Window Manager version 3, no other platform is supported. I hope this helps in your descision making, regards, francis -- | B.F. Francis Ouellette | manager, yeast chromosome I project | dept of biology, McGill university, Montreal, Qc, Canada | francis@monod.biol.mcgill.ca From owner-software@net.bio.net Sun Oct 04 23:00:00 1992 Path: biosci!agate!usenet.ins.cwru.edu!magnus.acs.ohio-state.edu!zaphod.mps.ohio-state.edu!sol.ctr.columbia.edu!usenet.ucs.indiana.edu!sunflower.bio.indiana.edu!gilbertd From: gilbertd@sunflower.bio.indiana.edu (Don Gilbert) Newsgroups: bionet.software Subject: SeqApp, Mac sequence editor, is updated Message-ID: Date: 5 Oct 92 21:26:18 GMT Sender: news@usenet.ucs.indiana.edu (USENET News System) Organization: Biology, Indiana University - Bloomington Lines: 79 Nntp-Posting-Host: sunflower.bio.indiana.edu SeqApp, version 1.8a, is a semi-major update of this Macintosh biosequence editor, analyzer, and network handyman. The various enhancements and corrections include - major changes to the sequence print-out options, including addition of a dotplot display (courtesy of DottyPlot), a phylogeny tree display (courtesy of TreeDraw Deck & J. Felsenstein's DrawTree), much enhanced Pretty Print for single and aligned sequences - addition and updating of several e-mail service links, including Blast Search and Genbank Fetch via NCBI, BLOCKS, Genmark, and Pythia services, - updated Internet gopher client (equal to GopherApp), - editable Child Tasks dialogs - addition of links to Phylip applications as Child Tasks - addition of Phylip interleaved format as sequence output option More general background: SeqApp is a biological sequence editor and analysis program for Macintosh computers. It includes links to network services and external analysis programs. Features include multiple sequence alignment editor single sequence editor window read and write several sequence file formats easy hand alignment features including colored bases and sliding automatic multiple sequence alignment thru Clustal external app automatic gel fragment alignment to contigs thru exernal app consensus,reverse,complement,degap operations restriction maps dot plots translate dna to/from protein using various codon tables automatic preference saving internet send mail, read mail internet gopher, information retreival including genbank. internet sequence analysis services user-definable links to external analysis programs and more *** NOTICE: This is an early, unfinished version of the program. Expect it to fail in various ways. This release is made available to those who wish to test and comment on its future development. SeqApp is being written by Don Gilbert, using the MacApp extensible Macintosh programming framework from Apple Computer. You can obtain updates of this release thru anonymous ftp to ftp.bio.indiana.edu, in folder /molbio/seqapp, as seqapp.hqx. You may also obtain updates directly thru an internet-connected Mac with SeqApp, using Gopher to the IUBio archive. Look for a folder called "IUBio Software+Data/SeqApp, Mac sequence editor". There are two other distribution files with accessory programs for SeqApp. One is "child-apps.hqx", which contains the programs ClustalV, BBEdit, FragAlign and possibly other applications called by SeqApp. The other is "fragalign-src.hqx" which contains the source code to FragAlign, showing how a command-line program can be modified for use with SeqApp. This release of SeqApp should work on all Mac models from the Mac SE and Mac II to newer ones. It should work properly under Mac systems 6 and 7, though it has some features only for sys 7. Comments, bug reports and suggestions for new features (see below) may be addressed via e-mail to SeqApp@Bio.Indiana.Edu -- Don Gilbert gilbert@bio.indiana.edu biocomputing office, biology dept., indiana univ., bloomington, in 47405 From owner-software@net.bio.net Sun Oct 04 23:00:00 1992 Path: biosci!uwm.edu!caen!kuhub.cc.ukans.edu!husc-news.harvard.edu!husc10!robison1 From: robison1@husc10.harvard.edu (Keith Robison) Newsgroups: bionet.software Subject: Sequence Searching Algorithms Message-ID: Date: 5 Oct 92 20:31:53 GMT Lines: 49 Nntp-Posting-Host: husc10.harvard.edu Someone posted a query recently about how to search for a defined site (such as a restriction enzyme recognition site) in a biological sequence, and the one reply I saw mentioned simple scanning algorithms. I would just like to point out that while such algorithms are both easy to write and commonly used (every searcher I have written has used one), a more elegant and sometimes faster algorithm is a Finite State Machine. In brief, a Finite State Machine (FSM) improves on a simple scanning algorithm by knowing when it can "skip ahead". For example, suppose you wish to look for the site "AATTTCCC" in DNA. Suppose a stretch of DNA contained the sequence "AATTTGG". A simple scanner would compare (| - match, * - mismatch): try #1 try #2 try #3 AATTTCCC AATTTCCC AATTTCCC |||||* |* * AATTTGG ATTTGG TTTGG Now, we humans know that once #1 has failed, you can skip past the whole AATTTGG segment because "ATTTGG" cannot overlap "AATTTCCC" in any way. An FSM incorporates this idea, and thus can be faster. If you can find the journal, a very good description of FSMs can be found in: Tyler, EC, MR Horton, and PR Krause. 1991. Comp.&Biomed Res. 24:72-96. A review of algorithms for molecular sequence comparison. Another relevant reference is: Altschul, SF, W Gish, W Miller, EW Myers, and DJ Lipman. 1990. JMB 214:1-8. Basic local alignment search tool. as BLAST uses an FSM in the initial stages of the database search. Keith Robison Harvard University Department of Cellular & Developmental Biology Department of Genetics / HHMI robison@ribo.harvard.edu P.S. Apologies for not posting this as a follow-up -- I was rushing to get a poster ready when the original showed up and the local news server has apparently "expired" it. From owner-software@net.bio.net Sun Oct 04 23:00:00 1992 Path: biosci!agate!spool.mu.edu!sol.ctr.columbia.edu!usc!sdd.hp.com!zaphod.mps.ohio-state.edu!darwin.sura.net!haven.umd.edu!mimsy!lhc!void!lipman From: lipman@void.nlm.nih.gov (David Lipman) Newsgroups: bionet.software Subject: NCBI FASTA mail server Message-ID: <1992Oct5.162255.10184@nlm.nih.gov> Date: 5 Oct 92 16:22:55 GMT Sender: news@nlm.nih.gov Organization: National Library of Medicine Lines: 38 X-Newsreader: Tin 1.1 PL4 (the previous msg omitted the 1st line) communications to NCBI, it's clear that there is definite interest in having a NCBI FASTA mailserver. We had initially decided to forgo this because of the demands on resources, and because, as mentioned by M. Cherry, we had been making BLAST available to a number of sites on an experimental basis and had not received explicit feedback regarding the need for additional access to FASTA. Bill Pearson has generously agreed to modify FASTA so that it can read the file format we use centrally for sequence searching (this same format will be