From owner-software@net.bio.net Wed Dec 01 08:55:21 1999 Path: hgmp.mrc.ac.uk!pegasus.csx.cam.ac.uk!daresbury!uninett.no!newsfeed.nacamar.de!rz.uni-karlsruhe.de!fu-berlin.de!jussieu.fr!u-psud.fr!not-for-mail From: "Yann Abraham" Newsgroups: bionet.software Subject: Re: Common DNA/Protein Seq Databases Date: Wed, 1 Dec 1999 09:49:50 +0100 Organization: Universite Paris-Sud, France. Lines: 18 Message-ID: <822ns5$ems$1@upsn21.u-psud.fr> References: NNTP-Posting-Host: mb-2414-6415.curie.fr X-Newsreader: Microsoft Outlook Express 4.72.3110.5 X-MimeOLE: Produced By Microsoft MimeOLE V4.72.3110.3 Xref: hgmp.mrc.ac.uk bionet.software:898 You can have a look at http://vectordb.atcg.com/, here you'll find a database of all plasmids with links to the corresponding sequence. Best of all, it is easily searchable with keywords. Hope this help ! Yann Abraham John Monahan a écrit dans le message ... >Does anybody have a URL to a site with all "common" plasmid, virus and >possibly protein sequences. Yes I know I can dig them out of Genbank etc. I >want to save some time! The best I have seen is the New England Biolabs >collection. However they have them in a non standard/mixed data format. > > > From owner-software@net.bio.net Wed Dec 01 19:20:52 1999 Path: hgmp.mrc.ac.uk!pegasus.csx.cam.ac.uk!warwick!fu-berlin.de!newsfeed.nacamar.de!newsfeed.icl.net!colt.net!baron.netcom.net.uk!netcom.net.uk!server3.netnews.ja.net!news.icnet!not-for-mail From: Arne Mueller Newsgroups: bionet.software Subject: Transmembrane prediction Date: Wed, 01 Dec 1999 19:11:57 +0000 Organization: Imperial Cancer Research Fund Lines: 22 Message-ID: <384572FD.50EDB1EB@icrf.icnet.uk> NNTP-Posting-Host: elm.lif.icnet.uk Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 4.61C-SGI [en] (X11; I; IRIX 6.5 IP32) X-Accept-Language: en Xref: hgmp.mrc.ac.uk bionet.software:899 Hi All, I'm looking for a transmembrane prediction program, the source code should be free available for academic use. I've to install the program on site for large scale use so I can't use a web-service. I've already tried MEMSAT and TOPPRED2. Both programs seem to overpredict transmembrane helices in some sequences. I'll be happy for any suggestions, thanks, Arne -- Arne Mueller Biomolecular Modelling Laboratory Imperial Cancer Research Fund 44 Lincoln's Inn Fields London WC2A 3PX, U.K. phone : +44-(0)171 2693405 | fax :+44-(0)171-269-3534 email : a.mueller@icrf.icnet.uk | http://www.icnet.uk/bmm/ From owner-software@net.bio.net Wed Dec 01 19:50:31 1999 Path: hgmp.mrc.ac.uk!warwick!fu-berlin.de!newspeer.ebone.net!newsfeed1.online.no!newsfeed.online.no!hydro.com!not-for-mail From: Ronald Govaert Newsgroups: bionet.software Subject: software? Date: Wed, 01 Dec 1999 20:48:50 +0100 Organization: Norsk Hydro ASA Lines: 2 Message-ID: <38457BA2.53CC1C1A@hydro.com> NNTP-Posting-Host: 163.34.37.141 Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 4.06 [en] (Win95; I) Xref: hgmp.mrc.ac.uk bionet.software:900 where i can find Pinnacle's Studio DV demo on the net From owner-software@net.bio.net Wed Dec 01 20:02:28 1999 Path: hgmp.mrc.ac.uk!not-for-mail From: "Guy St.C. Slater" Newsgroups: bionet.software Subject: ESTate - EST Analysis Tools Etc. First Release. Date: 1 Dec 1999 20:02:27 -0000 Organization: MRC Human Genome Mapping Project Resource Centre Lines: 52 Message-ID: <823usj$5ot$1@mercury.hgmp.mrc.ac.uk> NNTP-Posting-Host: mercury.hgmp.mrc.ac.uk X-Trace: niobium.hgmp.mrc.ac.uk 944078548 5214 193.62.192.80 (1 Dec 1999 20:02:28 GMT) X-Complaints-To: news@hgmp.mrc.ac.uk NNTP-Posting-Date: 1 Dec 1999 20:02:28 GMT Xref: hgmp.mrc.ac.uk bionet.software:901 --------------------------------------- ESTate 0.5.0 First Release Announcement --------------------------------------- The first public release of ESTate is now available. ESTate is a package of Expressed Sequence Tag Analysis Tools Etc. It may be downloaded from: http://www.hgmp.mrc.ac.uk/~gslater/ESTate/ Functionality includes: o EST clustering Rapid comparisons using finite state machines are combined with accurate comparisons from dynamic programming, by a graph theoretic approach to produce an anytime algorithm for EST clustering. o Consensus Translation An method for prediction of the translation implied by EST consensi, based on the use of multiple dynamic programming models and various strategies to achieve error tolerance. o Some experimental tools for database searching. All the programs are implemented in C, and have been tested under Linux, IRIX, Solaris and AIX. The source code is provided under the terms of the GNU public licence. Documentation is available from the URL above, and is also included in the package. All feedback is appreciated. Guy. -- %!PS % <------ Guy St.C. Slater ------> http://www.hgmp.mrc.ac.uk/~gslater/ 210 297/a{def}def/b{translate}a b 36/c{rotate}a c 0 1 0 1 12/d{exch moveto} a/e{closepath stroke}a/f{index}a/g{0 0 0 0 4 f}a/h{setlinewidth newpath dup g}a{pop exch 1 f add 0 h neg d lineto 72 c lineto e 2 h d 3 f 0 108 arc d e 18 c 0 2 f neg b 18 c}for 72 c newpath add g 0 7 arc d e pop showpage From owner-software@net.bio.net Wed Dec 01 21:38:10 1999 Path: hgmp.mrc.ac.uk!warwick!fu-berlin.de!logbridge.uoregon.edu!uwm.edu!biosci!NHGRI.NIH.GOV!jfryan From: jfryan@NHGRI.NIH.GOV (Joe Ryan) Newsgroups: bionet.software Subject: Re: Transmembrane prediction Date: 1 Dec 1999 13:41:18 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 33 Sender: daemon@net.bio.net Distribution: world Message-ID: <19991201163353.A976@nhgri.nih.gov> References: <384572FD.50EDB1EB@icrf.icnet.uk> NNTP-Posting-Host: net.bio.net Xref: hgmp.mrc.ac.uk bionet.software:902 > I'm looking for a transmembrane prediction program, the source code > should be free available for academic use. I've to install the program > on site for large scale use so I can't use a web-service. I've already > tried MEMSAT and TOPPRED2. Both programs seem to overpredict > transmembrane helices in some sequences. This is from an old post to this group. :> I am looking for software that can predict transmembrane domains in :> proteins. : :Here is a list in no particular order: : :TMPRED: http://www.ch.embnet.org/software/TMPRED_form.html :TopPred2: http://www.biokemi.su.se/~server/toppred2/ :DAS: http://www.biokemi.su.se/~server/DAS/ :SOSUI: http://www.tuat.ac.jp/~mitaku/adv_sosui/ :TMHMM: http://www.cbs.dtu.dk/services/TMHMM-1.0/ :HMMTOP: http://www.enzim.hu/hmmtop/ :PredictProtein: http://www.embl-heidelberg.de/predictprotein/ :PSIpred: http://globin.bio.warwick.ac.uk/psipred/ : :TMBASE: http://www.ch.embnet.org/software/tmbase/TMBASE_doc.html :(TMBASE is A Database of Membrane Spanning Protein Segments) : :Love, : Joe :-- :Joseph Ryan :Programmer :National Human Genome Research Institute From owner-software@net.bio.net Wed Dec 01 21:43:04 1999 Path: hgmp.mrc.ac.uk!warwick!fu-berlin.de!newsfeed.berkeley.edu!enews.sgi.com!news.corp.sgi.com!not-for-mail From: Haruna Cofer Newsgroups: bionet.software Subject: Parallel CLUSTAL X 1.8 available on SGI/IRIX Date: Wed, 01 Dec 1999 16:42:56 -0500 Organization: SGI Lines: 86 Message-ID: <38459660.FC1B05A9@columbus.sgi.com> NNTP-Posting-Host: catbert.columbus.sgi.com Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 4.7C-SGI [en] (X11; I; IRIX 6.5 IP22) X-Accept-Language: en Xref: hgmp.mrc.ac.uk bionet.software:903 Hello! This is just a quick message to let you know that SGI has implemented the parallel features of Parallel CLUSTAL W 1.8 into CLUSTAL X 1.8. So if any of you are interested in Parallel CLUSTAL X on SGI/IRIX, then simply go to the following page: http://www.sgi.com/chembio/resources/clustalw/parallel_clustalw.html And when you click the "I accept" button at the bottom of the page (the software is of course free), then both Parallel CLUSTAL W ("clustalw_mp") and Parallel CLUSTAL X ("clustalx_mp") will be downloaded in the same file together. Thank you very much for your support, and please do let me know if you have any questions or problems! Just FYI, I have attached the README file for Parallel CLUSTAL W and Parallel CLUSTAL X, which are available for IRIX 6.2 and IRIX 6.5. With regards, Haruna Cofer :) ===== 12 November 1999 This distribution contains a parallelized version of CLUSTAL W 1.8 and CLUSTAL X 1.8 for SGI systems running IRIX 6.5. Specifically, the Pairwise Alignments and Guide Tree computations are parallelized. It should be noted that these releases use a modification of the original pairalign.c file, which was modified to fix a memory access bug in the original code. Specifically, the original CLUSTAL W and CLUSTAL X codes read beyond the bounds of an allocated array, resulting in either a numerical error or a core dump of the program. The change made in pairalign.c (in both CLUSTAL W and CLUSTAL X) is as follows: Replace line 214 of pairalign.c: maxscore = diff(sb1, sb2, se1-sb1+1, se2-sb2+1, (sint)0, (sint)0); with the following line: maxscore = diff(sb1-1, sb2-1, se1-sb1+1, se2-sb2+1, (sint)0, (sint)0); To use the parallelized versions of CLUSTAL W and CLUSTAL X, simply set the MP_SET_NUMTHREADS environment variable to the number of processors you want to use. For example, to use 4 processors: setenv MP_SET_NUMTHREADS 4 If this environment variable is not set, then the default is to use the maximum number of processors on your machine. Then use the "clustalw_mp" executable to run the parallelized version of CLUSTAL W, and the "clustalx_mp" executable to run the parallelized version of CLUSTAL X, in the same way you would use the original "clustalw" and "clustalx" programs. With CLUSTAL X, however, there is an additional option available (-noinfo) that will suppress the status messages that are by default generated at the bottom of the CLUSTAL X window during the Pairwise Alignment calculation. Using the -noinfo option can significantly improve the performance of the Pairwise Alignments, since it eliminates the communication and synchronization required to write the status messages to the X window. To use the -noinfo option, simply call clustalx_mp with the -noinfo option: clustalx_mp -noinfo The clustalx_help file, included in this distribution, has been amended to include the additional -noinfo option. Please send questions or problems to Haruna Cofer (haruna@sgi.com). -- -------------------------------------------------------------------- Haruna N. Cofer 614-855-5245 (tel) Applications - Chem/Bio 248-848-5653 (fax) SGI 800-859-1020 x4553 (v-mail) 715 Affirmed Court x6-265-4553 (internal) Columbus, OH 43230 haruna@sgi.com (e-mail) -------------------------------------------------------------------- From owner-software@net.bio.net Thu Dec 02 02:21:44 1999 Path: hgmp.mrc.ac.uk!warwick!join.news.pipex.net!pipex!taps.news.pipex.net!pipex!bond.dk.uu.net!plug.news.pipex.net!pipex!bowl.news.pipex.net!pipex!warm.news.pipex.net!pipex!brown.telepac.pt!news.telepac.pt!duke.telepac.pt!news.telepac.pt!nntp.cprm.net!Pollux.Teleglobe.net!news.highway.telekom.at!newsfeed03.univie.ac.at!newscore.univie.ac.at!news-spur1.maxwell.syr.edu!news.maxwell.syr.edu!newspeer1.nac.net!news.mv.net!biosci!PANACOM.COM!hzzay From: hzzay@PANACOM.COM Newsgroups: bionet.software Subject: 2000 How to Books Date: 1 Dec 1999 08:46:45 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 60 Sender: daemon@net.bio.net Distribution: world Message-ID: <19991201144412.95F9C4E06@smtp.popsite.net> NNTP-Posting-Host: net.bio.net Xref: hgmp.mrc.ac.uk bionet.software:904 HELLO: THIS IS AN ADVERTISEMENT FOR THE PUBLISHERS CD-ROM, IF YOU HAVE NO INTEREST IN THIS INFORMATION, PLEASE CLICK DELETE. 