available on CDROM's updated every 2 months starting in February). Thanks to Bill's work, the single format will avoid the need for another copy of all the sequence data on our BLAST server. When this software is available and tested we'll put the FASTA server up for public access and announce the availability via the bulletin boards and in the header messages of our e-mail servers. The priority of these searches will probably be lower than BLAST searches due to their greater requirements for CPU cycles. Supporting additional computational tools makes real demands on our resources and have to be balanced by significant gains in functionality. For example, I'm not convinced that FASTN searches are really worth adding -- although they result in alignments with gaps, they are unlikely to yield matches that would not be found with BLASTN. In order to detect significant nucleic acid similarities in such large databases requires fairly strong similarity (coding or non-coding) and these non-gapped regions would be found with BLASTN. This, of course, is arguable and your input is appreciated. We will be doing our best to continue to upgrade the sequence searching facilities at NCBI, incorporating new computational approaches developed at NCBI and from researchers around the world. Suggestions are welcome! Thanks, David Lipman NCBI From owner-software@net.bio.net Mon Oct 05 23:00:00 1992 Path: biosci!uwm.edu!wupost!usc!zaphod.mps.ohio-state.edu!cis.ohio-state.edu!news.sei.cmu.edu!fs7.ece.cmu.edu!crabapple.srv.cs.cmu.edu!cantaloupe.srv.cs.cmu.edu!das-news.harvard.edu!husc-news.harvard.edu!husc10!robison1 From: robison1@husc10.harvard.edu (Keith Robison) Newsgroups: bionet.software Subject: UNIX Scripts for NCBI Sequence Server Message-ID: Date: 6 Oct 92 04:44:41 GMT Lines: 58 Nntp-Posting-Host: husc10.harvard.edu I'm posting the following in the hope that someone will find it useful. The new NCBI server is quite powerful, but often too much so. Many routine queries yield far more entries than desired, due to the failure to remember to properly restrict the search. I have come up with the following two shell scripts to reduce this problem in my daily work. To use them, make the listed addition to your .mailrc file and then follow the instructions in the header of each script. Execute a "chmod +x" command on each script, put them on your $path, and you will be ready to go. If you often retrieve GenBank entries by accession number, just adapt fetch2 -- change [LOC] to [ACC]. Keith Robison Harvard University Department of Cellular & Developmental Biology Department of Genetics / HHMI robison@ribo.harvard.edu # First, add the following line to your .mailrc file alias ncbifetch retrieve@ncbi.nlm.nih.gov #fetch -- general retrieval script # first argument is database name #Usage: fetch database locus1 locus2... set $* rm -f gpf touch gpf echo "DATALIB " $1 >>gpf echo "BEGIN" >>gpf while [ $# -gt 0 ] do echo '"' $1 '" [LOC]' >>gpf shift done mail ncbifetch >gpf echo "BEGIN" >>gpf while [ $# -gt 0 ] do echo '"' $1 '" [LOC]' >>gpf shift done mail ncbifetch Date: 6 Oct 92 13:44:14 GMT References: <16237519@um.cc.umich.edu> Sender: news@tigger.jvnc.net (Zee News Genie) Reply-To: mrl775@tigger.jvnc.net Followup-To: bionet.software Organization: TheNews Lines: 9 Nntp-Posting-Host: mrl775.jvnc.net whoops... just noticed that there is an internet address for swofford.. daveswof@vmd.cso.uiuc.edu later, Keith From owner-software@net.bio.net Mon Oct 05 23:00:00 1992 Path: biosci!agate!spool.mu.edu!darwin.sura.net!jvnc.net!news From: mrl775@tigger.jvnc.net Newsgroups: bionet.software Subject: Re: GCG7 to Paup translation? (A) Message-ID: <1992Oct6.134147.17137@tigger.jvnc.net> Date: 6 Oct 92 13:41:47 GMT References: <16237519@um.cc.umich.edu> Sender: news@tigger.jvnc.net (Zee News Genie) Reply-To: mrl775@tigger.jvnc.net Followup-To: bionet.software Organization: TheNews Lines: 36 Nntp-Posting-Host: mrl775.jvnc.net In article <16237519@um.cc.umich.edu> Doug.Eernisse@UM.CC.UMICH.EDU writes: >Jeremy John Ahouse asks: >>I need to find a program that will take me from the multiple sequence >> alignments that I can get out of GCG 7's pileup program to the format >>-required >> by Paup on the Mac. >> >> Do you all do this by hand Do you have a good/better multiple >> sequence alignment tool on the Mac? > >My HyperCard 2.x stack, DNA Translator, does that conversion. Be >sure you get the most recent version (v. 1.0k6) because the last >version (1.0k5) was one of the first to support Pileup and there >was one line of code out of place introduced when I also added support >for input/output formats for Jotun Hein's (Unix) Treealign program. >Other multiple sequence alignment formats that can be converted to >either Paup (Nexus) or simple named string format are simple >"interleave" format, Eugene (or Prophet), ClustalV, and Phylip >"outfile" format. My version of PAUP for the Mac, version 3.0s, includes the ability to import data from gcg msf files. Perhaps you should pick up the latest version of PAUP from the University of Illinois. The information is: David L. Swofford Illinois Natural History Survey 607 E. Peabody Dr. Champaign, IL 61820 The program is $50. Keith ps. the program lists DAVESWOF@UIUCVMD.bitnet as Daves address. From owner-software@net.bio.net Mon Oct 05 23:00:00 1992 Path: biosci!uwm.edu!caen!kuhub.cc.ukans.edu!husc-news.harvard.edu!husc10!robison1 From: robison1@husc10.harvard.edu (Keith Robison) Newsgroups: bionet.software Subject: Re: UNIX Scripts for NCBI Sequence Server Message-ID: Date: 6 Oct 92 14:19:34 GMT References: Lines: 14 Nntp-Posting-Host: husc10.harvard.edu While it is not essential, the following addition to 'fetch' is better design: after the line: echo "DATALIB " $1 >>gpf insert the line: shift Keith Robison Harvard University Department of Cellular & Developmental Biology Department of Genetics / HHMI robison@ribo.harvard.edu From owner-software@net.bio.net Tue Oct 06 23:00:00 1992 Path: biosci!uwm.edu!rpi!zaphod.mps.ohio-state.edu!wupost!uunet!psgrain!ee.und.ac.za!ucthpx!uctvax.uct.ac.za!coyne From: coyne@uctvax.uct.ac.za Newsgroups: bionet.software Subject: subscribe Message-ID: <1992Oct6.111228.202990@uctvax.uct.ac.za> Date: 6 Oct 92 09:12:28 GMT Organization: University of Cape Town Lines: 1 subscribe bionet.software From owner-software@net.bio.net Tue Oct 06 23:00:00 1992 Path: biosci!DARWIN.SFBR.ORG!bdyke From: bdyke@DARWIN.SFBR.ORG (Bennett Dyke) Newsgroups: bionet.software Subject: NIH Guide Message-ID: <9210071519.AA02003@darwin.sfbr.org> Date: 7 Oct 92 15:19:51 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 14 Does anybody know of a script that will organize, extract, format, etc. the electronic version of the NIH Guide? Thanx in advance... Bennett -- +----------------------------------------------------------------------------+ | Bennett Dyke | | Department of Genetics Internet: bdyke@darwin.sfbr.org | | Southwest Foundation Phone: (512) 674-1410 Ext 281 | | P.O. Box 