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From owner-software@net.bio.net Thu Dec 02 04:24:44 1999 Path: hgmp.mrc.ac.uk!warwick!fu-berlin.de!nf1.mgmt.sympatico.ca!news1.bellglobal.com!news20.bellglobal.com.POSTED!not-for-mail Message-ID: <3845F418.74AD918@ait.halifax.iti.ca> From: Angus Chisholm Reply-To: angus_chisholm@hotmail.com Organization: None X-Mailer: Mozilla 4.05 [en]C-SYMPA (Win95; I) MIME-Version: 1.0 Newsgroups: bionet.software Subject: Bioinformatics Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Lines: 8 Date: Thu, 02 Dec 1999 04:24:42 GMT NNTP-Posting-Host: 142.177.90.66 X-Trace: news20.bellglobal.com 944108682 142.177.90.66 (Wed, 01 Dec 1999 23:24:42 EDT) NNTP-Posting-Date: Wed, 01 Dec 1999 23:24:42 EDT Xref: hgmp.mrc.ac.uk bionet.software:906 I am a scientific IT professional with a diverse background in biology/ecotoxicology and computer programming. I have an insatiable thirst for knowledge, and I thoroughly enjoy being challenged, however, I am finding it difficult to land a Bioinformatics position. Does anyone have any suggestions as to how I crack this industry?? My email is listed below: angus_chisholm@hotmail.com From owner-software@net.bio.net Thu Dec 02 12:08:29 1999 Path: hgmp.mrc.ac.uk!warwick!fu-berlin.de!newspeer.ebone.net!amsnews01.chello.com!carrier1.net!newspeer.clara.net!news.clara.net!baron.netcom.net.uk!netcom.net.uk!server3.netnews.ja.net!news.icnet!m.mitchell From: m.mitchell@icrf.icnet.uk (Mike Mitchell) Newsgroups: bionet.software Subject: Re: Transmembrane prediction Date: Thu, 02 Dec 1999 11:57:09 +0000 Organization: Imperial Cancer Research Fund Lines: 27 Message-ID: References: <384572FD.50EDB1EB@icrf.icnet.uk> NNTP-Posting-Host: morpheus.lif.icnet.uk Mime-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit X-Newsreader: Yet Another NewsWatcher 2.4.0 Xref: hgmp.mrc.ac.uk bionet.software:907 In article <384572FD.50EDB1EB@icrf.icnet.uk>, Arne Mueller wrote: > I'm looking for a transmembrane prediction program, the source code > should be free available for academic use. I've to install the program > on site for large scale use so I can't use a web-service. I've already > tried MEMSAT and TOPPRED2. Both programs seem to overpredict > transmembrane helices in some sequences. In general the ExPASy website is a good starting point for protein analysis resources: http://www.expasy.ch/ and in particular: http://www.expasy.ch/tools/#transmem You may also want to try: http://azusa.proteome.bio.tuat.ac.jp/sosui/mem_pred.html -- Michael Mitchell "Smoke me a kipper, User Support I'll be back for breakfast." Molecular Biology Software Ace Rimmer, Test Pilot +44 (0)171 269 3115 BBC-TV Red Dwarf ENFJ From owner-software@net.bio.net Thu Dec 02 14:38:05 1999 Path: hgmp.mrc.ac.uk!pegasus.csx.cam.ac.uk!warwick!fu-berlin.de!newsfeed.direct.ca!logbridge.uoregon.edu!uwm.edu!biosci!HOTMAIL.COM!patsfan99 From: patsfan99@HOTMAIL.COM ("Patriot Nation") Newsgroups: bionet.software Subject: assmebly software Date: 2 Dec 1999 06:24:57 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 12 Sender: daemon@net.bio.net Distribution: world Message-ID: <19991202141703.50588.qmail@hotmail.com> NNTP-Posting-Host: net.bio.net Xref: hgmp.mrc.ac.uk bionet.software:908 Does anyone know the capacity of some of the popular desktop sequence assembly software? I have heard that the assembler sold with VectorNTI can't even assemble 500 fragments. Is that true? What is the capacity of Sequencher? How about DNASTAR's software? I've heard the DNASTAR stuff is very powerful. Any feedback would be very helpful. Thanks, Pat Fan ______________________________________________________ Get Your Private, Free Email at http://www.hotmail.com From owner-software@net.bio.net Thu Dec 02 15:26:48 1999 Path: hgmp.mrc.ac.uk!warwick!fu-berlin.de!isdnet!pasteur.fr!nefertiti.pasteur.fr!letondal From: letondal@pasteur.fr (Catherine Letondal) Newsgroups: bionet.software Subject: Re: Transmembrane prediction Date: 2 Dec 1999 15:25:51 GMT Organization: Institut Pasteur, Paris Lines: 47 Distribution: world Message-ID: <82631v$3v2$1@desdemone.pasteur.fr> References: <384572FD.50EDB1EB@icrf.icnet.uk> <19991201163353.A976@nhgri.nih.gov> Reply-To: letondal@pasteur.fr (Catherine Letondal) NNTP-Posting-Host: nefertiti.pasteur.fr X-Trace: desdemone.pasteur.fr 944148351 4066 157.99.64.20 (2 Dec 1999 15:25:51 GMT) X-Complaints-To: usenet@pasteur.fr NNTP-Posting-Date: 2 Dec 1999 15:25:51 GMT X-Newsreader: mxrn 6.18-31 Xref: hgmp.mrc.ac.uk bionet.software:909 You could as well use the BioNetbook : http://www.pasteur.fr/recherche/BNB/bnb-en.html and ask for the word: membrane or directly: http://www.pasteur.fr/cgi-bin/biology/bnb_s.pl?query=membrane&english=1 In article <19991201163353.A976@nhgri.nih.gov>, jfryan@NHGRI.NIH.GOV (Joe Ryan) writes: >> I'm looking for a transmembrane prediction program, the source code >> should be free available for academic use. I've to install the program >> on site for large scale use so I can't use a web-service. I've already >> tried MEMSAT and TOPPRED2. Both programs seem to overpredict >> transmembrane helices in some sequences. > >This is from an old post to this group. > >:> I am looking for software that can predict transmembrane domains in >:> proteins. >: >:Here is a list in no particular order: >: >:TMPRED: http://www.ch.embnet.org/software/TMPRED_form.html >:TopPred2: http://www.biokemi.su.se/~server/toppred2/ >:DAS: http://www.biokemi.su.se/~server/DAS/ >:SOSUI: http://www.tuat.ac.jp/~mitaku/adv_sosui/ >:TMHMM: http://www.cbs.dtu.dk/services/TMHMM-1.0/ >:HMMTOP: http://www.enzim.hu/hmmtop/ >:PredictProtein: http://www.embl-heidelberg.de/predictprotein/ >:PSIpred: http://globin.bio.warwick.ac.uk/psipred/ >: >:TMBASE: http://www.ch.embnet.org/software/tmbase/TMBASE_doc.html >:(TMBASE is A Database of Membrane Spanning Protein Segments) >: >:Love, >: Joe >:-- >:Joseph Ryan >:Programmer >:National Human Genome Research Institute > > > -- Catherine Letondal -- Pasteur Institute Computing Center From owner-software@net.bio.net Thu Dec 02 17:49:08 1999 Path: hgmp.mrc.ac.uk!warwick!fu-berlin.de!news.maxwell.syr.edu!newsswitch.lcs.mit.edu!uchinews!nntp-server.caltech.edu!seqaxp.bio.caltech.edu!MATHOG From: mathog@seqaxp.bio.caltech.edu Newsgroups: bionet.software Subject: SMP vs. Beowulf? Date: 2 Dec 1999 17:47:48 GMT Organization: Biology Division, Caltech, Pasadena CA 91125 Lines: 38 Message-ID: <826bc4$s1u@gap.cco.caltech.edu> Reply-To: mathog@seqaxp.bio.caltech.edu NNTP-Posting-Host: seqaxp.bio.caltech.edu Xref: hgmp.mrc.ac.uk bionet.software:910 Many of the key sequence analysis packages are now threaded. That means they can run on SMP machines and use multiple CPUs to speed things up. The other type of multicpu "machine" in common use these days is a distributed system, like a Beowulf cluster. In terms of $/Spec distributed machines tend to be a lot cheaper than the SMP equivalents, especially so when you start looking at N >> 2. For this reason, many "supercomputers" are now distributed machines. The database search algorithms are naturals for distributed calculations. Recent versions of Fasta come with both threaded and PVM variants. I've not seen a comparison of the performance though. Has anybody tried it with an N node SMP machine vs. an N node distributed machine, with equivalent CPUs on both? BLAST too seems like a good candidate for distributed computing. For instance, imagine BLAST on "nr" on an N node distributed machine: 1. format nr into N "equal" sized BLAST databases (for instance, by assigning sequence j to a database via modulo(j,N)). 2. run each query sequence on N machines, each with one chunk of the common database preloaded into memory. 3. merge the results from the N machines. Other than a requirement for putting in a correction for the true database size it at least seems straightforward. However, while BLAST is available threaded, I've not been able to find anything which appears to be for use in distributed systems. Is there a distributed implementation of BLAST as well? If not, is it because it's been tried and failed, or because nobody has attempted it yet? Thanks, David Mathog mathog@seqaxp.bio.caltech.edu Manager, sequence analysis facility, biology division, Caltech From owner-software@net.bio.net Thu Dec 02 20:30:49 1999 Path: hgmp.mrc.ac.uk!warwick!fu-berlin.de!howland.erols.net!newsfeed.fast.net!uunet!ffx.uu.net!hearst.acc.Virginia.EDU!murdoch.acc.Virginia.EDU!not-for-mail From: wrp@alpha0.bioch.virginia.edu (William R. Pearson) Newsgroups: bionet.software Subject: Re: SMP vs. Beowulf? Date: 02 Dec 1999 15:18:22 -0500 Organization: University of Virginia Lines: 33 Message-ID: References: <826bc4$s1u@gap.cco.caltech.edu> NNTP-Posting-Host: alpha0.bioch.virginia.edu X-Newsreader: Gnus v5.7/Emacs 20.4 Xref: hgmp.mrc.ac.uk bionet.software:911 We have not looked into SMP vs Beowulf exhaustively, but we have quite a bit of experience. (1) SMP is far easier to configure and run than PVM (or MPI or others). You just run the program; if its threaded SMP, it runs faster. SMP programs are also much easier to develop and debug. (2) Our current PVM implementation is not as CPU efficient as spawning a bunch of threaded fasta33_t runs when the algorithm is fast. For Smith-Waterman, which is compute bound, they are equally efficient. In line with point (1), I think it is easier to improve the performance of an SMP program. I don't think this is an inherent shortcoming of PVM, but reflect the fact that our PVM implementaion (and very primitive scheduling system) was build when machines and interconnections were much slower. (3) However, we have not yet found a version of Linux Pthreads that works 100% of the time. With the kernal and C-libraries that we use, we see failures which are almost certainly caused by Linux Pthreads. (We never see them in any other environment, and we don't see them unthreaded.) Linux PVM is very reliable. So we use both. We use PVM for genome-vs-genome Smith-Waterman searches, and we use SMP threaded versions for our WWW server. Starting up PVM (or any other system that spawns large numbers of jobs on other machines) has a high overhead, which isn't worth the cost when the search will be done in a few minutes - we don't see nearly as much overhead with SMP machines. But large SMP machines are considerably more expensive. A cost-effective solution is a WWW server that sends its searches to a bank of 1-CPU or 2-CPU machines. Bill Pearson From owner-software@net.bio.net Fri Dec 03 05:10:28 1999 Path: hgmp.mrc.ac.uk!warwick!fu-berlin.de!newsfeed.berkeley.edu!cgl.ucsf.edu!itssrv1.ucsf.edu!macmac-2.ucsf.edu!user From: spam@127.0.0.1 (Bernard Murray, PhD) Newsgroups: bionet.software Subject: Re: assmebly software Date: Thu, 02 Dec 1999 19:56:11 -0700 Organization: UCSF Lines: 22 Distribution: world Message-ID: References: <19991202141703.50588.qmail@hotmail.com> NNTP-Posting-Host: macmac-2.ucsf.edu Xref: hgmp.mrc.ac.uk bionet.software:912 In article <19991202141703.50588.qmail@hotmail.com>, patsfan99@HOTMAIL.COM ("Patriot Nation") wrote: > Does anyone know the capacity of some of the popular desktop sequence > assembly software? I have heard that the assembler sold with VectorNTI > can't even assemble 500 fragments. Is that true? What is the capacity of > Sequencher? How about DNASTAR's software? I've heard the DNASTAR stuff is > very powerful. Any feedback would be very helpful. Have a look at Miller & Powell (1994) "A quantitative comparison of DNA sequence assembly programs" J Comput Biol 1994 Winter;1(4):257-69 Mark did a very thorough job with the offerings at the time but I don't think they looked at DNASTAR or VectorNT. Bernard -- Bernard P. Murray, PhD bpmurray at cgl . ucsf . edu Department of Cellular & Molecular Pharmacology, UCSF From owner-software@net.bio.net Fri Dec 03 11:32:04 1999 Path: hgmp.mrc.ac.uk!pegasus.csx.cam.ac.uk!not-for-mail From: Tim Cutts Newsgroups: bionet.software Subject: Re: SMP vs. Beowulf? Date: 03 Dec 1999 11:30:28 +0000 (GMT) Organization: Linux Unlimited Lines: 46 Message-ID: References: <826bc4$s1u@gap.cco.caltech.edu> NNTP-Posting-Host: rrw1000.sel.cam.ac.uk X-Newsreader: trn 4.0-test70 (17 January 1999) Originator: timc@news.chiark.greenend.org.uk ([127.0.0.1]) Xref: hgmp.mrc.ac.uk bionet.software:913 William R. Pearson wrote: > >We have not looked into SMP vs Beowulf exhaustively, but we have quite >a bit of experience. > >(1) SMP is far easier to configure and run than PVM (or MPI or > others). You just run the program; if its threaded SMP, it runs > faster. SMP programs are also much easier to develop and debug. There are a couple of points to make here. 1) MPI is far more efficient than PVM. No-one should be using PVM these days. 2) MPI is more flexible than threads in that an MPI version of a program can still be run on an SMP machine, as well as on a distributed network. Programs like BLAST and FASTA have a problem in that their I/O requirements are large, and this can be a real performance problem on a distributed network. For example, you could think of implementing your parallel program by giving each MPI process part of the database to work on. The problem there is that you have a large overhead in getting the database to the processor. Ethernet is too slow, and will destroy any performance gain from the parallel code. A better solution, easier to implement, and probably more useful for most purposes, is a workstation farm with each node having a local copy of all the target databases, and run normal single threaded blast on each. For large scale work, you typically want to blast lots of sequences against several databases, so such coarse grained parallelisation is fine. You just need some way of distributing the blast jobs to your farm. You can either do this with some fairly trivial perl scripting, or you can use some more flexible commercial offering. I can highly recommend platform computing's LSF package. It's expensive, but it extremely good at managing workstation farms, in particular with cycle stealing from machines when they're idle. Using LSF at the University of Cambridge, I got 100 %CPU utilisation on a 20 workstation farm. These were interactive workstations too; people doing NMR spectrum assignment at the workstations weren't even aware their machines were also performing highly CPU intensive analysis jobs in the background. Efficient use of the workstations like this ultimately saved money, since they realised that they no longer needed to buy further machines. Tim. From owner-software@net.bio.net Fri Dec 03 17:08:06 1999 Path: hgmp.mrc.ac.uk!server1.netnews.ja.net!fu-berlin.de!logbridge.uoregon.edu!uwm.edu!biosci!HOTMAIL.COM!patsfan99 From: patsfan99@HOTMAIL.COM ("Patriot Nation") Newsgroups: bionet.software Subject: Re: RE: assembly software Date: 3 Dec 1999 09:05:16 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 8 Sender: daemon@net.bio.net Distribution: world Message-ID: <19991203165717.12232.qmail@hotmail.com> NNTP-Posting-Host: net.bio.net Xref: hgmp.mrc.ac.uk bionet.software:914 Thanks for the reply, but 1994 was a long time ago in terms of software. The VectorNTI stuff has only been around for a few months (and is likely still full of bugs). DNASTAR has been around for a long time, but has had many upgrades and improvements since 1994. Does anyone have more recent experience with these packages? ______________________________________________________ Get Your Private, Free Email at http://www.hotmail.com From owner-software@net.bio.net Fri Dec 03 17:08:10 1999 Path: hgmp.mrc.ac.uk!server1.netnews.ja.net!fu-berlin.de!logbridge.uoregon.edu!uwm.edu!biosci!HACKERGENE.UCDAVIS.EDU!akozik From: akozik@HACKERGENE.UCDAVIS.EDU (Alexander Kozik) Newsgroups: bionet.software Subject: 3700 crashes very often Date: 3 Dec 1999 09:14:16 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 17 Sender: daemon@net.bio.net Distribution: world Message-ID: <3847F911.4EAE5B78@hackergene.ucdavis.edu> NNTP-Posting-Host: net.bio.net Xref: hgmp.mrc.ac.uk bionet.software:915 Hi! Recently our lab got 3700 machine. However our 3700 crashes very often (almost every second run). The tech support from PE repairs it three times a week without any success. I would like to know from other 3700 users: Is it a regular 3700 life / behavior or our lab is unlucky with given machine? What is known about 3700 reliability? Thanks a lot in advance, Alexander Kozik, Dept. of Biological Chemistry University of California at Davis. From owner-software@net.bio.net Fri Dec 03 17:25:54 1999 Path: hgmp.mrc.ac.uk!server1.netnews.ja.net!fu-berlin.de!news.uni-stuttgart.de!news.belwue.de!chevreux From: chevreux@mbp-lserv1.inet.dkfz-heidelberg.de (Bastien Chevreux) Newsgroups: bionet.software Subject: Re: assmebly software Date: 3 Dec 1999 17:25:51 GMT Organization: Speaking for myself (really) Lines: 27 Message-ID: References: <19991202141703.50588.qmail@hotmail.com> Reply-To: b.chevreux@dkfz-heidelberg.de NNTP-Posting-Host: mbp-lserv1.inet.dkfz-heidelberg.de X-Newsreader: slrn (0.9.5.2 UNIX) Xref: hgmp.mrc.ac.uk bionet.software:916 On 2 Dec 1999 06:24:57 -0800, Patriot Nation wrote: >Does anyone know the capacity of some of the popular desktop sequence >assembly software? I have heard that the assembler sold with VectorNTI >can't even assemble 500 fragments. Is that true? What is the capacity of >Sequencher? How about DNASTAR's software? I've heard the DNASTAR stuff is >very powerful. Any feedback would be very helpful. You might want to have a look at http://www.dkfz-heidelberg.de/mbp_ased/ where we have downloadable snapshots of our MIRA assembly software which also uses an integrated trace signal analyser (EdIt) to detect and _correct_ many of the trivial and not so trivial errors that occur in reads. It has been tested with projects up to 10,000 reads, we're currently investigating 20,000+ read projects with it. Tested with ABI and ALF sequences. Hope I could help, Bastien ------------------------------------------------------------------------------- Dipl.-Inform. Med. Bastien Chevreux -- b.chevreux@dkfz-heidelberg.de Deutsches Krebsforschungszentrum Heidelberg -- Abteilung Molekulare Biophysik Im Neuenheimer Feld 280 -- 69120 Heidelberg -- Phone: +49 6221 42 2336 ------------------------------------------------------------------------------- -It's mine. =Nope, it's my one. *CRASH* =Alright. It WAS yours. From owner-software@net.bio.net Fri Dec 03 17:34:30 1999 From: "Burluth Enterprises" Newsgroups: bionet.software Subject: Y2K T-SHIRTS Date: Thu, 2 Dec 1999 20:50:26 -0700 Lines: 14 X-Newsreader: Microsoft Outlook Express 4.72.3110.1 X-MIMEOLE: Produced By Microsoft MimeOLE V4.72.3110.3 NNTP-Posting-Host: 216.146.167.101 Message-ID: <38473db1_7@news.newsfeeds.com> X-Trace: 2 Dec 1999 21:49:05 -0600, 216.146.167.101 X-Authenticated-User: rambo_boy X-Report: Report abuse to abuse@newsfeeds.com X-Abuse-Info: Please be sure to forward a copy of ALL headers, INCLUDING the body X-Abuse-Info2: ALL Spam complaints are acted upon within 24 hours! Organization: Newsfeeds.com http://www.newsfeeds.com 73,000+ UNCENSORED Newsgroups. Path: hgmp.mrc.ac.uk!pegasus.csx.cam.ac.uk!daresbury!uninett.no!news.maxwell.syr.edu!newsfeed.enteract.com!news.compuserve.com!news-master.compuserve.com!feed3.newsfeeds.com!newsfeeds.com!feed2.newsfeeds.com!newsfeeds.com!news.newsfeeds.com!newsfeeds.com!216.146.167.101 Xref: hgmp.mrc.ac.uk bionet.software:917 Please pardon us if this is an off-topic post, but due to the unique nature of these y2k related t-shirts, we thought you would like to know. The t-shirts we have available right now, will be funny (or serious) to certain groups. Although they are for everyone, typically the computer buff type people will find them the most amusing. Stop by and check out what we have right now. They are great for yourself or as gifts for others. http://www.y2k-fun.com -----------== Posted via Newsfeeds.Com, Uncensored Usenet News ==---------- http://www.newsfeeds.com The Largest Usenet Servers in the World! ------== Over 73,000 Newsgroups - Including Dedicated Binaries Servers ==----- From owner-software@net.bio.net Sat Dec 04 03:15:26 1999 Path: hgmp.mrc.ac.uk!pegasus.csx.cam.ac.uk!daresbury!server5.netnews.ja.net!nntp.news.xara.net!xara.net!gxn.net!dispose.news.demon.net!demon!news.maxwell.syr.edu!logbridge.uoregon.edu!news.Arizona.EDU!not-for-mail From: John Little Newsgroups: bionet.software Subject: Software to locate mutations in a known sequence? Date: Fri, 03 Dec 1999 19:49:06 -0700 Organization: University of Arizona Message-ID: <38488121.CDBD3DE2@u.arizona.edu> NNTP-Posting-Host: biochem5.biosci.arizona.edu Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 4.61 [en] (Win95; I) X-Accept-Language: en Lines: 13 Xref: hgmp.mrc.ac.uk bionet.software:918 We isolate lots of mutants in a sequenced organism (phage lambda), and would like to find software in which we can have a "template" showing the wild-type sequence, with multiple landmarks including genes, to which we can compare the sequence of a mutant. Ideally, it would identify any changes, then tell us either 1. which gene is altered and the amino acid change or 2. which cis-acting site is changed. Any suggestions for such software? John Little Department of Biochemistry University of Arizona jlittle@u.arizona.edu From owner-software@net.bio.net Sat Dec 04 09:38:04 1999 Path: hgmp.mrc.ac.uk!server1.netnews.ja.net!fu-berlin.de!logbridge.uoregon.edu!uwm.edu!biosci!PRTB.COM.RU!foi11 From: foi11@PRTB.COM.RU (anderson) Newsgroups: bionet.software Subject: SECRETS REVEALED!!! Date: 4 Dec 1999 01:21:08 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 52 Sender: daemon@net.bio.net Distribution: world Message-ID: <199912042927HAA35610@378h33kim398.infocomm.it> NNTP-Posting-Host: net.bio.net Xref: hgmp.mrc.ac.uk bionet.software:919 ******************************************************* This list is opt-in only. We are linked to many web sites that offer free subscriptions to our opt-in list. You will be removed from this list at any time by following the simple instructions that can be found at the end of this email. THIS IS NOT SPAM! 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To help us insure quality control, you may inform P.J. Software Company management directly at micro82@angelfire.com if you have any concerns regarding the delivery of this message. This message has been delivered by a third party marketing agency in compliance with federal guidelines. You may rcmove your name from our opt-in list by sending an e-mail to the address below with the word rcmove in the subj. 4e To From owner-software@net.bio.net Sat Dec 04 10:08:19 1999 Path: hgmp.mrc.ac.uk!server1.netnews.ja.net!fu-berlin.de!logbridge.uoregon.edu!uwm.edu!biosci!MEPHI.RU!geja33 From: geja33@MEPHI.RU (dane482) Newsgroups: bionet.software Subject: ARE YOU BEING INVESTIGATED?? Date: 4 Dec 1999 02:03:11 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 53 Sender: daemon@net.bio.net Distribution: world Message-ID: <199912042481LAA1003@sj28book27uw.cit.chalmers.se> NNTP-Posting-Host: net.bio.net Xref: hgmp.mrc.ac.uk bionet.software:920 ******************************************************* This list is opt-in only. We are linked to many web sites that offer free subscriptions to our opt-in list. You will be removed from this list at any time by following the simple instructions that can be found at the end of this email. THIS IS NOT SPAM! You are on our mailing list because you subscribed or someone you know subscribed for you at one of our associate web sites. ******************************************************* Cyber Investigator "EASY WAY TO FIND OUT ANYTHING ABOUT ANYONE" http://3437342643/10.html Cyber Investigator TAKES YOU BEYOND WHAT SEARCH ENGINES CAN DO! Cyber Investigator is an amazing new tool that allows you to find EVERYTHING you ever wanted to know about your EMPLOYEES, FRIENDS, RELATIVES, SPOUSE, NEIGHBORS, even your BOSS! You can check out ANYONE, ANYTIME, ANYWHERE, right on the internet... Here's the best part: With our SECURE ORDER SYSTEM you can have this amazing tool in your hands right away and you can be doing your own on-line investigations IMMEDIATELY. To find out more about what Cyber Investigator can do for YOU! CLICK HERE: http://3437342643/10.html Thanks, P.J. Software Company Security Software Developers Since 1995 P.J. Software Company respects others right to privacy. To help us insure quality control, you may inform P.J. Software Company management directly at micro82@angelfire.com if you have any concerns regarding the delivery of this message. This message has been delivered by a third party marketing agency in compliance with federal guidelines. You may rcmove your name from our opt-in list by sending an e-mail to the address below with the word rcmove in the subj. DHD87-28I28-29 Q From owner-software@net.bio.net Sat Dec 04 14:11:29 1999 Path: hgmp.mrc.ac.uk!server1.netnews.ja.net!fu-berlin.de!news.icm.edu.pl!not-for-mail From: Piotr Kozbial Newsgroups: bionet.software Subject: Re: SMP vs. Beowulf? Date: Sat, 04 Dec 1999 15:11:40 +0100 Organization: http://news.icm.edu.pl/ Lines: 26 Message-ID: <3849211C.8AA04ACE@ibb.waw.pl> References: <826bc4$s1u@gap.cco.caltech.edu> Reply-To: piotrk-NO@SPAMM-ibb.waw.pl NNTP-Posting-Host: arete.ibb.waw.pl Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Trace: sunsite.icm.edu.pl 944316686 10988 212.87.28.79 (4 Dec 1999 14:11:26 GMT) X-Complaints-To: abuse@news.icm.edu.pl NNTP-Posting-Date: 4 Dec 1999 14:11:26 GMT X-Accept-Language: en X-Mailer: Mozilla 4.7 [en] (X11; U; Linux 2.2.10 i686) Xref: hgmp.mrc.ac.uk bionet.software:921 There are other kinds of Linux clusters. You can read discussion about "Choosing the Right Cluster System" http://slashdot.org/article.pl?sid=99/11/12/0354238 For example (posted by SEWilco): Beowulf is one of a family of parallel programming API tools. Programs must use the API to accomplish parallel programming. http://cesdis.gsfc.nasa.gov/linux/beowulf/beowulf.html SCI is fast hardware with support for distributed shared memory, messaging, and data transfers. Again, if you don't use the API then no gain. http://nicewww.cern.ch/~hmuller/sci.htm DIPC is distributed System V IPC. Programs which use the IPC API can be converted to DIPC easily, such as just by adding the DIPC flag to the IPC call. http://wallybox.cei.net/dipc/dipc.html MOSIX is the most general-purpose. Processes are scattered across a cluster automatically without having to modify the programs. No API needed other than usual Unix-level process use. Allows parallel execution of any program, although full use requires a parallel program design. http://www.cnds.jhu.edu/mirrors/mosix/ From owner-software@net.bio.net Sat Dec 04 17:35:15 1999 Path: hgmp.mrc.ac.uk!server1.netnews.ja.net!fu-berlin.de!news.idt.net!netnews.com!newspeer1.nac.net!easynet-tele!easynet.net!tank.news.pipex.net!pipex!warm.news.pipex.net!pipex!krypton.inbe.net!INbe.net!not-for-mail From: "louis vanuytsel" Newsgroups: bionet.software Subject: visioneer paperport Date: Sat, 4 Dec 1999 18:32:08 +0100 Organization: UUNET Benelux (post does not reflect views of UUNET Benelux) Lines: 7 Message-ID: <82bjcd$bb$1@xenon.inbe.net> NNTP-Posting-Host: uu212-190-7-204.unknown.uunet.be