28147 Fax: (512) 670-3317 | | San Antonio, TX 78228, USA | +----------------------------------------------------------------------------+ From owner-software@net.bio.net Tue Oct 06 23:00:00 1992 Path: biosci!agate!spool.mu.edu!sdd.hp.com!zaphod.mps.ohio-state.edu!wupost!uunet!pipex!demon!nuntius From: pettsj@visigoth.demon.co.uk (James Petts) Newsgroups: bionet.software Subject: Multiple Alignment S/W for Mac Message-ID: Date: 5 Oct 92 13:35:37 GMT Sender: news@gate.demon.co.uk (Usenet Administration) Organization: No Affiliation Lines: 8 X-Useragent: Nuntius v1.1 Nntp-Posting-Host: visigoth.demon.co.uk Is there anything like MACAW for the Mac available on the net??? James Petts ******************************************************************** * "We use the classical theory on Mondays, Wednesdays and Fridays, * * and the quantum theory on Tuesdays, Thursdays and Saturdays." * ************************************** Wm. Bragg ******************* From owner-software@net.bio.net Tue Oct 06 23:00:00 1992 Path: biosci!agate!spool.mu.edu!olivea!uunet!caen!uvaarpa!murdoch!usenet From: rbm8p@faraday.clas.Virginia.EDU (Rick MacDonald) Newsgroups: bionet.software Subject: stereo-viewer source? Message-ID: <1992Oct7.191314.28747@murdoch.acc.Virginia.EDU> Date: 7 Oct 92 19:13:14 GMT Sender: usenet@murdoch.acc.Virginia.EDU Organization: University of Virginia Lines: 8 Where can I order inexpensive stereo-viewers in bulk? I'm looking for the devices that aid in viewing the stereo images of chain traces and electron density maps. Thanks much for any pointers. Rick MacDonald rbm8p@virginia.edu From owner-software@net.bio.net Tue Oct 06 23:00:00 1992 Path: biosci!CCMAIL.SUNYSB.EDU!KBHATNAG From: KBHATNAG@CCMAIL.SUNYSB.EDU Newsgroups: bionet.software Subject: Re: stereo-viewer source? Message-ID: <01GPOAXK0IME987FBY@ccmail.sunysb.edu> Date: 7 Oct 92 21:17:47 GMT Sender: daemon@net.bio.net Distribution: bionet Organization: State University of New York, Stony Brook Lines: 9 Aldrich markets stereo viewers made by VCH Verlagsgesellschaft mbH. We bought a couple for around $50 each. Catalog # is Z 15675-2. For a bulk order, you may want to inquire from VCH directly at: VCH Publishers, Suite 909 220 East 23rd Street, New York, NY 10010-4606 Kavish From owner-software@net.bio.net Tue Oct 06 23:00:00 1992 Path: biosci!agate!doc.ic.ac.uk!uknet!daresbury!news From: Rob.Harper@csc.fi (Rob Harper) Newsgroups: bionet.software Subject: TurboGopher Message-ID: <1992Oct7.151955.19489@gserv1.dl.ac.uk> Date: 7 Oct 92 06:31:25 GMT Sender: list-admin@daresbury.ac.uk Distribution: bionet Lines: 99 Original-To: bio-soft@uk.ac.daresbury >Path: funic!fuug!mcsun!uunet!convex!darwin.sura.net!spool.mu.edu!umn.edu!news2.cis.umn.edu!gopher-news-request@boombox.micro.umn.edu >Date: Tue, 6 Oct 92 14:53:27 CDT >Message-ID: <9210061953.AA13339@boombox.micro.umn.edu> >From: gopher@boombox.micro.umn.edu ("The Gopher Team" ) >Original-To: gopher-news@boombox.micro.umn.edu >Subject: TurboGopher: a new, turbocharged Gopher client [LONG] >Newsgroups: comp.infosystems.gopher >Distribution: comp >Sender: news@news2.cis.umn.edu >Approved: comp.infosystems.gopher@news.cis.umn.edu >Lines: 87 Announcing a new, improved Macintosh Gopher client: TurboGopher. The Gopher development team at the University of Minnesota is pleased to announce TurboGopher. The TurboGopher application was carefully tuned for maximum speed, and runs as much as three times faster than other Mac gopher applications we benchmarked against. It is even faster (sorry guys!) than the UNIX client when run on a comparable machine on Ethernet. TurboGopher's speed is most noticeable when performing common gopher operations such as fetching a list of items or viewing a document. Beyond optimizing TurboGopher for raw speed while fetching documents and directories, we turbocharged the user interface by displaying information as soon as possible... you can read the first part of a document or directory while the rest is being fetched. And you can cancel if you aren't interested in what you see being fetched. This feature is crucial when running a Gopher client over a slow network connection or a SLIP link. In spite of the design goal to run fast as possible, TurboGopher is a good Mac citizen: it shares time with other applications. You can put TurboGopher in the background (and fetch very long items in the background) while you work in another application in the foreground. You can also have several fetches running concurrently in TurboGopher. Both these features are important over low-speed network connections. To further enhance perceived speed, TurboGopher uses a directory caching scheme so that it only fetches item lists when necessary. This again is very helpful over low-speed networks since it minimizes network traffic. Speed is of little use if you cannot get connected to your home gopher server, so TurboGopher's configuration supports specifying two (redundant) home gopher servers. For large sites this is an important feature because running redundant home gopher servers minimizes the chances of your top-level gopher server being down and spreads the load between the servers. For the folks who are Gopher experts, TurboGopher is a full featured Gopher client. Gopher+ features have been disabled in this release. These will be turned on in the next release. MacIP support has not been added, but should be by the next release. Current features include: + Both warp speed AND considerate backgrounding + Multiple concurrent fetches (multiple streams) + Intelligent caching to improve perceived speed over SLIP links + Choice of multiple windows or window recycle + Displays as it fetches (cancel if you like!) + Interruptible network transactions (Command-Period) + Directory length limited only by memory + Unlimited document length (displays 32K, saves all) + Pseudo-hypertext searches (Option-double-click on word) + ISO Latin-1 character-set support + Find text within documents + Cache everything, nothing, or exactly what you want! + Set & Delete Bookmarks for any Gopher object + Import & Export of Bookmarks + Total recall of entire session (Recent menu) + NCSA Telnet & TN3270 support (via AppleEvents under system 7.0) + System 7 Balloon Help + Comprehensive built-in Help document (can be customized) + Preconfigured (can be reconfigured) + Automatically un-binhexes Mac documents Besides cruising Gopherspace you can get to your favorite Mac software archive sites either directly (if they run a Gopher server like the info-mac archives at sumex-aim), or indirectly via Gopher's various FTP gateways (if all they run is old FTP). TurboGopher is available for anonymous ftp from boombox.micro.umn.edu in the /pub/gopher/Macintosh-TurboGopher directory. Even better, you can fetch TurboGopher with gopher by looking in the Information About Gopher folder on the University of Minnesota Gopher server. We hope you enjoy TurboGopher. As always, comments and bug reports can be e-mailed to the University