X-Priority: 3 X-MSMail-Priority: Normal X-Newsreader: Microsoft Outlook Express 5.00.2615.200 X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2615.200 Xref: hgmp.mrc.ac.uk bionet.software:922 Does anybody knows where I can download Visioneer Paperport? Thanks Louis Vanuytsel From owner-software@net.bio.net Sat Dec 04 19:21:30 1999 Path: hgmp.mrc.ac.uk!server1.netnews.ja.net!fu-berlin.de!headwall.stanford.edu!newsfeed.stanford.edu!newsfeed.berkeley.edu!newshub.sdsu.edu!franklin.ljcrf.edu!not-for-mail From: greg@franklin.burnham-inst.org (Dr. Greg Quinn) Newsgroups: bionet.software Subject: Readseq dll? Date: 4 Dec 1999 19:26:12 GMT Organization: COMPUTATIONAL BIOLOGY at The BURNHAM INSTITUTE Lines: 6 Message-ID: <82bpsk$i7d$1@franklin.ljcrf.edu> NNTP-Posting-Host: franklin.ljcrf.edu X-Newsreader: TIN [UNIX 1.3 950824BETA PL0] Xref: hgmp.mrc.ac.uk bionet.software:923 I'm writing a little VB app to do some housekeeping for my sequences; does anyone know of a windows dll port of Don Gilberts readseq, to efficiently allow me to make calls to convert formats? (I'm just interested in the dynamic linked library and not a windows program). Thanks for any help Greg From owner-software@net.bio.net Sat Dec 04 20:38:42 1999 Path: hgmp.mrc.ac.uk!server1.netnews.ja.net!fu-berlin.de!logbridge.uoregon.edu!news.indiana.edu!not-for-mail From: gilbertd@bio.indiana.edu (Don Gilbert) Newsgroups: bionet.software Subject: Re: Readseq dll? Date: 4 Dec 1999 20:38:39 GMT Organization: Biology, Indiana University - Bloomington Lines: 12 Message-ID: <82bu4f$44u$1@flotsam.uits.indiana.edu> References: <82bpsk$i7d$1@franklin.ljcrf.edu> NNTP-Posting-Host: chipmunk.bio.indiana.edu Xref: hgmp.mrc.ac.uk bionet.software:924 Greg, I'm not aware of a readseq dll for windows. I don't build dll's so don't know what is involved, but if it is a matter of compiling c code with thr right switches, it may be easy to do with verison 1 of readseq. If MSoft would want to do something useful to support java on its os, you might use readseq version 2 java jar in place of a dynamic link library. - Don -- -- d.gilbert--bioinformatics--indiana-u--bloomington-in-47405 -- gilbertd@bio.indiana.edu From owner-software@net.bio.net Sat Dec 04 22:28:47 1999 Path: hgmp.mrc.ac.uk!not-for-mail From: Keith James Newsgroups: bionet.software Subject: Re: RE: assembly software Date: 04 Dec 1999 22:28:47 +0000 Organization: MRC Human Genome Mapping Project Resource Centre Lines: 27 Message-ID: References: <19991203165717.12232.qmail@hotmail.com> NNTP-Posting-Host: fes18.sanger.ac.uk Mime-Version: 1.0 (generated by tm-edit 7.106) Content-Type: text/plain; charset=NIL X-Trace: niobium.hgmp.mrc.ac.uk 944346527 2963 193.62.207.222 (4 Dec 1999 22:28:47 GMT) X-Complaints-To: news@hgmp.mrc.ac.uk NNTP-Posting-Date: 4 Dec 1999 22:28:47 GMT X-Newsreader: Gnus v5.5/Emacs 20.3 Xref: hgmp.mrc.ac.uk bionet.software:925 >>>>> "Patriot" == "Patriot Nation" writes: Patriot> Thanks for the reply, but 1994 was a long time ago in Patriot> terms of software. The VectorNTI stuff has only been Patriot> around for a few months (and is likely still full of Patriot> bugs). DNASTAR has been around for a long time, but has Patriot> had many upgrades and improvements since 1994. Does Patriot> anyone have more recent experience with these packages? I've used the DNAStar package to do small scale assembly (about a year ago now) and found it to be an unpleasant experience. My main gripe with it was instability (the Windows version anyway - I've never used it on a Mac). I was constantly finding bugs, to the extent that I would only expect to see in early beta software. They probably still distribute a demo CD, so the best thing would be to try before you buy, especially at that price. Their web page says it can handle 64,000 reads. That's enough for a bacterial whole genome shotgun. I'd want to be really, really sure of its stability to use it to that capacity. -- Keith From owner-software@net.bio.net Sun Dec 05 01:36:22 1999 Path: hgmp.mrc.ac.uk!server1.netnews.ja.net!fu-berlin.de!news-peer.gip.net!news.gsl.net!gip.net!spring.edu.tw!netnews.hinet.net!news From: uk03@hello.com.tw Newsgroups: bionet.software Subject: 200¤¸ªººô¸ô§Q¾¹ Date: 5 Dec 1999 01:36:18 GMT Organization: DCI HiNet Lines: 41 Message-ID: <82cfii$idf@netnews.hinet.net> NNTP-Posting-Host: h151.s130.ts32.hinet.net Xref: hgmp.mrc.ac.uk bionet.software:926 Á`­p¦W³æ370¸Uµ§...¥u­n¤j¯S»ù200!!!!! 120-130¸Uµ§ªÖ©wokªº¦W³æ!!((ªá¤F¥b¦~¾ã²z¥X¨Óªº..¦]¦Û¤v¾ã²zªºÁÙ¦b¼W¥[¬G¤£¤Óª¾¹D¦h¤Öµ§¤F..)) 150¸Uµ§¾ã²z¤£­«½Æªº¦W³æ!!((¶R¤F4¤ùµo«H¾ã²z¥X¨Óªº)) 100¸Uµ§¥¼¾ã²zªº¦W³æ!!((¨ì·s»D¸s²Õ§ìªº)) 1¤ù¦X5¤ùºëµØ...»ù¿ú¯À§O¤H¤@¤ùªº4¤À¤§¤@.. ¾÷·|¬O¦³¦ý¬O¤£ªø¦³.. ¦ý¬O§ÚªÖ©w³o¬O20¥@¬öªº³Ì«á¤@¦¸...!!! ¥H«á¤@¤ùöt¨ì800..¤£­n«á®¬­ò!! ¥þ³¡370¸Uµ§!!! ¦h¤Ö...600...¤£...400...¤£... ²{¦b¥u­n""" 2 0 0 !!"""..­­¤@¤H¶R5¤ù.. ¶R¤F¦bÂà½æ..¤£ÄF§A..¦Ü¤Ööt3­¿.. ¦]¤£¦b¿N¤ù.£®¤£¦b·Qµo«H.. ©Ò¥H¤j½â½æ.. ¶R5¤ùªÌ¥iÀ°¥L°µ¤@­Ó²³æªººô­¶..^^ §O¤£¬Û«H..·Q¦Û¤vºô¸ô³Ð·~¾a²{¦b­ò!! ³t¼·0937638256 ©Î http://www.hello.com.tw/~uk99/ ¦¹ºô§ó·s¤¤¦p¤£¯à¶i¥h½Ð¨£¶q.. °ª¶¯«ÌªF¦a°Ï..¥iª½±µ¨ú³f..¤£¥Î±¾¸¹... §A·QÅý¦Û¤vªººô§}öt°_¨Ó¶Ü??... §A·Q¦Û¤v¿ì¹q¤l³ø..¦ý¬O¥Ó½Ðªººô¯¸Àt¤ò¤SÃø¿ì¶Ü?? §A·Q¦Û¤v·í¦ÑÁó¶Ü?? §A·Q¾aºô¸ôÁÈ¿ú¶Ü?? §A·Qª¾¹D¹q¤l¼s§i«Hªº¥\¤O¶Ü.?? ¥~­±ªºµo«H..20¸U«Ê..1000...!! §A¤]·QÁÈÁȬݨººØ´þ¨ý¶Ü?? §Öcall§Ú§a... §O¦h»¡...¦n±d¦Û¤vª¾´N¦n...§Ö¨Ó¹q§a..0937638256 E-MAIL: uk01@hello.com.tw From owner-software@net.bio.net Mon Dec 06 04:15:18 1999 Path: hgmp.mrc.ac.uk!pegasus.csx.cam.ac.uk!daresbury!uninett.no!news.maxwell.syr.edu!newsfeed.atl.bellsouth.net.MISMATCH!newsfeed.atl!news4.mia.POSTED!not-for-mail From: bakerweb@bellsouth.net (DAVID BAKER) Newsgroups: bionet.software Subject: Information on Windows y2k Compliance (Very Critical) Message-ID: <384b4b70.21069482@news1.lig.bellsouth.net> X-Newsreader: Forte Free Agent 1.11/32.235 Lines: 12 Date: Mon, 06 Dec 1999 05:43:26 GMT NNTP-Posting-Host: 209.214.174.50 X-Trace: news4.mia 944453342 209.214.174.50 (Sun, 05 Dec 1999 23:09:02 EST) NNTP-Posting-Date: Sun, 05 Dec 1999 23:09:02 EST Xref: hgmp.mrc.ac.uk bionet.software:927 This five minutes of your time (to read and apply the test) could very well be the most important time you spend with your computer for the remainder of 1999. You be the judge at: Click Here Do your friends a big favor and share this site with them. I'm set. Are you? From owner-software@net.bio.net Mon Dec 06 04:55:19 1999 Path: hgmp.mrc.ac.uk!pegasus.csx.cam.ac.uk!daresbury!uninett.no!news.algonet.se!algonet!newsfeed.berkeley.edu!newsgate.cuhk.edu.hk!hkusud.hku.hk!hkunae.hku.hk!hkusub.hku.hk!not-for-mail From: Xia Xuhua Newsgroups: bionet.software Subject: Re: Readseq dll? Date: 6 Dec 1999 04:46:27 GMT Organization: The University of Hong Kong Lines: 47 Message-ID: <82ff33$19he5@hkunae.hku.hk> References: <82bpsk$i7d$1@franklin.ljcrf.edu> NNTP-Posting-Host: hkusub.hku.hk X-Newsreader: TIN [UNIX 1.3 release 961025] Xref: hgmp.mrc.ac.uk bionet.software:928 Dr. Greg Quinn wrote: : I'm writing a little VB app to do some housekeeping for my sequences; : does anyone know of a windows dll port of Don Gilberts readseq, to : efficiently allow me to make calls to convert formats? (I'm just : interested in the dynamic linked library and not a windows program). : Thanks for any help : Greg The earlier versions of my program DAMBE included a DLL compiled from readseq (readseq2.dll) that include functions callable from VB, but I no long keep the earlier versions of DAMBE. If you know someone who still runs an early version of DAMBE, then you can ask them for the readseq2.dll in their windows\system directory and I will tell you how to make calls. The new versions of DAMBE includes extensive sequence utilities much beyond READSEQ. I have released a new version of DAMBE with many enhancement and a comprehensive help system. The software is available from my web site: http://web.hku.hk/~xxia/software/software.htm DAMBE is an integrated software package for retrieving, organizing, manipulating, aligning, graphically displaying, and analyzing molecular sequence data. Many tools for comparative sequences analysis and extensive tests of alternative phylogenetic hypotheses have been implemented. Although DAMBE is mainly for molecular sequence data, allele frequency data can also be used by DAMBE for calculating genetic distances or phylogenetic reconstruction. DAMBE runs on Windows 95/98/NT (including the MACs that installed the virtual PC software). Two installation problems have been addressed by Microsoft and I have included the links to the Microsoft solutions related to DAMBE installation. Best. Xuhua ================================================================== Dr. Xuhua Xia | Tel: (852) 2857 8239 (lab) Dept. Ecol. & Biod. | Tel: (852) 2975 5629 (office) Rm 603, T.T. Tsui Building | Fax: (852) 2517 6082 The University of Hong Kong | Email: xxia@hkusua.hku.hk Pukfulam Road | WWW: http://web.hku.hk/~xxia Hong Kong | ================================================================== From owner-software@net.bio.net Mon Dec 06 08:15:22 1999 Path: hgmp.mrc.ac.uk!pegasus.csx.cam.ac.uk!daresbury!uninett.no!news.maxwell.syr.edu!newsfeed.berkeley.edu!newshub.sdsu.edu!franklin.ljcrf.edu!not-for-mail From: greg@franklin.burnham-inst.org (Dr. Greg Quinn) Newsgroups: bionet.software Subject: Re: Readseq dll? Date: 6 Dec 1999 08:11:12 GMT Organization: COMPUTATIONAL BIOLOGY at The BURNHAM INSTITUTE Lines: 69 Message-ID: <82fr30$k6n$1@franklin.ljcrf.edu> References: <82bpsk$i7d$1@franklin.ljcrf.edu> <82ff33$19he5@hkunae.hku.hk> NNTP-Posting-Host: franklin.ljcrf.edu X-Newsreader: TIN [UNIX 1.3 950824BETA PL0] Xref: hgmp.mrc.ac.uk bionet.software:929 Thanks Don and Xuhua for the replies; I seem to remember installing a scientific freeware program a while back that included a dll called readseq; that must have been Xuhua's program. I'll hunt around for an old copy; that will probably be faster for me than exporting functions from the readseq source. Thanks again. Xia Xuhua (xxia@hkusub.hku.hk) wrote: : Dr. Greg Quinn wrote: : : I'm writing a little VB app to do some housekeeping for my sequences; : : does anyone know of a windows dll port of Don Gilberts readseq, to : : efficiently allow me to make calls to convert formats? (I'm just : : interested in the dynamic linked library and not a windows program). : : Thanks for any help : : Greg : : The earlier versions of my program DAMBE included a DLL compiled from : readseq (readseq2.dll) that include functions callable from VB, but I no : long keep the earlier versions of DAMBE. If you know someone who still runs : an early version of DAMBE, then you can ask them for the readseq2.dll in : their windows\system directory and I will tell you how to make calls. : : The new versions of DAMBE includes extensive sequence utilities much beyond : READSEQ. : : I have released a new version of DAMBE with many enhancement and a : comprehensive help system. The software is available from my web site: : : http://web.hku.hk/~xxia/software/software.htm : : DAMBE is an integrated software package for retrieving, organizing, : manipulating, aligning, graphically displaying, and analyzing molecular : sequence data. Many tools for comparative sequences analysis and extensive : tests of alternative phylogenetic hypotheses have been implemented. : Although DAMBE is mainly for molecular sequence data, allele frequency : data can also be used by DAMBE for calculating genetic distances or : phylogenetic reconstruction. : : DAMBE runs on Windows 95/98/NT (including the MACs that installed the : virtual PC software). : : Two installation problems have been addressed by Microsoft and I have : included the links to the Microsoft solutions related to DAMBE : installation. : : Best. : Xuhua : ================================================================== : Dr. Xuhua Xia | Tel: (852) 2857 8239 (lab) : Dept. Ecol. & Biod. | Tel: (852) 2975 5629 (office) : Rm 603, T.T. Tsui Building | Fax: (852) 2517 6082 : The University of Hong Kong | Email: xxia@hkusua.hku.hk : Pukfulam Road | WWW: http://web.hku.hk/~xxia : Hong Kong | : ================================================================== -- ***************************************** Computational Biology Group The Burnham Institute (formerly La Jolla Cancer Research Inst.) 10901 North Torrey Pines road La Jolla CA92037 Phone:(619) 646 3103 Email: greg@franklin.ljcrf.edu http://franklin.ljcrf.edu/greg http://www.greg.com/ ***************************************** From owner-software@net.bio.net Mon Dec 06 15:58:05 1999 Path: hgmp.mrc.ac.uk!server1.netnews.ja.net!fu-berlin.de!logbridge.uoregon.edu!infeed.is.co.za!feeder.is.co.za!helios.is.co.za!not-for-mail Message-ID: <384BDBB3.DB0DFE55@sanbi.ac.za> Date: Mon, 06 Dec 1999 17:52:19 +0200 From: Win Hide X-Mailer: Mozilla 4.05 [en] (Win95; U) MIME-Version: 1.0 Newsgroups: bionet.software Subject: STACK GENE INDEX 2.31 + CLUSTERING and MANAGEMENT TOOLS RELEASED Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Lines: 53 NNTP-Posting-Host: 196.38.142.74 X-Trace: helios.is.co.za 944495840 63354 196.38.142.74 Xref: hgmp.mrc.ac.uk bionet.software:930 SANBI announces the release of STACK - 2.31 : A Whole aligned Gene Index of Human sequences, as well as underlying tissue specific indices. The release is regularly updated with cross-links to UniGene and is supported with consensus, assembly analysis and alignment viewing and extraction at SANBI's website www.sanbi.ac.za/Dbases.html. The database is the only currently existing system that includes a co-distribution of the tools used to cluster and manage the production of the data. STACK_PACK 0.8 alpha: Serial-capable, Parallelised versions of the clustering code(s) are currently available for SGI, SUN and LINUX platforms, (COMPAQ to be released very shortly). STACKdb 2.31 is the first STACKdb release that contains the whole-body-index section derived from the tissue-based clusters of the same release. In the past, the whole-body index section was delivered after the tissue-based clusters. The method employed and assessment of quality of the resource is fully described in: A Comprehensive Approach to Clustering of Expressed Human Gene Sequence: The Sequence Tag Alignment and Consensus Knowledge Base Robert T. Miller, Alan G. Christoffels, Chella Gopalakrishnan, John Burke, Andrey A. Ptitsyn, Tania R. Broveak, and Winston A. Hide. November 1999: Genome Research: 9:1143-1155 And d2_cluster: A Validated Method for Clustering EST and Full-Length cDNA Sequences. John Burke, Dan Davison, and Winston Hide. November 1999: Genome Research: 9:1135-1142 The distribution contains documentation such as: * HOWTO.txt how to get the most from searching STACKdb * STACK2.31_notes.txt release notes and statistics for tissue-based clusters * index2_31.txt release notes and statistics for whole-body-index * tissue_tree.txt strategy for separating ESTs into tissue categories From owner-software@net.bio.net Tue Dec 07 01:28:05 1999 Path: hgmp.mrc.ac.uk!server1.netnews.ja.net!fu-berlin.de!newsfeed.berkeley.edu!newsgate.cuhk.edu.hk!hkusud.hku.hk!hkunae.hku.hk!hkusub.hku.hk!not-for-mail From: Xia Xuhua Newsgroups: bionet.software Subject: New version of DAMBE Date: 7 Dec 1999 01:20:18 GMT Organization: The University of Hong Kong Lines: 32 Message-ID: <82hnci$f462@hkunae.hku.hk> NNTP-Posting-Host: hkusub.hku.hk X-Newsreader: TIN [UNIX 1.3 release 961025] Xref: hgmp.mrc.ac.uk bionet.software:932 Dear All, I have released a new version of DAMBE with many enhancement and a comprehensive help system. The software is available from my web site: http://web.hku.hk/~xxia/software/software.htm DAMBE (Data Analysis in Molecular Biology and Evolution) is an integrated software package for retrieving, organizing, manipulating, aligning, graphically displaying, and analyzing molecular sequence data. Many tools for comparative sequences analysis and extensive tests of alternative phylogenetic hypotheses have been implemented. Although DAMBE is mainly for molecular sequence data, allele frequency data can also be used by DAMBE for calculating genetic distances or phylogenetic reconstruction. DAMBE runs on Windows 95/98/NT (including the MACs that installed the virtual PC software). Two rare installation problems have been addressed by Microsoft and I have included the links to the Microsoft solutions related to DAMBE installation. Best. Xuhua ================================================================== Dr. Xuhua Xia | Tel: (852) 2857 8239 (lab) Dept. Ecol. & Biod. | Tel: (852) 2975 5629 (office) Rm 603, T.T. Tsui Building | Fax: (852) 2517 6082 The University of Hong Kong | Email: xxia@hkusua.hku.hk Pukfulam Road | WWW: http://web.hku.hk/~xxia Hong Kong | ================================================================== From owner-software@net.bio.net Tue Dec 07 12:45:12 1999 Path: hgmp.mrc.ac.uk!pegasus.csx.cam.ac.uk!daresbury!uninett.no!news.maxwell.syr.edu!logbridge.uoregon.edu!uwm.edu!biosci!AOL.COM!bsn2 From: bsn2@AOL.COM Newsgroups: bionet.software Subject: Accept Visa and Mastercard - Lowest Rates !!! Date: 7 Dec 1999 04:25:31 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 23 Sender: daemon@net.bio.net Distribution: world Message-ID: <199912071341.NAA11424@hobbes.sfi.com.ph> Reply-To: bsn2@aol.com NNTP-Posting-Host: net.bio.net Xref: hgmp.mrc.ac.uk bionet.software:933 This is a multi-part message in MIME format. ------=_NextPart_000_018C_01BD9940.715D52A0 Content-Type: text/html; ACCEPT ALL MAJOR CREDIT CARDS
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 From owner-software@net.bio.net Tue Dec 07 12:45:12 1999 Path: hgmp.mrc.ac.uk!pegasus.csx.cam.ac.uk!daresbury!uninett.no!news.algonet.se!algonet!newsfeed.berkeley.edu!newsfeed.stanford.edu!biosci!FUNDCVMEJOR.COM.AR!consultando From: consultando@FUNDCVMEJOR.COM.AR ("CONSULTANDO") Newsgroups: bionet.software Subject: Invitación a participar en lista de educación Date: 7 Dec 1999 04:46:44 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 35 Sender: daemon@net.bio.net Distribution: world Message-ID: <199912062333843.SM00146@mail.fundcvmejor.com.ar> NNTP-Posting-Host: net.bio.net Xref: hgmp.mrc.ac.uk bionet.software:934 Le estamos invitando a participar de un servicio de consultas en temas relacionados con la educación. La FUNDACION VOY CADA VEZ MEJOR, ha creado la lista "CONSULT@NDO" cuyo propósito es el de brindar a estudiantes, docentes, profesionales, instituciones educativas y entidades relacionadas con la educación, la posibilidad de facilitar y promover la circulación y el intercambio de información educativa. No se permitirán consultas políticas, gremiales, amorales o de temas deportivos profesionales. No se distribuirá publicidad comercial encubierta, en forma de consulta. El mecanismo para realizar las consultas es muy fácil, pues las mismas se podrán hacer enviando un mensaje a la lista "CONSULT@NDO" a la dirección: consultando@fundcvmejor.com.ar , para realizar esta operación es necesario antes estar inscripto. Para inscribirse en la lista le solicitamos envíe un mail a: consultando@fundcvmejor.com.ar con el comando (SUBSCRIBE) (sin parentesis) en el subject o asunto y en cuerpodel mensaje, escribes tu nombre y tu e-mail. La temática de la lista "CONSULT@NDO", entre otros, esta relacionada con PEDIDOS DE: Información para la realización de trabajos a ser presentados o tesis. Información o colaboración acerca de la realización de proyectos educativos. Información acerca de becas y pasantías. Libros y apuntes o intercambio de los mismos. Información sobre requisitos de ingreso a establecimientos educacionales. Intercambio de alumnos de diferentes lugares. Comunicación de la realización de y certámenes estudiantiles y docentes. Información sobre cursos, eventos y actividades. Información sobre paginas Web, foros y listas educativas. Y temas relacionados con la educación y la docencia. La lista "CONSULT@NDO", tiene la característica de ser moderada y el idioma será el español y el portugués, sin ñ, ni acentos. Agradeceremos la difusión de esta invitación, a listas y boletines donde Ud. este inscripto, a instituciones o personas relacionadas con la educación. Agradecemos la atención dispensada al presente e-mail, deseando el mayor de los éxitos en vuestras tareas, lo saludamos muy atte. FUNDACION VOY CADA VEZ MEJOR Humberto Pedraza Alvarez Presidente Nilza Duarte Secretaria E-mail: consultando@fundcvmejor.com.ar info@fundcvmejor.com.ar URL: http://www.fundcvmejor.com.ar From owner-software@net.bio.net Tue Dec 07 20:15:24 1999 From: "yariv aviv" Newsgroups: bionet.software Subject: NEW PROGRAM !!! ONE OF THE BEST !!! Date: Tue, 7 Dec 1999 22:16:14 +0200 Lines: 17 X-Newsreader: Microsoft Outlook Express 4.72.3110.37 X-MimeOLE: Produced By Microsoft MimeOLE V4.72.3110.37 NNTP-Posting-Host: 212.29.228.200 X-NNTP-Posting-Host: 212.29.228.200 Message-ID: <384d6ad7.0@news.barak.net.il> X-Trace: 7 Dec 1999 22:15:19 +0200, 212.29.228.200 Path: hgmp.mrc.ac.uk!server1.netnews.ja.net!fu-berlin.de!newspeer.ebone.net!diablo.theplanet.net!diablo2!news-lond.gip.net!news.gsl.net!gip.net!news.barak.net.il!212.29.228.200 Xref: hgmp.mrc.ac.uk bionet.software:935 HI IF YOU HAVE A WEB END YOU WANT OT SEND A CHAT TO YOUR VISITORS , WITHOUT ANY PROGRAM THAT THEY NEED TO DOWNLOAD , END YOU CAN KNOW HOW MANY PEPPOLE IN YOUR SITE IN THIS MOMENT END MORE INF' GO TO : humanclick.com hope that you enjoy with this program end ITS FREE !!!!!!! From owner-software@net.bio.net Tue Dec 07 22:35:04 1999 Path: hgmp.mrc.ac.uk!server1.netnews.ja.net!fu-berlin.de!newsfeed.germany.net!newsfeed.tli.de!newsfeed1.uni2.dk!news.net.uni-c.dk!not-for-mail From: "S.W. Rasmussen" Newsgroups: bionet.software Subject: DNATools revision 5.1.647 Date: Tue, 07 Dec 1999 23:36:49 +0000 Organization: UNI-C Lines: 39 Message-ID: <384D9A11.87AEE3E3@crc.dk> NNTP-Posting-Host: ppp1.crc.dk Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Trace: news.net.uni-c.dk 944605511 47720 130.226.184.128 (7 Dec 1999 22:25:11 GMT) X-Complaints-To: usenet@news.net.uni-c.dk NNTP-Posting-Date: 7 Dec 1999 22:25:11 GMT X-Mailer: Mozilla 4.5 [en] (WinNT; I) X-Accept-Language: en Xref: hgmp.mrc.ac.uk bionet.software:936 Dear DNATools user, This revision contains a number of improvements and refinements especially relevant for people using DNATools to manage small (4-6,000) EST projects: The speed of file loading has been improved a bit, the structure of sequence headers has been refined to facilitate searching, selected search results can be viewed by right-clicking items in file lists or in the main editor form (without first opening the sequence header), sub-groups of sequences can easily be extracted from a project with the 'Close File' and 'Search Project' functions (this makes it a simple operation to repeat database searching for sequences with poor blast match), building local data libraries (with NCBI, formatdb) and batch-searching the project (with NCBI, Blast) now works quite well. The functions for SAGE (serial analysis of gene expression) analysis now allows you to retrieve tags from the dropdown lists simply typing a few character of the tag ID or its sequence in the dropdown box. A number of small bugs here and there have been removed (which does not imply that DNATools is bug-free!!) You can read more about this revision of DNATools if you visit: http://www.crc.dk/phys/dnatools.htm PS. Looking at the log file for our ftp site, it appears that many people have problems downloading the large (app. 7Mb) installation file. It is now possible to download DNATools in three separate zip-files. Regards Soeren -- Soeren W. Rasmussen, Dr. scient. Department of Physiology Carlsberg Laboratory Copenhagen, Denmark swr@crc.dk, http://www.crc.dk/phys From owner-software@net.bio.net Wed Dec 08 09:10:18 1999 Path: hgmp.mrc.ac.uk!guardian!warwick!server1.netnews.ja.net!fu-berlin.de!newsfeed.direct.ca!newsfeed.bctel.net!news.bctel.net!not-for-mail From: amanita@telus.net (Mycos) Newsgroups: bionet.software Subject: Mycological ID Software ? Message-ID: <384ded28.40920475@news.bctel.net> X-Newsreader: Forte Free Agent 1.11/32.235 Lines: 20 Date: Wed, 08 Dec 1999 05:33:05 GMT NNTP-Posting-Host: 209.52.33.28 X-Complaints-To: news@bctel.net X-Trace: news.bctel.net 944631100 209.52.33.28 (Tue, 07 Dec 1999 21:31:40 PDT) NNTP-Posting-Date: Tue, 07 Dec 1999 21:31:40 PDT Xref: hgmp.mrc.ac.uk bionet.software:937 Spoke to a fellow who was developing some software regarding mycological databases for ID purposes. Unfortunately, this was several "Format C:'s" ago and I can't remember the guys name. If you know of whom I'm talking about can you please direct me to the aforesaid or to anyone who can give me info on the current state of devopment. In my correspondence at that time I also mentioned how nice it would be if there were a palm-sized type of gadget that had highly portable, lightweight ID keys on a variety of natural history subjects. Again, anyone hear of such a device being in devopment? As a naturalist, I would find such a thing to be an answer to my prayers, pagan though they may be (that's what He said in that rather thunderous tone I'm sure your all familiar with. No ? Hmmm). Anyway, it seems that all to often, that the more extraordinary finds on my forays are regarding a specimen that would be found in a book that I decided to leave OUT of the backpack due to weight. Anyhow, thanks in advance for any help anyone might offer. Gary Williams From owner-software@net.bio.net Wed Dec 08 19:24:02 1999 Path: hgmp.mrc.ac.uk!sunlight.pku.edu.cn!pku!newsgate.cuhk.edu.hk!newsfeed.berkeley.edu!xmission!news.cc.utah.edu!cs.utexas.edu!news.uh.edu!news.uth.tmc.edu!not-for-mail From: Markus Hoenicka Newsgroups: bionet.software,comp.text.sgml Subject: ANN: SOP DTD package released Date: 08 Dec 1999 18:52:41 +0000 Organization: University of Texas Health Science Center Lines: 34 Sender: mhoen@GIRCH19 Message-ID: NNTP-Posting-Host: ibp104.med.uth.tmc.edu Mime-Version: 1.0 Content-Type: text/plain;charset=US-ASCII Content-Transfer-Encoding: 7bit X-Newsreader: Gnus v5.7/Emacs 20.4 Xref: hgmp.mrc.ac.uk bionet.software:938 comp.text.sgml:1111 The SOP DTD is a SGML document type definition for writing biomedical method sheets and standard operating procedures. The package contains the DTD, DSSSL stylesheets to render the documents in either HTML, RTF, Postscript, PDF, DVI or MIF format, a set of m4 macros to retrieve information and textual contents from your documents with sgrep, a full documentation, and some more stuff. Please visit: http://ourworld.compuserve.com/homepages/hoenicka_markus/sopdtd.html The aim of this package is to facilitate the use of a central method or SOP repository in a workgroup or a department. All documents can be made available as HTML in the intranet, and any print format can be used to create a hardcopy for the lab bench. sgrep and the m4 macros allow to search for specific information in the pool of method sheets, and they also allow to selectively retrieve parts of existing documents (without having to know in which document they are stored) to piece together new documents. This is the initial public release, so parts may be missing or too restrictive for general use. I'll be happy to incorporate any feedback to improve the stuff. Markus -- Markus Hoenicka UT Houston Medical School Dept. of Integrative Biology and Pharmacology 6431 Fannin MSB4.114 Houston, TX 77030 (713) 500-6313, -7476, -7477 (713) 500-7444 (fax) mhoen@farmr1.med.uth.tmc.edu http://ourworld.compuserve.com/homepages/hoenicka_markus/ From owner-software@net.bio.net Thu Dec 09 13:53:14 1999 Path: hgmp.mrc.ac.uk!server1.netnews.ja.net!fu-berlin.de!news.uni-stuttgart.de!news.belwue.de!chevreux From: chevreux@mbp-lserv1.inet.dkfz-heidelberg.de (Bastien Chevreux) Newsgroups: bionet.software Subject: Re: assembly software Date: 9 Dec 1999 13:53:01 GMT Organization: Speaking for myself (really) Lines: 18 Message-ID: References: <19991203165717.12232.qmail@hotmail.com> <384F42BF.8F3D0E71@cts.com> Reply-To: b.chevreux@dkfz-heidelberg.de NNTP-Posting-Host: mbp-lserv1.inet.dkfz-heidelberg.de X-Newsreader: slrn (0.9.5.2 UNIX) Xref: hgmp.mrc.ac.uk bionet.software:939 On Wed, 08 Dec 1999 21:48:47 -0800, Mike Parlee wrote: >I used DNASTAR on Macintosh extensively for large (20-40kb +) shotgun >assemblies. [...] Did I miss anything crucial? 20-40kb (500-1000 reads) shotguns are, in my point of view, tiny and cute little projects which are assembled and conservatively (but automatically) edited within minutes. Fun starts at 200kb+ :) Salut, Bastien ------------------------------------------------------------------------------- Dipl.-Inform. Med. Bastien Chevreux -- b.chevreux@dkfz-heidelberg.de Deutsches Krebsforschungszentrum Heidelberg -- Abteilung Molekulare Biophysik Im Neuenheimer Feld 280 -- 69120 Heidelberg -- Phone: +49 6221 42 2336 ------------------------------------------------------------------------------- -It's mine. =Nope, it's my one. *CRASH* =Alright. It WAS yours. From owner-software@net.bio.net Thu Dec 09 14:10:05 1999 Path: hgmp.mrc.ac.uk!server1.netnews.ja.net!news.uhi.ac.uk!server6.netnews.ja.net!server4.netnews.ja.net!news5-gui.server.ntli.net!ntli.net!news-lond.gip.net!news-peer.gip.net!news.gsl.net!gip.net!newsfeed.berkeley.edu!nntp.flash.net!mercury.cts.com!thoth.cts.com!not-for-mail From: Mike Parlee Newsgroups: bionet.software Subject: Re: assembly software Date: Wed, 08 Dec 1999 21:48:47 -0800 Organization: CTS Network Services Lines: 39 Message-ID: <384F42BF.8F3D0E71@cts.com> References: <19991203165717.12232.qmail@hotmail.com> Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Trace: thoth.cts.com 944718187 38095 204.216.199.3 (9 Dec 1999 05:43:07 GMT) X-Complaints-To: newsmaster@cts.com To: Patriot Nation X-Mailer: Mozilla 4.61 [en] (X11; I; Linux 2.2.12-20 i686) X-Accept-Language: en Xref: hgmp.mrc.ac.uk bionet.software:940 Patriot Nation wrote: > Thanks for the reply, but 1994 was a long time ago in terms of software. > The VectorNTI stuff has only been around for a few months (and is likely > still full of bugs). DNASTAR has been around for a long time, but has had > many upgrades and improvements since 1994. Does anyone have more recent > experience with these packages? I used DNASTAR on Macintosh extensively for large (20-40kb +) shotgun assemblies. The Macintosh version of SeqMan II (the assembly program) has been around for a long time and is quite stable. There were serious stability issues with other programs in the Lasergene package though. The multiple alignment tool (MegAlign) was particularly prone to crash. My current employer uses Sequencher. In my experience Sequencher offers some nice features for small assemblies with low coverage. Manual edits are automatically tracked and there are some nice summary views. When I tried using Sequencher for large assemblies I was aggravated by the length of time it took to import each chromatogram. I am unimpressed with VectorNTI as a sequence assembly tool. It is excellent for creating and editing plasmid maps, but the sequence assembly is definately not there yet. My favorite sequence assembly tool set would be the Phred/Phrap/Consed trio. If you are not familiar with the Unix command line the learning curve is steep, but its availability on Linux means you don't have to invest in expensive hardware to try it out. On the plus side, huge alignments go together in a snap, on the down side you need lots of coverage for reliable assemblies. As far as I know there is no way to split contigs or remove sequences from the assembly. The selling point for me was assembling a highly repetitive region of human chromosome (~80kb I think) in just a couple of hours after a post-doc had been working on it for about a month in DNASTAR. Good luck, Mike Parlee From owner-software@net.bio.net Thu Dec 09 16:38:04 1999 Path: hgmp.mrc.ac.uk!server1.netnews.ja.net!fu-berlin.de!nntp.flash.net!newsfeed.enteract.com!chicago-news-feed1.bbnplanet.com!news.gtei.net!uwm.edu!biosci!FRODO.MGH.HARVARD.EDU!bongard From: bongard@FRODO.MGH.HARVARD.EDU ("Deverie K. Bongard-Pierce") Newsgroups: bionet.software Subject: assmebly software Date: 9 Dec 1999 08:43:51 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 36 Sender: daemon@net.bio.net Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net Xref: hgmp.mrc.ac.uk bionet.software:941 On 12/2 Pat Fan wrote >Does anyone know the capacity of some of the popular desktop sequence >assembly software? .... I routinely use Squencher3.1 on my MAC to assemble EST projects containing 10,000 sequences. These sequences range in size from 100bp to 700bp- the average being around 400. I have heard a rumor that Sequencher 4 can assemble projects larger then 10K sequences. I believe that the version 4 software is currently available for the PC but the MAC version is not quite out. I too have used Phred/Phrap/Consed trio and while it is great for large assembly projects (>10K sequences) I find editing in Consed to be a bit clumsy & slow when compared with Sequencher. It also does not output the data in a fashion thats easy to use with other systems & programs. Squencher does take longer to import the chromatographs and assemble the alignments then P/P/C but if you start a large project just before going home its usually done in the morning. I find the time I save in editing with Sequencher to be will worth the longer setup times. Version 3 of Sequencher does not do as well as the Phred/Phrap/Consed trio when it comes to aligning EST sequences with their genomic counterparts- alot more editing is need around intron borders, but again I have heard that the ver.4 software does a much better job with these kinds of alignments. ----------------------------------------------------- Deverie K. Bongard-Pierce Sr.Tech./Lab Manager- Howard Goodman's Lab Dept. of Molecular Biology Fax: (617) 726-6893 Mass. General Hospital Lab: (617) 726-5938 Boston MA 02114 email: bongard@molbio.mgh.harvard.edu ----------------------------------------------------- From owner-software@net.bio.net Fri Dec 10 12:21:23 1999 Date: Fri, 10 Dec 1999 13:28:06 +0100 From: hans.engkvist@REMOVEFORREPLYgenpat.uu.se (Hans Engkvist) Newsgroups: bionet.software Subject: format/file type of ABI sequencing gel files? Message-ID: X-Newsreader: MT-NewsWatcher 2.4.4 NNTP-Posting-Host: pan.genpat.uu.se X-Trace: 10 Dec 1999 13:21:18 +0100, pan.genpat.uu.se Lines: 15 Path: hgmp.mrc.ac.uk!server1.netnews.ja.net!fu-berlin.de!feed2.news.luth.se!luth.se!newsfeed.sunet.se!news01.sunet.se!news99.sunet.se!newsfeed.uu.se!hans.engkvist Xref: hgmp.mrc.ac.uk bionet.software:942 Hello, someone here who knows? I would like to do my own analysis of the data in a ABI sequencing gel file. Unfortuantely I can't figure out in what format/file type the data is in. Is it a image format? Other kind of matrix data? TIA, Hans Engkvist -- /Hans Engkvist ...before e-mail replying make necessary changes in my e-mail adress... "Nothing shocks me, I'm a scientist" /Indiana Jones From owner-software@net.bio.net Fri Dec 10 14:19:58 1999 Path: hgmp.mrc.ac.uk!server1.netnews.ja.net!fu-berlin.de!jussieu.fr!ext.jussieu.fr!mac2-info.sb-roscoff.fr!user From: crepinau@sb-roscoff.fr (Crepineau florent) Newsgroups: bionet.software Subject: Re: assembly software Date: 10 Dec 1999 14:19:56 GMT Organization: Station biologique de Roscoff Lines: 27 Message-ID: References: <19991203165717.12232.qmail@hotmail.com> <384F42BF.8F3D0E71@cts.com> NNTP-Posting-Host: mac2-info.sb-roscoff.fr Mime-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit Xref: hgmp.mrc.ac.uk bionet.software:943 Sequencher is nice to use but a bit slow when assembling. I usually did it overnight. Phred/Phrap/consed is powerful however as already mentioned the editing part is not very user friendly and as mentioned a few very useful possibilities are not available. Has anyone mentioned the Staden package? I think it can do assembly and it is free now. Acembly which goes with ACEDB database can do assembly as well. TIGR assembler can do assembly, assembled sequences can be edited in GDE or consed. You may have a look at the EBI, they have a database of software, maybe you could find something interesting. Hope it helps Florent -- Florent Crépineau Station Biologique de Roscoff BP 74 29682 Roscoff cedex From owner-software@net.bio.net Fri Dec 10 15:21:10 1999 Path: hgmp.mrc.ac.uk!server1.netnews.ja.net!fu-berlin.de!howland.erols.net!pants.skycache.com!newsfeed.skycache.com!cyclone1.gnilink.net!typhoon1.gnilink.net.POSTED!not-for-mail From: "cudaman2k" Newsgroups: bionet.software Subject: PC Accessories Lines: 8 X-Newsreader: Microsoft Outlook Express 4.72.3612.1700 X-MimeOLE: Produced By Microsoft MimeOLE V4.72.3612.1700 Message-ID: Date: Fri, 10 Dec 1999 15:23:27 GMT NNTP-Posting-Host: 151.204.210.11 X-Trace: typhoon1.gnilink.net 944839407 151.204.210.11 (Fri, 10 Dec 1999 10:23:27 EST) NNTP-Posting-Date: Fri, 10 Dec 1999 10:23:27 EST Xref: hgmp.mrc.ac.uk bionet.software:944 PC Accessories Another great place to find PC hardware and software Secure online purchasing!!!! http://pconline.vstoreoffice.com From owner-software@net.bio.net Fri Dec 10 16:50:26 1999 Path: hgmp.mrc.ac.uk!server1.netnews.ja.net!fu-berlin.de!news.idt.net!newsfeed.cwix.com!argos.tel.hr!not-for-mail From: "Ivan Petrovic" Newsgroups: alt.consumers.free-stuff,bionet.software Subject: EasyZip 2000 v4.6 - BH (BlakHole) support, improved integration with Windows, redesigned web page, ... Date: Fri, 10 Dec 1999 16:13:05 +0100 Organization: HiNet Lines: 70 Message-ID: <82raea$au0$2@as102.tel.hr> NNTP-Posting-Host: zgis01.ina.hr Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit X-Trace: as102.tel.hr 944844042 11200 194.152.228.18 (10 Dec 1999 16:40:42 GMT) X-Complaints-To: abuse@tel.hr NNTP-Posting-Date: 10 Dec 1999 16:40:42 GMT X-Priority: 3 X-MSMail-Priority: Normal X-Newsreader: Microsoft Outlook Express 5.00.2314.1300 X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2314.1300 Xref: hgmp.mrc.ac.uk bionet.software:945 * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * EasyZip 2000 v4.6 SR-1 [12/08/1999] The most powerful Freeware Archive Utility that exists... * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * What is EasyZip? EasyZip is a great, powerful, and totally FREE Archive Utility for Windows 95/98/NT/2000. 