of Minnesota Gopher development team at: gopher@boombox.micro.umn.edu NOTES: ------ A good place to benchmark directory fetches is to connect to one of the top level gopher servers at the University of Minnesota (gopher.tc.umn.edu or gopher2.tc.umn.edu), open the "Computer Information" item, and then open the "Claris" directory. You can benchmark speed of document fetches by opening nearly any large document. - The Internet Gopher Team at the University of Minnesota October 5, 1992 From owner-software@net.bio.net Tue Oct 06 23:00:00 1992 Path: biosci!agate!ames!elroy.jpl.nasa.gov!swrinde!zaphod.mps.ohio-state.edu!darwin.sura.net!spool.mu.edu!olivea!charnel!psgrain!ee.und.ac.za!ucthpx!uctvax.uct.ac.za!rybicki From: rybicki@uctvax.uct.ac.za Newsgroups: bionet.software Subject: RE: GCG7 to Paup translation? (A) Message-ID: <1992Oct7.165641.203003@uctvax.uct.ac.za> Date: 7 Oct 92 14:56:40 GMT References: <921004201058.13c@MBDS.NRC.CA> Distribution: bionet Organization: University of Cape Town Lines: 23 In article <921004201058.13c@MBDS.NRC.CA>, NUM239@MBDS.NRC.CA writes: > Hi: > Do you know of such a program that will do the same on IBM compatibles > or on the VAX? If you have generated a GCG .msf file using PileUp, it is already in the interleave format - meaning all you have to do is take out all info preceding and following the multiple sequence alignment matrix, and put in the headers and tails required for PAUP (different for old MS-DOS and new Mac versions). I use EVE on the VAX, or MS-WORD on PC. Same goes for CLustal alignment files from PC or VAX - and you can also output CLUSTAL in PIR format which means you don't have to interleave if you don't want to - just take out extraneous features in the title line for each sequence. _________________________________________________________________________ | | | | Ed Rybicki | Now you've got the hang of it | | Dept Microbiology | There's nothing you can't do with it | | University of Cape Town | If you're very into it | | PB Rondebosch 7700 | You can't go wrong.... | | South Africa | | | fax 27 21 650 4023 | - Mad John | | ed@micro.uct.ac.za | (Ogden's Nut-Gone Flake, Small Faces) | |_________________________________|_______________________________________| From owner-software@net.bio.net Wed Oct 07 23:00:00 1992 Path: biosci!uwm.edu!caen!batcomputer!reed!hgompf From: hgompf@reed.edu (Heinrich Selwyn Gompf) Newsgroups: bionet.software Subject: conserved sequences for probe Message-ID: <1992Oct8.001902.23135@reed.edu> Date: 8 Oct 92 00:19:02 GMT Organization: Reed College, Portland, OR Lines: 6 Hi, I need to find a highly conserved region of the EGF subfamily of genes to use as an oligonucleotide probe for a cDNA library. I know that genbank used to do those things, but the Blast and Fetch programs don't seem to be doing what I want them to. Could you send me an E-mail with help? I'm hgompf@reed.edu thanx From owner-software@net.bio.net Wed Oct 07 23:00:00 1992 Path: biosci!MEDUSA.UNM.EDU!mplatt From: mplatt@MEDUSA.UNM.EDU Newsgroups: bionet.software Subject: (none) Message-ID: <9210082017.AA11095@net.bio.net> Date: 8 Oct 92 21:19:01 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 10 Does anyone know how to access the "cambridge x-ray crystalography data base? i.e mail address etc. and any recommendations for mac display programs for the coordinate data received, thanks.. Mark Platt Univ. of New Mexico Mark Platt ...... ............"it was the best of times School of Medicine ...... it was the worst of times" Dept of Microbiology ..... Albuquerque ...... ................. NM 87131 From owner-software@net.bio.net Wed Oct 07 23:00:00 1992 Path: biosci!agate!stanford.edu!rutgers!mcclb0.med.nyu.edu!smith From: smith@mcclb0.med.nyu.edu Newsgroups: bionet.software Subject: Re: NIH Guide Message-ID: <1992Oct7.203729.7154@mcclb0.med.nyu.edu> Date: 8 Oct 92 01:37:29 GMT References: <9210071519.AA02003@darwin.sfbr.org> Distribution: bionet,world Organization: NYU Medical Center, New York, NY 10016, USA Lines: 19 In article <9210071519.AA02003@darwin.sfbr.org>, bdyke@DARWIN.SFBR.ORG (Bennett Dyke) writes: > Does anybody know of a script that will organize, extract, format, etc. > the electronic version of the NIH Guide? Thanx in advance... We have written and made available programs to accept the incomming E-Guide, create a database with it and present it to a user. The user program allows searching on text items and NIH keywords, printing, file extraction, mailling or whole Guides, or selected fragments of them. The program also performs automatic updating of guide items as errata are posted. To get a copy, send mail to our MAILSERVer (MAILSERV@MCCLB0.MED.NYU.EDU) with the lines HELP and INDEX in the body of the message. Then follow the instructions. The program is for VAX/VMS and the distribution is packaged using VMS_SHARE. +----------------------------------------------------------------------------+ |Ross Smith, Research Computing Resource, Department of Cell Biology, NYU-MC| |E-Mail: SMITH@NYUMED.BITNET (BITNET), SMITH@MCCLB0.MED.NYU.EDU (Internet)| +----------------------------------------------------------------------------+ From owner-software@net.bio.net Wed Oct 07 23:00:00 1992 Path: biosci!agate!ames!elroy.jpl.nasa.gov!usc!zaphod.mps.ohio-state.edu!sol.ctr.columbia.edu!usenet.ucs.indiana.edu!sunflower.bio.indiana.edu!gilbertd From: gilbertd@sunflower.bio.indiana.edu (Don Gilbert) Newsgroups: bionet.software Subject: Re: 3D RNA Editor wanted Message-ID: Date: 8 Oct 92 01:38:40 GMT References: Sender: news@usenet.ucs.indiana.edu (USENET News System) Organization: Biology, Indiana University - Bloomington Lines: 25 Nntp-Posting-Host: sunflower.bio.indiana.edu You and others with interests in 3D RNA drawings may want to look at the Macintosh RNA 3D toolkit that Jim Brown here put together for his work. These are a selection of RNA building blocks drawn with the Mac application Swivel 3D, which is a general Mac 3D drawing program. You ask for "tetraloops, stacks, helices, bends, pseudoknots" and I seem to recall that this collection includes those. Here is the brief description of these drawing tools: 3D RNA toolkit is a "toolkit" of RNA pencil-type structures in Swivel 3D format. These files can be used to construct 3D models of RNAs either from known structures (e.g. tRNA) or to test potential tertiary models. from James W. Brown, jwbrown@bio.indiana.edu You can pick these up by anonymous ftp to ftp.bio.indiana.edu, currently in folder Incoming/ as rna-3d-tools.hqx ( a 1.9 megabyte file). -- Don Gilbert gilbert@bio.indiana.edu biocomputing office, biology dept., indiana univ., bloomington, in 47405 From owner-software@net.bio.net Wed Oct 07 23:00:00 1992 Path: biosci!uwm.edu!ux1.cso.uiuc.edu!news.cso.uiuc.edu!geta!mrmike From: mrmike@geta.life.uiuc.edu (Mike McCaughey) Newsgroups: bionet.software Subject: 3D RNA Editor wanted Message-ID: Date: 8 Oct 92 01:11:41 GMT Sender: usenet@news.cso.uiuc.edu (Net Noise owner) Organization: University of Illinois at Urbana Lines: 34 Colleagues, I am in search for a computer graphics 3D editing tool to esily compose RNA and protein spatial structure models at low as well as atomic resolution. Known structure element coordinates for e.g. tetraloops, stacks, helices, bends, pseudoknots and for protein zippers, fingers, sheets, a-helices etc etc should be part of a toolbox where one can pick structure templates for the buildup. Structures must be seen and treated with varying detail, for example an RNA A-helix is either a simple cylinder, a carved cylinder (showing grooves), same with bases and sugars shown as simple tiles, and with atoms shown. Only X-ray (and sometimes NMR) data justify the latter, but lower resolution models from other data can be very useful. I have seen MacroModel, Insight, Quanta, and brochures for Sybyl/Biopolymer module. The focus of these programs are either molecular dynamics or the price is out of line. Would any readers of this know reasonably priced programs like described, either finished or in the works? Sincerely, Niels Larsen E-mail niels@darwin.life.uiuc.edu _____________________________________________________________________ / ______ / / Department of Microbiology / 1611 B Lyndhurst West / / / / University of Illinois / Savoy, IL 61874 /_____/ / / 131 Burrill Hall / U.S.A. / / 407 South Goodwin Avenue / / / Urbana, IL 61801, U.S.A. / -------------------------- / / / -------------------------- / / Phone (217)-333-9369 / / / Shared FAX (217)-244-6697 / (217)-356-5451, ans. mach. / /____________________________________________________________________/ From owner-software@net.bio.net Wed Oct 07 23:00:00 1992 Path: biosci!uwm.edu!ux1.cso.uiuc.edu!news.cso.uiuc.edu!geta!mrmike From: mrmike@geta.life.uiuc.edu (Mike McCaughey) Newsgroups: bionet.software Subject: Programmer Wanted Message-ID: Date: 8 Oct 92 16:14:58 GMT Sender: usenet@news.cso.uiuc.edu (Net Noise owner) Organization: University of Illinois at Urbana Lines: 41 RESEARCH PROGRAMMER The Department of Microbiology, University of Illinois at Urbana-Champaign, seeks a qualified Research Programmer for the ribosomal database project (RDP), which functions in a world-wide capacity to facilitate research in some of the more interesting and important areas of biology; evolution, microbial ecology, nucleic acid structure, taxonomy, etc. Duties will include work on software for the database, automated mechanisms for exchanging information with other biological databases and construction of useful and tools for the user community's handling of the data. Duties may also include part-time systems administration of a Unix/MacIntosh network. Experience should include familiarity with Unix and MacIntosh operating systems, C or Fortran, X-windows, and preferably Prolog. Knowledge of (and interest in) biology is also highly desirable. A B.S. or M.S. degree is required (preferably in computer science, engineering, or in combination with biology). Position is full time; duration is dependent upon continuation of funds (from NSF). Salary is negotiable; starting date is as soon as possible after closing date. Applicants should send a resume, a summary of relevant experience, and the names and addresses (incl. electronic) of three references to: Ms. Carolyn Corn, Administrative Assistant, Department of Microbiology, Univerisy of Illinois, 131 Burrill Hall, 407 S. Goodwin Avenue, Urbana, IL 61801; Phone: 217-333-1736. To receive full consideration, applications should be received by November 1, 1992. Interviews may be conducted as soon as applications are received. However, all applications that are received by the above date will be given equal consideration. The University of Illinois is an Equal Opportunity/Affirmative Action Employer. From owner-software@net.bio.net Thu Oct 08 23:00:00 1992 Path: biosci!KRSNUCC1.BITNET!HYUNERHO From: HYUNERHO@KRSNUCC1.BITNET Newsgroups: bionet.software Subject: Info Needed on EMBL-connection status ... Message-ID: <9210090624.AA27135@net.bio.net> Date: 9 Oct 92 06:24:02 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 13 Dear Netters ... I am wondering about EMBL-Netserv connection status via e-mail recent days . Is anybody out there who knows and are willing to let me know the connection status or opration status of EMBL ? One of my colleague is trying to register his sequence to EMBL data library . And any comments would be very helpful to us . Thanks for reading me and in advance . Sincerely Rhee Hwan-Seok Dept. Mol.Biol Seoul National Univ. e-mail : hyunerho@krsnucc1.BITNET From owner-software@net.bio.net Thu Oct 08 23:00:00 1992 Path: biosci!bcm!cs.utexas.edu!convex!darwin.sura.net!jvnc.net!yale.edu!nigel.msen.com!emory!sol.ctr.columbia.edu!destroyer!news.iastate.edu!iscsvax.uni.edu!klier From: klier@iscsvax.uni.edu Newsgroups: bionet.software Subject: Image analysis software wanted\ Message-ID: <1992Oct9.103749.7443@iscsvax.uni.edu> Date: 9 Oct 92 15:37:49 GMT Organization: University of Northern Iowa Lines: 10 Can someone point me at a good image analysis software package for an IBM 386 compatible system (we have a frame grabber board)-- currently running Jandel's Java. We'd like to shift to a dynamic image analysis from still frames. NIH had a Mac-compatible package a few years back-- anything comparable for the IBM? And preferably ultra-low cost? (Like free???) Thanks! Kay Klier Biology Dept UNI in%klier@iscsvax.uni.edu From owner-software@net.bio.net Thu Oct 08 23:00:00 1992 Path: biosci!bcm!cs.utexas.edu!natinst.com!news.dell.com!swrinde!zaphod.mps.ohio-state.edu!wupost!uunet!mcsun!sunic!corax.udac.uu.se!embnet.se!daresbury!news From: BIONET@FRCGM51.EARN Newsgroups: bionet.software Subject: Readseq Message-ID: <1992Oct9.085757.14238@gserv1.dl.ac.uk> Date: 9 Oct 92 09:57:00 GMT Sender: list-admin@daresbury.ac.uk Distribution: bionet Lines: 26 X-Envelope-To: bio-software@daresbury.ac.uk Original-To: bio-software@UK.AC.DARESBURY X-Vms-To: IN%"bio-software@daresbury.ac.uk" Hello, Some time ago, I downloaded the well known program READSEQ from D. Gilbert onto our Vax/VMS, compiled, linked and run it without any problem. Now I'd like to have it on our PC's. Problem: impossible to compile it without severe errors or, in those rare cases where we could link, run it without run-time errors (stack overflow). I used the Microsoft QuickC compiler (various releases, including the Windows version). D. Gilbert mailed me that he is not aware of such problems. Is there anybody on the net who experienced similar problems? If so, what is the trick to compile Readseq on a PC? Thanks for the help, --------------------------------------------------------------- | Jean-Loup Risler | | | CNRS | | | Centre de Genetique Moleculaire | Risler@frcgm51.bitnet | | 91190 Gif sur Yvette France | | --------------------------------------------------------------- From owner-software@net.bio.net Thu Oct 08 23:00:00 1992 Path: biosci!daresbury!doc.ic.ac.uk!agate!ames!elroy.jpl.nasa.gov!sdd.hp.com!zaphod.mps.ohio-state.edu!darwin.sura.net!sgiblab!sgigate!olivea!charnel!sifon!monod!francis From: francis@monod.Biol.McGill.CA (Francis Ouellette) Newsgroups: bionet.software Subject: Re: Info Needed on EMBL-connection status ... Message-ID: Date: 9 Oct 92 20:16:48 GMT References: <9210090624.AA27135@net.bio.net> Sender: news@sifon.cc.mcgill.ca Distribution: bionet Organization: McGill University Lines: 39 Nntp-Posting-Host: monod.biol.mcgill.ca HYUNERHO@KRSNUCC1.BITNET writes: >I am wondering about EMBL-Netserv connection status via e-mail >recent days . Is anybody out there who knows and are willing to >let me know the connection status or opration status of EMBL ? >One of my colleague is trying to register his sequence to EMBL >data library . And any comments would be very helpful to us . >Thanks for reading me and in advance . >Sincerely Rhee Hwan-Seok >Dept. Mol.Biol >Seoul National Univ. >e-mail : hyunerho@krsnucc1.BITNET Well someone at EMBL was telling me (unnamed for the protection of the innocent) that some over-zealous person had requested 8000 (yes, 8 thousands) seperate files from the email server, and when these were not comming in (???) had put in the request a second time! (yes, another 8000 files!) No wonder email to and from Germany has been a bit slow of late! It is quite an irresponsible thing to do, and the people who did this should be "reprimended" (like being told that what they did was *very* bad ... I do not want to suggest that "big brother" should cut anybody off the net ) and hopefully we can all learn from this and try to make sure it does not happen again. kindest regards to all, francis -- | B.F. Francis Ouellette | manager, yeast chromosome I project | dept of biology, McGill university, Montreal, Qc, Canada | francis@monod.biol.mcgill.ca From owner-software@net.bio.net Sat Oct 10 23:00:00 1992 Path: biosci!SERVER.UGA.EDU!arnold%gandal.dnet From: arnold%gandal.dnet@SERVER.UGA.EDU Newsgroups: bionet.software Subject: (none) Message-ID: <9210111508.AA22066@server.uga.edu> Date: 11 Oct 92 15:08:08 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 142 TO: Those Interested FROM: Jonathan Arnold, ARNOLD@BSCF.UGA.EDU SUBJECT: ODS DISTRIBUTION INFORMATION ON Ordering DNA Sequences (ODS) ver 1.1 (c) 1990 The Univ of GA & A. Jamie Cuticchia PROGRAM DESCRIPTION: Programs are now available to assist in the in vitro reconstruction of chromosomes or chromosome fragments ("contig mapping") from a clonal library. The theory behind the ODS program for "contig mapping" can be found in: Cuticchia, A.J., Arnold, J., and W.E. Timberlake. (1992a). The use of simulated annealing in chromosome reconstruction experiments based on binary scoring. Genetics 132: 591-601 ODS is a program that orders DNA sequences based on similarity of their binary profiles assigned to clones in a library by one of several experimental approaches. DNA fragments with a high degree of overlap are expected to show a high degree of similarity in their profiles. The ordering process is based on minimizing the sum of the linking distances between clones as a function of their ordering along the chromosome. The algorithm used to minimize this criterion is a combinatorial optimization method called simulated annealing. The algorithm is described in: Cuticchia, A.J., Arnold, J., and W.E. Timberlake. (1992b). ODS: Ordering DNA Sequences, a physical mapping algorithm based on simulated annealing. CABIOS, in press Any published use of these programs should cite this reference. Simulated annealing allows approximate solutions to Np complete problems in a finite amount of time. The annealing parameters in this program are set at the following values: Temperature = 50 Maximum Trials = 500000 Maximum Successes = 25000 Decrease in T = 0.5 PROGRAM INPUT: The program requires answers to three questions. The first is the name of the file which has the binary profile data (INFILE). The second is the name of the file to which the order should be written (OUTFILE). The third is one seed for the random number generator (IDUM). The program will not prompt you for this input, if run interactively, to keep it streamlined for use in a batch queue. PROGRAM OUTPUT: The program outputs the inferred minimum linking distance on the first line, and on succeeding lines, the inferred ordering of clones in the first column and the linking distance between successive clones in the second column. PROGRAM INPUT LIMITATIONS: The length of a binary profile (the number of probes) is limited to 100. The number of clones must be between 1 and 1000. Filenames (with directory path, if specified) must be no longer than 80 characters. The seed can be any integer between -2147483648 and 2147483647. OBTAINING THE SOFTWARE: The software is only distributed via Internet using EMAIL. Please send an EMAIL request to: ARNOLD@BSCF.UGA.EDU if you wish copies of the program. I will EMAIL you: 1) a FORTRAN program, ODS.FOR 2) this documentation file, ODS.DOC 3) a test input file, ODS.DAT 4) an example output file, ODS.OUT 5) a command file, ODS.COM. This file is what you would use to submit a batch job in the VAX/VMS operating system to generate ODS.OUT. The values were used to generate the output in Cuticchia et al. (1992b). USING THE SOFTWARE WITHOUT THE PROGRAMS: The programs also have been incorporated into a DNA sequence analysis package (Arnold et al., 1986), and can be accessed directly on the Biological Sequence/Structure Computational Facility (BS/SCF). Contact Dr. Weise for a guest account at: WEISE@BSCF.UGA.EDU OBTAINING FURTHER DOCUMENTATION: The best source of documentation are the papers by Cuticchia et al. (1992a, 1992b). A reprint can be obtained by writing: Dr. Jonathan Arnold Genetics Department University of Georgia Athens, GA 30602 or by emailing: ARNOLD%BSCF.UGA.EDU SOFTWARE SUPPORT IN THE USE OF THE PROGRAMS: If you have questions about the programs, please contact Dr. A. Jamie Cuticchia currently located at Johns Hopkins University: JAMIE@WELCHGATE.WELCH.JHU.EDU HARDWARE LIMITATIONS: The programs have been run with minor modification on VAXstations, a DECstation 3100, and on a Silicon Graphics IRIS 4D70/GT workstation. . - - - - - - - - - - - Jonathan Arnold - - - - - - - - - - - - - - - . | Dept. of Genetics, | | University of Georgia | | Athens, Georgia 30602 | | Phone: (706) 542-1449 | | messages: (706) 542-8000 | | FAX: (706) 542-3910 | | Internet: ARNOLD@BSCF.UGA.EDU | . - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - . From owner-software@net.bio.net Sat Oct 10 23:00:00 1992 Path: biosci!bcm!cs.utexas.edu!usc!zaphod.mps.ohio-state.edu!wupost!uunet!portal!cup.portal.com!HRWood From: HRWood@cup.portal.com (Harold R Wood) Newsgroups: bionet.software Subject: Re: stereo-viewer source Message-ID: <67504@cup.portal.com> Date: 11 Oct 92 00:36:29 GMT Organization: The Portal System (TM) Lines: 8 It is possible, with a little practice, to see sterio without a viewer. By superimposing the two images by "kinda crossing