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Support: EasyZip and more and more information about EasyZip you can find at: http://ipsoft.cjb.net and my e-mail address is: easyzip@ipsoft.cjb.net Thanks in advance... Ivan Petrovic -- ___________________________________________________________ EasyZip 2000 - Great, powerful and totally FREE Archive Utility for Windows 95/98/NT/2000 that has built-in support for many, many formats (ZIP, CAB, LHA, BH, ARJ, RAR, ACE, ARC, ZOO, TAR, GZ, XXE, UUE)... * * * * * * * * * * * * * * * * * * * * * * * * * * * * http://ipsoft.cjb.net ivanpetrov@ipsoft.cjb.net * * * * * * * * * * * * * * * * * * * * * * * * * * * * From owner-software@net.bio.net Fri Dec 10 18:46:02 1999 Path: hgmp.mrc.ac.uk!server1.netnews.ja.net!fu-berlin.de!headwall.stanford.edu!newsfeed.stanford.edu!uchinews!nntp-server.caltech.edu!seqaxp.bio.caltech.edu!MATHOG From: mathog@seqaxp.bio.caltech.edu Newsgroups: bionet.software Subject: Re: format/file type of ABI sequencing gel files? Date: 10 Dec 1999 18:43:50 GMT Organization: Biology Division, Caltech, Pasadena CA 91125 Lines: 1717 Message-ID: <82rhl6$iav@gap.cco.caltech.edu> References: Reply-To: mathog@seqaxp.bio.caltech.edu NNTP-Posting-Host: seqaxp.bio.caltech.edu Xref: hgmp.mrc.ac.uk bionet.software:946 In article , hans.engkvist@REMOVEFORREPLYgenpat.uu.se (Hans Engkvist) writes: >Hello, >someone here who knows? >I would like to do my own analysis of the data in a ABI sequencing gel file. >Unfortuantely I can't figure out in what format/file type the data is in. >Is it a image format? Other kind of matrix data? I had to figure this out by working backwords from a trace file, and dumping the data in different hex formats using a true hack of a program I wrote called DATASNIFFER.FOR. See ABI.TXT after my signature for the layout I arrived at. I did this on an OpenVMS Alpha machine so byte orders needed to be reversed relative to the Macintosh types used in the the file. I also wrote a small fortran program to test my observations/convert an ABI file to a text format. It's called ABIBREAKOUT.FOR and also follows my signature. Note that to use it you'll have to be sure that float is a 4 byte IEEE value and you may need to change around the byte swapping routines if your machine goes the other way. Just for good measure, I put DATASNIFFER.FOR in here too. Use any or all of it as you wish. Regards, David Mathog mathog@seqaxp.bio.caltech.edu Manager, sequence analysis facility, biology division, Caltech ************************************************************************** *** abi.txt ************************************************************ !Absolute positions here start at 1 and INCLUDE 128 byte MacBinary header !Offsets in an ABI file are C standard - they start 0 for the first byte and ! do NOT include the MacBinary header (which may or may not be present) !Convert these absolute positions to offsets by subtracting 129 (and vice versa) ! ! Byte order from Macintosh is REVERSE of that under OpenVMS on ALPHA ! !INT1 = unsigned integer 1 !INT2 = unsigned integer 2, most significant byte at N+1, least at N ! Except for Matrix, where it is a signed integer 2, holding ! value * 1000 !INT4 = unsigned integer 4, most significant byte at N+3, least at N !INT10 = unknown 10 byte data structure that some fields use !INT28 = FLAG structures !FLT4 = signed floating point number, 4 bytes, IEEE float format ! ! consist of: ! FLAG = 4 INT1 = text, case specific (apparently) like "DATA" ! INSTANCE = INT4, the instance of this type of FLAG, >= 1. ! DATATYPE = INT2, the data type this flag structure contains. Known ! types are: ! 1023 FLAG structures (28 bytes) ! 2 Text (no count byte, see 18 below) Used for text ! <4 bytes and stored as immediate values, or long ! text, like DNA sequences ! 4 (Series) of INT2 ! 7 (Series) of FLT4 ! 10 DATE structure (4 bytes) ! 11 TIME structure (4 bytes) ! 12 ?? (Series) of INT10, used by THUM ! 13 ?? (Series) of INT1, used by AUTO and CAGT ! 18 Text (first byte is length, rest is text) ! DATASIZE = INT2, the size of the data type in bytes ! NRECORDS = INT4, the number of records of this datatype present ! NBYTES = INT4, the number of bytes in all of these records ! VALUE = 4 bytes. A space that holds one of these: ! 1. INT4 POINTER to actual data elsewhere in file (value of ! zero for a pointer indicates no field contents) ! OR ! 2. The DATA itself (packed into this space, may leave ! zero bytes) ! REMAINDER = If the VALUE does not use all 4 bytes. ! SPARE = INT4. Not quite sure yet what this does, but it looks ! like it might be just uninitialized data. ! !FLAGs are 4 consecutive bytes, visible ASCII characters, like "DATA" !"text" = string of bytes 129 VALUE = (A,B,I,F) "FLAG" 4 X INT1 (ABI File type marker) 133 VALUE = 0 INT1 (unknown purpose) 134 VALUE = 65 INT1 ("e") (unknown purpose) 135 tdir FLAG (Pointer to Multiple FLAG region) INSTANCE = 1 INT4 DATATYPE = 1023 INT2 DATASIXE = 28 INT2 NRECORDS = 69 INT4 NBYTES = 2240 INT4 VALUE = POINTER to Front of Multiple FLAG region INT4 SPARE = 30594184 INT4 160 VALUE = FFx, padding up to and including offset 128 N X INT2 257 THUM structure 1, INT10 (???) 267 THUM structure 2, INT10 (???) 277 MACHINE length INT1 278 MACHINE text 284 RUN STARTED AT TITLE length INT1 285 RUN STARTED AT TITLE text N X INT1 300 RUN STOPPED AT TITLE length INT1 301 RUN STOPPED AT TITLE text N X INT1 316 MATRIX FILE 1 length INT1 317 MATRIX FILE 1 text N X INT1 342 MATRIX FILE 2 length INT1 343 MATRIX FILE 2 text N X INT1 368 GEL FILE NAME length INT1 369 GEL FILE NAME text N X INT1 377 GEL FILE PATH length INT1 378 GEL FILE PATH text N X INT1 437 MATRIX 1 (4 x 4 INT2) "Primer Matrix" 501 MATRIX 2 (4 x 4 INT2) "Taq Term. Matrix" 565 MATRIX 3 (4 x 4 INT2) "T7 Term. Matrix" 469 MATRIX 101 (4 x 4 INT2) These three seem to be duplicates of the 533 MATRIX 102 (4 x 4 INT2) first three 615 MATRIX 103 (4 x 4 INT2) Values for MATRIX structures are Inverse Matrix * 1000 stored as signed INT2 629 SAMPLE length INT1 630 SAMPLE text N X INT1 642 DYESET/PRIMER 1 length INT1 643 DYESET/PRIMER 1 text N X INT1 666 DYESET/PRIMER 2 length INT1 667 DYESET/PRIMER 2 text N X INT1 690 COMMENT TITLE length INT1 691 COMMENT TITLE text N X INT1 699 VOLTAGE? N X INT2 1159 CURRENT? N X INT2 2079 POWER? N X INT2 1619 TEMPERATURE N X INT2 2539 RAW G TRACE N X INT2 17243 RAW A TRACE N X INT2 31947 RAW C TRACE N X INT2 46651 RAW T TRACE N X INT2 61355 PROCESSED TRACE G N X INT2 79445 PROCESSED TRACE A N X INT2 97175 PROCESSED TRACE C N X INT2 115625 PROCESSED TRACE T N X INT2 133715 BASE TO TRACE ARRAY 1 N X INT2 135139 CALLED SEQUENCE 1 N X INT1 135851 BASE TO TRACE ARRAY 2 N X INT2 137275 CALLED SEQUENCE 2 N X INT1 137987 #(G,A,T,C) in CALLED SEQUENCE 2 4 X INT2 137995 BASECALLER length INT1 137996 BASECALLER text N X INT1 138001 BASECALLER VERSION length INT1 138002 BASECALLER VERSION text N X INT1 138013 AEPt FLAG (Number of Scans) INSTANCE = 1 INT4 DATATYPE = 4 INT2 DATASIZE = 2 INT2 NRECORDS = 1 INT4 NBYTES = 2 INT4 VALUE = 7352 INT2 REMAINDER= 0 INT2 SPARE = 0 INT4 138041 AEPt FLAG (Number of Scans) INSTANCE = 2 INT4 DATATYPE = 4 INT2 DATASIZE = 2 INT2 NRECORDS = 1 INT4 NBYTES = 1 INT4 VALUE = 7352 INT2 REMAINDER= 0 INT2 SPARE = 0 INT4 138069 ASPF FLAG (???) INSTANCE = 1 INT4 DATATYPE = 4 INT2 DATASIZE = 2 INT2 NRECORDS = 1 INT4 NBYTES = 1 INT4 VALUE = 0 INT2 REMAINDER= 0 INT2 SPARE = 0 INT4 138097 ASPt FLAG (Base Call Start, Primer Peak Loc.?) INSTANCE = 1 INT4 DATATYPE = 4 INT2 DATASIZE = 2 INT2 NRECORDS = 1 INT4 NBYTES = 2 INT4 VALUE = 805 INT2 REMAINDER= 0 INT2 SPARE = 0 INT4 138125 ASPt FLAG (Base Call Start, Primer Peak Loc.?) INSTANCE = 2 INT4 DATATYPE = 4 INT2 DATASIZE = 2 INT2 NRECORDS = 1 INT4 NBYTES = 2 INT4 VALUE = 805 INT2 REMAINDER= 0 INT2 SPARE = 0 INT4 138153 AUTO FLAG (???) INSTANCE = 1 INT4 DATATYPE = 13 INT2 DATASIZE = 1 INT2 NRECORDS = 3 INT4 NBYTES = 3 INT4 VALUE = (0,0,0) 3 X INT1 REMAINDER= 0 INT1 SPARE = 0 INT4 138181 B1Pt FLAG (Base Call 1 Start) INSTANCE = 1 INT4 DATATYPE = 4 INT2 DATASIZE = 2 INT2 NRECORDS = 1 INT4 NBYTES = 2 INT4 VALUE = 805 INT2 REMAINDER= 0 INT2 SPARE = 0 INT4 138209 B1Pt FLAG (Base Call 2 Start) INSTANCE = 2 INT4 DATATYPE = 4 INT2 DATASIZE = 2 INT2 NRECORDS = 1 INT4 NBYTES = 2 INT4 VALUE = 805 INT2 REMAINDER= 0 INT2 SPARE = 0 INT4 138237 CAGT FLAG (???) INSTANCE = 1 INT4 DATATYPE = 13 INT2 DATASIZE = 1 INT2 NRECORDS = 4 INT4 NBYTES = 4 INT4 VALUE = (0,0,0,0) 4 X INT1 SPARE = 0 INT4 138265 CMBF FLAG (Comb field/file??) INSTANCE = 1 INT4 DATATYPE = 18 INT2 DATASIZE = 1 INT2 NRECORDS = 1 INT4 NBYTES = 1 INT4 VALUE = 0 INT1 REMAINDER= (0,0,0) 3 X INT1 SPARE = 0 INT4 138293 CMNT FLAG (Comment field) INSTANCE = 1 INT4 DATATYPE = 18 INT2 DATASIZE = 1 INT2 NRECORDS = 1 INT4 NBYTES = 1 INT4 VALUE = POINTER to COMMENT FIELD INT4 SPARE = 0 INT4 138321 CTTL FLAG (Comment Title) INSTANCE = 1 INT4 DATATYPE = 18 INT2 DATASIZE = 1 INT2 NRECORDS = 9 INT4 NBYTES = 9 INT4 VALUE = POINTER TO COMMENT TITLE, INT4 SPARE = 0 INT4 138349 DATA FLAG (Raw G Trace) INSTANCE = 1 INT4 DATATYPE = 4 INT2 DATASIZE = 2 INT2 NRECORDS = 7352 INT4 NBYTES = 14704 INT4 VALUE = POINTER TO RAW G TRACE INT4 SPARE = 0 INT4 138377 DATA FLAG (Raw A Trace) INSTANCE = 2 INT4 DATATYPE = 4 INT2 DATASIZE = 2 INT2 NRECORDS = 7352 INT4 NBYTES = 14704 INT4 VALUE = POINTER TO RAW A TRACE INT4 SPARE = 0 INT4 138405 DATA FLAG (Raw C Trace) INSTANCE = 3 INT4 DATATYPE = 4 INT2 DATASIZE = 2 INT2 NRECORDS = 7352 INT4 NBYTES = 14704 INT4 VALUE = POINTER TO RAW C TRACE INT4 SPARE = 0 INT4 138433 DATA FLAG (Raw T Trace) INSTANCE = 4 INT4 DATATYPE = 4 INT2 DATASIZE = 2 INT2 NRECORDS = 7352 INT4 NBYTES = 14704 INT4 VALUE = POINTER TO RAW T TRACE INT4 SPARE = 0 INT4 138461 DATA FLAG (Voltage?) INSTANCE = 5 INT4 DATATYPE = 4 INT2 DATASIZE = 2 INT2 NRECORDS = 230 INT4 NBYTES = 460 INT4 VALUE = POINTER TO VOLTAGE? INT4 SPARE = 0 INT4 138489 DATA FLAG (Current?) INSTANCE = 6 INT4 DATATYPE = 4 INT2 DATASIZE = 2 INT2 NRECORDS = 230 INT4 NBYTES = 460 INT4 VALUE = POINTER TO CURRENT? INT4 SPARE = 0 INT4 138517 DATA FLAG (Power?) INSTANCE = 7 INT4 DATATYPE = 4 INT2 DATASIZE = 2 INT2 NRECORDS = 230 INT4 NBYTES = 460 INT4 VALUE = POINTER TO POWER? INT4 SPARE = 0 INT4 138545 DATA FLAG (Temperature?) INSTANCE = 8 INT4 DATATYPE = 4 INT2 DATASIZE = 2 INT2 NRECORDS = 230 INT4 NBYTES = 460 INT4 VALUE = POINTER TO TEMPERATURE INT4 SPARE = 0 INT4 138573 DATA FLAG ( Final G Trace) INSTANCE = 9 INT4 DATATYPE = 4 INT2 DATASIZE = 2 INT2 NRECORDS = 9045 INT4 NBYTES = 18090 INT4 VALUE = POINTER TO PROCESSED TRACE G INT4 SPARE = 30594116 INT4 138601 DATA FLAG ( Final A Trace) INSTANCE = 10 INT4 DATATYPE = 4 INT2 DATASIZE = 2 INT2 NRECORDS = 9045 INT4 NBYTES = 18090 INT4 VALUE = POINTER TO PROCESSED TRACE A INT4 SPARE = 30594152 INT4 138629 DATA FLAG ( Final C Trace) INSTANCE = 11 INT4 DATATYPE = 4 INT2 DATASIZE = 2 INT2 NRECORDS = 9045 INT4 NBYTES = 18090 INT4 VALUE = POINTER TO PROCESSED TRACE C INT4 SPARE = 30594172 INT4 138657 DATA FLAG ( Final T Trace) INSTANCE = 12 INT4 DATATYPE = 4 INT2 DATASIZE = 2 INT2 NRECORDS = 9045 INT4 NBYTES = 18090 INT4 VALUE = POINTER TO PROCESSED TRACE T INT4 SPARE = 30594136 INT4 138685 EVNT FLAG ( Run started at title) INSTANCE = 1 INT4 DATATYPE = 18 INT2 DATASIZE = 1 INT2 NRECORDS = 16 INT4 NBYTES = 16 INT4 VALUE = POINTER to RUN STARTED AT TITLE SPARE = 0 INT4 138713 EVNT FLAG ( Run stopped at title) INSTANCE = 2 INT4 DATATYPE = 18 INT2 DATASIZE = 1 INT2 NRECORDS = 16 INT4 NBYTES = 16 INT4 VALUE = POINTER to RUN STOPPED AT TITLE SPARE = 0 INT4 138741 FWO_ FLAG ( Field order ) INSTANCE = 1 INT4 DATATYPE = 2 INT2 DATASIZE = 1 INT2 NRECORDS = 4 INT4 NBYTES = 4 INT4 VALUE = "GATC" 4 X INT1 SPARE = 0 INT4 138769 GLEN FLAG (Gel file name) INSTANCE = 1 INT4 DATATYPE = 18 INT2 DATASIZE = 1 INT2 NRECORDS = 9 INT4 NBYTES = 9 INT4 VALUE = POINTER TO GEL FILE NAME INT4 SPARE = 0 INT4 138797 GELP FLAG (Gel file path) INSTANCE = 1 INT4 DATATYPE = 18 INT2 DATASIZE = 1 INT2 NRECORDS = 60 INT4 NBYTES = 60 INT4 VALUE = POINTER TO GEL FILE PATH INT4 SPARE = 0 INT4 138825 LANE FLAG (number of lane) INSTANCE = 1 INT4 DATATYPE = 4 INT2 DATASIZE = 1 INT2 NRECORDS = 2 INT4 NBYTES = 2 INT4 VALUE = (0,8) 2 X INT2 SPARE = 0 INT4 138853 MCHN FLAG (Name of machine) INSTANCE = 1 INT4 DATATYPE = 18 INT2 DATASIZE = 1 INT2 NRECORDS = 7 INT4 NBYTES = 7 INT4 VALUE = POINTER to MACHINE, INT4 SPARE = 0 INT4 138881 MODL FLAG (Name of model) INSTANCE = 1 INT4 DATATYPE = 2 INT2 DATASIZE = 1 INT2 NRECORDS = 4 INT4 NBYTES = 4 INT4 VALUE = "373" 4 X INT1 SPARE = 0 INT4 138909 MTRX FLAG (Matrix 1 "Primer Matrix") INSTANCE = 1 INT4 DATATYPE = 4 INT2 DATASIZE = 2 INT2 NRECORDS = 16 INT4 NBYTES = 32 INT4 VALUE = POINTER to MATRIX 1 INT4 SPARE = 0 INT4 138937 MTRX FLAG (Matrix 2 "Taq Term. Matrix") INSTANCE = 2 INT4 DATATYPE = 4 INT2 DATASIZE = 2 INT2 NRECORDS = 16 INT4 NBYTES = 32 INT4 VALUE = POINTER to MATRIX 2 INT4 SPARE = 0 INT4 138965 MTRX FLAG (Matrix 3 "T7 Term. Matrix") INSTANCE = 3 INT4 DATATYPE = 4 INT2 DATASIZE = 2 INT2 NRECORDS = 16 INT4 NBYTES = 32 INT4 VALUE = POINTER to MATRIX 3 INT4 SPARE = 0 INT4 138993 MTRX FLAG (Matrix 101) INSTANCE = 101 INT4 <-- Out of ORDER, missing a bunch in between DATATYPE = 4 INT2 DATASIZE = 2 INT2 NRECORDS = 16 INT4 NBYTES = 32 INT4 VALUE = POINTER to MATRIX 101 INT4 SPARE = 30594132 INT4 139021 MTRX FLAG (Matrix 102) INSTANCE = 102 INT4 DATATYPE = 4 INT2 DATASIZE = 2 INT2 NRECORDS = 16 INT4 NBYTES = 32 INT4 VALUE = POINTER to MATRIX 102 INT4 SPARE = 30594128 INT4 139049 MTRX