your eyes" you can see the sterio effect. This is a useful tech. to learn if you regularly need to see sterios, no good if you are demonstrating to a class. I have used the technique with sterio X-rays, sterio aerial maps, and sterio protein configurations. Rick Wood From owner-software@net.bio.net Sat Oct 10 23:00:00 1992 Path: biosci!uwm.edu!zaphod.mps.ohio-state.edu!sol.ctr.columbia.edu!ira.uka.de!math.fu-berlin.de!news.belwue.de!news.uni-tuebingen.de!mailserv!zxmkr08 From: zxmkr08@mailserv.zdv.uni-tuebingen.de (Cornelius Krasel) Newsgroups: bionet.software Subject: Re: Sequence film scanning systems? Message-ID: Date: 11 Oct 92 17:47:39 GMT References: Sender: news@softserv.zdv.uni-tuebingen.de (News Operator) Organization: Comp. Center (ZDV) U of Tuebingen, FRG Lines: 18 Some weeks ago I asked for sequence film scanning systems. The replies I got were all (without exception) rather discouraging. It seems that the main problem is the identifying of bands on the autoradiographs. For that reason we now have decided to spend the money on a graphic tablet made by Hitachi (sold by Pharmacia, at least here in Germany) and try to get it running with MacVector (we had a look at the 1.0 demo of DNasis and found it rather terrific; the guy from Pharmacia told us something that Version 2.0 should come out RSN, but anyways...). Thank you for your responses (my colleagues were rather impressed :-). --Cornelius. -- /* Cornelius Krasel, Department of Physiological Chemistry, U Tuebingen */ /* email: krasel@mailserv.zdv.uni-tuebingen.de (Internet) */ /* krasel@chemie.uni-tuebingen.dbp.de (WIN/X400) */ /* "People are DNA's way of making more DNA." (anonymous) */ From owner-software@net.bio.net Sun Oct 11 23:00:00 1992 Path: biosci!UTSPH.SPH.UTH.TMC.EDU!gsbs1022 From: gsbs1022@UTSPH.SPH.UTH.TMC.EDU (Zharkikh Andrey) Newsgroups: bionet.software Subject: Re: What Genomes have been Sequenced? Message-ID: <00961F97.01EC8940.24594@UTSPH.SPH.UTH.TMC.EDU> Date: 12 Oct 92 13:13:13 GMT Sender: daemon@net.bio.net Reply-To: gsbs1022@UTSPH.SPH.UTH.TMC.EDU Distribution: bionet Lines: 20 Note added in proof: Jean-Loup Risler at BIONET@FRCGM51.EARN wrote: >3) About a former posting: in yeast chromosome III, there are 182 > open reading frames longer than 300 bp (thus coding for proteins longer > than 100 aa). Some of them correspond to already known genes, and 145 > ORFs are novel (see the Nature paper). Note that these figures are > consistent with a study of the chrIII transcripts, hence most of these > ORFs are actually translated. ... >That more than 50% of the ORFs in ChrIII do not resemble anything >previously known is one great information afforded by its sequencing. As Monte Carlo simulation shows, about 24 of these ORF are expected to be found by chance (in a random sequence of length 300,000 with the same base frequencies as in yeast III chromosome: A=0.31, T=0.30, G=0.19, and C=0.20). Andrey. From owner-software@net.bio.net Sun Oct 11 23:00:00 1992 Path: biosci!daresbury!news From: DKIRSCHT@UVMVM.EARN (David Kirschtel) Newsgroups: bionet.software Subject: Plant Genetics Position Message-ID: <1992Oct12.054005.21313@gserv1.dl.ac.uk> Date: 11 Oct 92 20:52:45 GMT Sender: list-admin@daresbury.ac.uk Distribution: bionet Lines: 90 Original-To: bio-software@UK.AC.DARESBURY POSITION ANNOUNCEMENT PLANT GENETICIST Title: Assistant Professor (9-month appointment, tenure-track) Location: Department of Botany College of Agriculture and Life Sciences University of Vermont Burlington, VT 05405-0086 Date Available: Academic year, 1993. Responsibilities: Participate in the undergraduate and graduate teaching program of the Department. Prosecute a competitive research program in contemporary molecular plant genetics. Serve as academic and research advisor to undergraduate and graduate students. Participate in departmental, college and university committees and faculty governance. Qualifications: Plant molecular geneticist with post-doctoral experience. Demonstrated ability in teaching and research. Salary: Competitive and commensurate with experience. Application Procedure: Send letter of application, curriculum vitae, statements of teaching and research interests. Also arrange to have letters of reference sent from three referees. Documents should be sent to: GENETICS SEARCH COMMITTEE Department of Botany Life Science Building University of Vermont Burlington, VT 05405-0086 Women and representatives of diverse racial, ethnic and cultural groups are strongly encouraged to apply. AA/EO employer and educator. Application Deadline: Review will begin Dec. 15, 1992. ----------------------------------------------------------------- BOTANY AT UVM: The Department of Botany has a prominent history of both excellent undergraduate and graduate education and active research in a broad array of plant biology disciplines. Our emphases are in plant molecular biology, physiology, ecology and evolution. Most of the faculty of the Department are located in Marsh Life Science Building, a modern facility with teaching and research instrumentation to match. Other facilities of the University directly of interest to those conducting teaching and research in Botany include: the Proctor Maple Research Center, the University Horticultural Farm, the University Farm, the Pringle Herbarium, extensive natural holdings of diverse ecological types, the School of Natural Resources and the College of Medicine. The candidate should benefit from interactions with a large number of successful scholars with diverse interests in the area of molecular genetics and molecular biology including Departments of Agricultural Biochemistry, Animal Sciences, Biochemistry, Microbiology and Molecular Genetics, Nutritional Sciences, Plant and Soil Science, Zoology, and interdisciplinary programs in Cell and Molecular Biology (graduate) and Biological Sciences (undergraduate). Both the department and the University as a whole enjoy extensive collabora- tions between faculty in both research and teaching functions. THE UVM/BURLINGTON COMMUNITY: The University of Vermont is located in Burlington in the rural Lake Champlain Valley, nestled between the Adirondack State Park in New York (the largest wilderness park in the United States) and the Green Mountains of Vermont. Opportunities for outdoor activities abound during all four seasons of the year. Additionally, the University of Vermont and the population center of greater Burlington attract a diverse array of cultural activities. Also, several large metropolitan centers are within easy travel by auto or plane (Montreal, 100 mi., Boston, 225 mi. and New York City 275 mi.). From owner-software@net.bio.net Sun Oct 11 23:00:00 1992 Path: biosci!daresbury!news From: BIONET@FRCGM51.EARN Newsgroups: bionet.software Subject: Re: What Genomes have been Sequenced? Message-ID: <1992Oct12.051255.20790@gserv1.dl.ac.uk> Date: 11 Oct 92 15:34:00 GMT Sender: list-admin@daresbury.ac.uk Distribution: bionet Lines: 40 X-Envelope-To: bio-software@daresbury.ac.uk Original-To: bio-software@UK.AC.DARESBURY X-Vms-To: IN%"bio-software@daresbury.ac.uk" 1) The "landmark paper" on Yeast Chromosome III appeared in NATURE, vol. 357 pp. 38-46 and not in Science. I'm not quite sure whether the cited number of authors (>100) was ironical or not. If so, why (I'm not a co- author)? 2) Keith Robison has forgotten *Bacillus subtilis* in his review of partly but well under way sequenced genomes (no sweat, this is not my favourite organism). 3) About a former posting: in yeast chromosome III, there are 182 open reading frames longer than 300 bp (thus coding for proteins longer than 100 aa). Some of them correspond to already known genes, and 145 ORFs are novel (see the Nature paper). Note that these figures are consistent with a study of the chrIII transcripts, hence most of these ORFs are actually translated. My point is that an ORF or a gene is not weird or strange if one gets no phenotype upon its disruption: a) not getting a phenotype *in your laboratory conditions* does not mean that the gene is useless! b) it is quite possible that these genes may be duplicated, triplicated, etc... on other chromosomes. Disrupting one copy will make no harm. That more than 50% of the ORFs in ChrIII do not resemble anything previously known is one great information afforded by its sequencing. Remember also that yeast is a small eukaryotic organism, whose genome contains introns and exons, and that reverse genetic experiments are easy with yeast. The choice of this organism for a collaborative project was not done by chance... --------------------------------------------------------------- | Jean-Loup Risler | | | CNRS | | | Centre de Genetique Moleculaire | Risler@frcgm51.bitnet | | 91190 Gif sur Yvette France | | --------------------------------------------------------------- From owner-software@net.bio.net Sun Oct 11 23:00:00 1992 Path: biosci!agate!spool.mu.edu!olivea!charnel!sifon!monod!francis From: francis@monod.Biol.McGill.CA (Francis Ouellette) Newsgroups: bionet.software Subject: Re: What Genomes have been Sequenced? Message-ID: Date: 12 Oct 92 15:31:46 GMT References: <1992Oct12.051255.20790@gserv1.dl.ac.uk> Sender: news@sifon.cc.mcgill.ca Distribution: bionet Organization: McGill University Lines: 58 Nntp-Posting-Host: monod.biol.mcgill.ca Jean-Loup Risler (BIONET@FRCGM51.EARN) e'crit: >1) The "landmark paper" on Yeast Chromosome III appeared in NATURE, vol. 357 > pp. 38-46 and not in Science. I'm not quite sure whether the cited > number of authors (>100) was ironical or not. If so, why (I'm not a co- > author)? 147 authors from 35 labs in Europe. If I was one of those labs, I sure would want my name on it. This papers, and others in the near future to come from Europe shows one way to do a mini-mega sequencing project. Many (in the human and C. elegans) project have made fun of the Yeast project but the Nature paper has silenced many, and it works! We can sequence a small genome (14,000,000 bp +/-) by "conventional" cloning and sequencing methods. They will not be able to do this for the human genome project ... they will need new technology. >2) Keith Robison has forgotten *Bacillus subtilis* in his review of partly Keith also mentions 3 yeast chromosome on their way to completion ... it is more like 4 ... I, II, III (finished) and XI. >3) About a former posting: in yeast chromosome III, there are 182 > open reading frames longer than 300 bp (thus coding for proteins longer and there are probably more, and some of the already identified ones may be bogus. Many carreers are spent on a single gene ... so more than 180 for CHIII and more than a thousand (2000?) for the yeast genome will keep many many people very busy. The task of genome sequencing is very altruistic (well, I think it is ;-). We are producing data which will be used (and corrected!) by thousands of scientist worldwide, and not just yeast biologists. >That more than 50% of the ORFs in ChrIII do not resemble anything >previously known is one great information afforded by its sequencing. >Remember also that yeast is a small eukaryotic organism, whose genome >contains introns and exons, and that reverse genetic experiments are easy >with yeast. The choice of this organism for a collaborative project was not >done by chance... I think you meant very few introns here (?) ... and yes, not much "chance" in choosing yeast here ... if I can quote somebody from my yeast mailling list (yes, yes, it is comming folks ;-) ... "Yeast is Best" regards to all francis (PS maybe this should move from bionet.software to bionet.general?) (PPS salut Jean-Loup!) -- | B.F. Francis Ouellette | manager, yeast chromosome I project | dept of biology, McGill university, Montreal, Qc, Canada | francis@monod.biol.mcgill.ca From owner-software@net.bio.net Sun Oct 11 23:00:00 1992 Path: biosci!UTSPH.SPH.UTH.TMC.EDU!gsbs1022 From: gsbs1022@UTSPH.SPH.UTH.TMC.EDU (Zharkikh Andrey) Newsgroups: bionet.software Subject: Re: What Genomes have been Sequenced? Message-ID: <00961FBA.C0726920.24668@UTSPH.SPH.UTH.TMC.EDU> Date: 12 Oct 92 17:29:05 GMT Sender: daemon@net.bio.net Reply-To: gsbs1022@UTSPH.SPH.UTH.TMC.EDU Distribution: bionet Lines: 8 One small addition to my previous estimation of the number of ORF longer than 100 bp expected by chance: I considered only one DNA strand. Hence, the total number of such long ORFs is about 48, that is 26% of all discovered ORFs (182) or 33% of all novel ORFs. Andrey From owner-software@net.bio.net Sun Oct 11 23:00:00 1992 Path: biosci!daresbury!news From: Rob.Harper@csc.fi (Rob Harper) Newsgroups: bionet.software Subject: Recent msdos uploads to SIMTEL20 (27-Sep - 8-Oct 1992) Message-ID: <1992Oct12.082818.23659@gserv1.dl.ac.uk> Date: 12 Oct 92 08:30:26 GMT Sender: list-admin@daresbury.ac.uk Distribution: bionet Lines: 200 Content-Type: text/plain; charset=us-ascii Original-To: bio-soft@uk.ac.daresbury Mime-Version: 1.0 X-Mailer: ELM [version 2.4beta PL17] Content-Length: 9845 The following files have been recently uploaded to WSMR-SIMTEL20.ARMY.MIL (between 27-Sep-92 and 8-Oct-92): NOTE: Type B is Binary; Type A is ASCII Filename Type Length Date Description ============================================== Directory PD1: GUS_160.ZIP B 31515 920927 Convert between any two archive types SHEZ81.ZIP B 242028 921008 Shell for archive manipulation, w/virus check SQZ1082E.EXE B 80258 921005 SQUEEZE archiver from Sweden. Compresses small Directory PD1: SKYGLB35.ZIP B 171583 921004 Skyglobe v3.5: Educational map of the sky Directory PD1: USBBS101.ZIP B 86297 920927 Darwin's nationwide IBM BBS listing: 920926 Directory PD1: GW4WIN11.ZIP B 3735558 920929 *Complete* Bible search program for Windows3.x Directory PD1: BOWLS21A.ZIP B 249718 921007 BowlStat V2.1: Bowling stats program, 1/2 BOWLS21B.ZIP B 158795 921007 BowlStat V2.1: Bowling stats program, 2/2 ROCV2.ZIP B 671254 921006 Resumes On Computer (ROC), a resume database Directory PD1: AN300.ZIP B 192263 921007 Ample notice: Powerfu