FLAG (Matrix 103) INSTANCE = 103 INT4 DATATYPE = 4 INT2 DATASIZE = 2 INT2 NRECORDS = 16 INT4 NBYTES = 32 INT4 VALUE = POINTER to MATRIX 103 INT4 SPARE = 30671314 INT4 139077 MTXF FLAG (Matrix File) INSTANCE = 1 INT4 DATATYPE = 18 INT2 DATASIZE = 1 INT2 NRECORDS = 26 INT4 NBYTES = 26 INT4 VALUE = POINTER to MATRIX FILE 1 INT4 SPARE = 0 INT4 139105 MTXF FLAG (Matrix File) INSTANCE = 2 INT4 DATATYPE = 18 INT2 DATASIZE = 1 INT2 NRECORDS = 26 INT4 NBYTES = 26 INT4 VALUE = POINTER to MATRIX FILE 2 INT4 SPARE = 30594148 INT4 139133 NAVG FLAG (Number of Channels Averaged) INSTANCE = 1 INT4 DATATYPE = 4 INT2 DATASIZE = 2 INT2 NRECORDS = 1 INT4 NBYTES = 2 INT4 VALUE = 3 INT2 REMAINDER= 0 INT2 SPARE = 0 INT4 139161 NChn FLAG (Number of Channels in Machine) INSTANCE = 1 INT4 DATATYPE = 4 INT2 DATASIZE = 2 INT2 NRECORDS = 1 INT4 NBYTES = 2 INT4 VALUE = 388 INT2 REMAINDER= 0 INT2 SPARE = 0 INT4 139189 NLNE FLAG (Number of Lanes on Gel) 48 lanes INSTANCE = 1 INT4 DATATYPE = 4 INT2 DATASIZE = 2 INT2 NRECORDS = 1 INT4 NBYTES = 2 INT4 VALUE = 48 INT2 REMAINDER= 0 INT2 SPARE = 0 INT4 139217 PBAS FLAG (Called Sequence 1) INSTANCE = 1 INT4 DATATYPE = 2 INT2 DATASIZE = 1 INT2 NRECORDS = 712 INT4 NBYTES = 712 INT4 VALUE = POINTER to CALLED SEQUENCE 1 INT4 SPARE = 30594160 INT4 139245 PBAS FLAG (Called Sequence 2) INSTANCE = 2 INT4 DATATYPE = 2 INT2 DATASIZE = 1 INT2 NRECORDS = 712 INT4 NBYTES = 712 INT4 VALUE = POINTER to CALLED SEQUENCE 2 INT4 SPARE = 30594164 INT4 139273 PDMF FLAG (Dyeset/Primer 1) INSTANCE = 1 INT4 DATATYPE = 18 INT2 DATASIZE = 1 INT2 NRECORDS = 24 INT4 NBYTES = 24 INT4 VALUE = POINTER to DYESET/PRIMER 1 INT4 SPARE = 0 INT4 139301 PDMF FLAG (Dyeset/Primer 2) INSTANCE = 2 INT4 DATATYPE = 18 INT2 DATASIZE = 1 INT2 NRECORDS = 24 INT4 NBYTES = 24 INT4 VALUE = POINTER to DYESET/PRIMER 2 INT4 SPARE = 30594144 INT4 139329 PLOC FLAG (Base to Trace 1) INSTANCE = 1 INT4 DATATYPE = 4 INT2 DATASIZE = 2 INT2 NRECORDS = 712 INT4 NBYTES = 1424 INT4 VALUE = POINTER TO BASE to TRACE ARRAY 1 INT4 SPARE = 30594192 INT4 139357 PLOC FLAG (Base to Trace 2) INSTANCE = 2 INT4 DATATYPE = 4 INT2 DATASIZE = 2 INT2 NRECORDS = 712 INT4 NBYTES = 1424 INT4 VALUE = POINTER TO BASE to TRACE ARRAY 2 INT4 SPARE = 30594124 INT4 139385 PPOS FLAG (Primer Position in raw) INSTANCE = 1 INT4 DATATYPE = 4 INT2 DATASIZE = 2 INT2 NRECORDS = 1 INT4 NBYTES = 2 INT4 VALUE = 940 INT2 REMAINDER= 0 INT2 SPARE = 0 INT4 139413 PPOS FLAG (Primer position in raw) INSTANCE = 2 INT4 DATATYPE = 4 INT2 DATASIZE = 2 INT2 NRECORDS = 1 INT4 NBYTES = 2 INT4 VALUE = 940 INT2 REMAINDER= 0 INT2 SPARE = 0 INT4 139441 RSPN FLAG (???) INSTANCE = 1 INT4 DATATYPE = 4 INT2 DATASIZE = 2 INT2 NRECORDS = 1 INT4 NBYTES = 2 INT4 VALUE = 3 INT2 REMAINDER= 0 INT2 SPARE = 0 INT4 139469 RUND FLAG (Date Started) INSTANCE = 1 INT4 DATATYPE = 10 INT2 DATASIZE = 4 INT2 NRECORDS = 1 INT4 NBYTES = 4 INT4 VALUE = (1997 INT2 (year),2 INT1 (month), 14 INT1 (day) ) SPARE = 0 INT4 139497 RUND FLAG (Date stopped) INSTANCE = 2 INT4 DATATYPE = 10 INT2 DATASIZE = 4 INT2 NRECORDS = 1 INT4 NBYTES = 4 INT4 VALUE = (1997 INT2 (year),2 INT1 (month), 15 INT1 (day) ) SPARE = 0 INT4 139525 RUNT FLAG (Time started) INSTANCE = 1 INT4 DATATYPE = 11 INT2 DATASIZE = 4 INT2 NRECORDS = 1 INT4 NBYTES = 4 INT4 VALUE = (16 (h), 36 (m), 40 (s), 0 (ignored) ) 4 X INT1 SPARE = 0 INT4 139553 RUNT FLAG (Time ended) INSTANCE = 2 INT4 DATATYPE = 11 INT2 DATASIZE = 4 INT2 NRECORDS = 1 INT4 NBYTES = 4 INT4 VALUE = (4 (h), 37 (m), 11 (s), 0 (ignored) ) 4 X INT1 SPARE = 0 INT4 139581 S/N% FLAG (Sum of Each Base Type) INSTANCE = 1 INT4 DATATYPE = 4 INT2 DATASIZE = 2 INT2 NRECORDS = 4 INT4 NBYTES = 8 INT4 VALUE = POINTER to #(G,A,T,C) in CALLED SEQUENCE 2 INT4 SPARE = 0 INT4 139609 SMPL FLAG (Sample Name) INSTANCE = 1 INT4 DATATYPE = 18 INT2 DATASIZE = 1 INT2 NRECORDS = 13 INT4 NBYTES = 13 INT4 VALUE = POINTER TO SAMPLE INT4 SPARE = 0 INT4 139637 SPAC FLAG (Base Spacing Used) INSTANCE = 1 INT4 DATATYPE = 7 INT2 DATASIZE = 4 INT2 NRECORDS = 1 INT4 NBYTES = 4 INT4 VALUE = 9.67 FLT4 SPARE = 0 INT4 139665 SPAC FLAG (Basecaller) INSTANCE = 2 INT4 DATATYPE = 18 INT2 DATASIZE = 1 INT2 NRECORDS = 6 INT4 NBYTES = 6 INT4 VALUE = POINTER to BASECALLER INT4 SPARE = 30594140 INT4 139693 SPAC FLAG (Base Spacing Calculated) INSTANCE = 3 INT4 DATATYPE = 7 INT2 DATASIZE = 4 INT2 NRECORDS = 1 INT4 NBYTES = 4 INT4 VALUE = 9.67 FLT4 SPARE = 0 INT4 139721 SVER FLAG (Collection Version) INSTANCE = 1 INT4 DATATYPE = 18 INT2 DATASIZE = 1 INT2 NRECORDS = 4 INT4 NBYTES = 4 INT4 VALUE = "2.0" 4 X INT1 SPARE = 0 INT4 139749 SVER FLAG (Basecaller Version) INSTANCE = 2 INT4 DATATYPE = 18 INT2 DATASIZE = 1 INT2 NRECORDS = 12 INT4 NBYTES = 12 INT4 VALUE = POINTER to BASECALLER VERSION INT4 SPARE = 30594196 INT4 139777 THUM FLAG (???) INSTANCE = 1 INT4 DATATYPE = 12 INT2 DATASIZE = 10 INT2 NRECORDS = 1 INT4 NBYTES = 10 INT4 VALUE = POINTER to THUM structure 1 INT4 SPARE = 30594112 INT4 139805 THUM FLAG (???) INSTANCE = 2 INT4 DATATYPE = 12 INT2 DATASIZE = 10 INT2 NRECORDS = 1 INT4 NBYTES = 10 INT4 VALUE = POINTER to THUM structure 2 INT4 SPARE = 30594120 INT4 139833 TRKC FLAG (Tracking Channels???) INSTANCE = 1 INT4 DATATYPE = 4 INT2 DATASIZE = 2 INT2 NRECORDS = 2 INT4 NBYTES = 4 INT4 VALUE = (70, 69) 2 X INT2 SPARE = 0 INT4 139861 TRKI FLAG (???) INSTANCE = 1 INT4 DATATYPE = 4 INT2 DATASIZE = 2 INT2 NRECORDS = 1 INT4 NBYTES = 2 INT4 VALUE = 32 INT2 REMAINDER = 0 INT2 SPARE = 0 INT4 139889 TRKP FLAG (???) INSTANCE = 1 INT4 DATATYPE = 4 INT2 DATASIZE = 2 INT2 NRECORDS = 2 INT4 NBYTES = 4 INT4 VALUE = (0, 1246) 2 X INT2 SPARE = 0 INT4 139917 drty FLAG ( End of file?) INSTANCE = 1 INT4 DATATYPE = 4 INT2 DATASIZE = 2 INT2 NRECORDS = 1 INT4 NBYTES = 2 INT4 VALUE = 0 INT2 REMAINDER= 0 INT2 SPARE = 0 INT4 139945 Zeroes to end of file *** abibreakout.for ******************************************************** c ABIBreakout.FOR C 26-FEB-1997 David Mathog C C This program opens an ABI trace file and then dumps fields C to a text format. C For OpenVMS/ALPHA - compile with /float=IEEE_FLOAT C Other platforms - you may need to change byte swapping routines. C ***************************************************** c implicit none integer*4 MAXFILE parameter (MAXFILE=2**20) character*1 array(MAXFILE) !A 1Mb array to hold the file character*120 infile,outfile, search integer flagsum parameter (flagsum=40) character*7 flagtypes(flagsum) integer*4 irec,brec,istat,incount,inlen,numstrings,ipoint integer*4 begin,length,step,swap,slen integer*4 inlenarray(10) integer*4 lastbyte integer*4 offset integer*4 action c character*4 flag integer*4 datatype,datasize integer*4 instance,nrecords,nbytes,value integer*4 spare c byte sbyte(80,10) logical ok c logical flagcompare c data flagtypes/ 1 ' tdir 0' !jump to offset, no action 1 ,' AEPt 1' !immediate single value 1 ,' ASPF 1' !immediate single value 1 ,' ASPt 1' !immediate single value 1 ,' AUTO 2' !immediate multiple value 1 ,' B1Pt 1' !immediate single value 1 ,' CAGT 2' !immediate multiple value 1 ,' CMBF 3' !indirect multiple value 1 ,' CMNT 3' !indirect multiple value 1 ,' CTTL 3' !indirect multiple value 1 ,' DATA 3' !indirect multiple value 1 ,' EVNT 3' !indirect multiple value 1 ,' FWO_ 2' !immediate multiple value 1 ,' GLEN 3' !indirect multiple value 1 ,' GELP 3' !indirect multiple value 1 ,' LANE 2' !immediate multiple value 1 ,' MCHN 3' !indirect multiple value 1 ,' MODL 2' !immediate multiple value 1 ,' MTRX 3' !indirect multiple value 1 ,' MTXF 3' !indirect multiple value 1 ,' NAVG 1' !immediate single value 1 ,' NCHn 1' !immediate single value 1 ,' NLNE 1' !immediate single value 1 ,' PBAS 3' !indirect multiple value 1 ,' PDMF 3' !indirect multiple value 1 ,' PLOC 3' !indirect multiple value 1 ,' PPOS 1' !immediate single value 1 ,' RSPN 1' !immediate single value 1 ,' RUND 1' !immediate single value 1 ,' RUNT 1' !immediate single value 1 ,' S/N% 3' !indirect multiple value 1 ,' SMPL 3' !indirect multiple value 1 ,' SPAC 6' !immediate single value or indirect multiple value 1 ,' SVER 5' !immediate or indirect multiple value 1 ,' THUM 4' !indirect single value 1 ,' TRKC 2' !immediate multiple value 1 ,' TRKI 1' !immediate single value 1 ,' TRKP 2' !immediate multiple value 1 ,' TRKP 2' !immediate multiple value 1 ,' drty 0' !jump to offset, no action 1/ external flagcompare c c c write(6,*)'ABIbreakout' write(6,*)' This program converts a binary ABI file to' write(6,*)' a text format.' c write(6,*)' ' write(6,*)'Input the name of the file to process' read(5,'(q,a)')inlen,infile(1:inlen) c open(unit=10 1 ,file=infile(1:inlen) 1 ,form='UNFORMATTED',status='OLD' 1 ,ORGANIZATION='SEQUENTIAL' 1 ,RECORDTYPE='FIXED' 1 ,READONLY,iostat=istat) if(istat.ne.0)stop 'Fatal error, something wrong with input file' c inquire(10,RECL=irec) !longwords, because unformmated if(irec.lt.0)then !error... stop 'ABIBreakout fatal error, illegal record size' else brec=irec*4 !bytes/record write(6,*)' ' write(6,*)'Each record is ',brec,' bytes long' end if c write(6,*)' ' write(6,*)'Now reading in the input file' ipoint=1 incount=0 istat = 0 do while(istat .ge. 0 .and. ipoint .le. MAXFILE - brec + 1) call getrec(array(ipoint),irec*4,istat) if(istat.eq.0)then ipoint=ipoint+brec incount = incount + 1 end if end do lastbyte = incount*brec write(6,*)' ' write(6,*)'Read in ',incount,' records' write(6,*)'Read in ',lastbyte,' bytes' write(6,*)' ' close(10) c write(6,*)'Input the name of the output file' read(5,'(q,a)')inlen,infile(1:inlen) open(unit=11 1 ,file=infile(1:inlen) 1 ,form='FORMATTED',status='NEW' 1 ,CARRIAGECONTROL='LIST' 1 ,iostat=istat) if(istat.ne.0)stop 'Fatal error, something wrong with output file' C C Determine if it is a MacBinary or not by the position of the ABIF C flag C if(flagcompare(array(1),'ABIF'))then offset = 1 !correction from file pointer to Fortran array pointers ipoint = 7 !position of first FLAG structure else if(flagcompare(array(129),'ABIF'))then offset = 129 ipoint = 135 else stop 'Fatal error - input file is not an ABI trace file' end if call getflag(array(ipoint) 1 ,flag,instance,datatype,datasize,nrecords 1 ,nbytes,value,spare,1) call getaction(flagtypes,flagsum,flag,instance,action) if(action .ne. 0)stop 'Fatal error, input file invalid' ipoint = offset + value action = 1 c c do while(action .ne. 0) call getflag(array(ipoint) 1 ,flag,instance,datatype,datasize,nrecords 1 ,nbytes,value,spare,0) call getaction(flagtypes,flagsum,flag,instance,action) C C Matrix overlays an odd, signed integer 2 onto the unsigned C integer 2 datatype (4). Make up a datatype for use in this C program that does not exist in ABI files C if(flag .eq. 'MTRX')datatype = 1004 call writefield(11, array,action, offset 1 ,flag,instance,datatype,datasize 1 ,nrecords,nbytes,value,spare) ipoint = ipoint + 28 end do close (11) stop 'ABIBreakout: normal completion' end subroutine getrec(scratch,size,stat) implicit none integer*4 size,stat character*1 scratch(size) read(10,iostat=stat)scratch return end subroutine tellem(array,begin,length,step,swap) implicit none integer*4 begin,length,step,swap,i,j,k byte array(*) byte ba(4),btemp integer*2 wa(2),wtemp integer*4 la, longword integer*4 sbyte,sword integer*4 ubyte,uword character*2 outc equivalence (ba,wa,la) c write(6,2000)'*******************************************************************************' write(6,2000)'|-Abs-Position--|-Rel-Position--|---byte-----|---word----------------|-----longword-------|char|' write(6,2000)' int hex int hex int uint hex int uint int hex' do i =begin,begin+length-1,step c c load the 4 bytes into the equivalenced byte array c k = i do j=1,4 ba(j)=array(k) k = k + 1 end do c c pull off the byte and unsigned byte c sbyte=ba(1) ubyte=jiand('ff'x,la) c c pull off the word and unsigned word c sword=wa(1) uword=jiand('ffff'x,la) c c pull off the longword c longword=la c c swap as needed c if(swap .eq. 1)then c la = uword btemp=ba(1) ba(1)=ba(2) ba(2)=btemp uword=la c la = sword btemp=ba(1) ba(1)=ba(2) ba(2)=btemp sword=wa(1) c la = longword do j = 0,1 btemp=ba(4-j) ba(4-j)=ba(j+1) ba(j+1)=btemp end do longword=la end if c c if(ubyte .ge. '40'o .and. ubyte .le. '177'o)then outc=char(ubyte) if(ubyte .eq.'40'o)outc='SP' else outc='**' endif write(6,1000)i,i,i-begin,i-begin,sbyte,ubyte,ubyte,sword,uword, 1 longword,longword,outc end do 1000 format(2(' ',i7,' ',z8),2(' ',i4),' ',z2,3(' ',i11),' ',z8,' ',a) 2000 format(' ',a) return end logical function flagcompare(array,text) implicit none character*1 array(4) character*4 text c integer i c flagcompare = .true. do i = 1,4 if(array(i) .ne. text(i:i))then flagcompare = .false. return end if end do return end subroutine getflag(array 1 ,flag,instance,datatype,datasize,nrecords 1 ,nbytes 1 ,value 1 ,spare,swap) implicit none c character*1 array(28) character*4 flag integer*4 datatype,datasize integer*4 instance,nrecords,nbytes integer*4 value integer*4 spare,swap c integer*4 i c character*1 ca(4) byte ba(4) integer*2 wa(2) integer*4 la real*4 ra equivalence (ca,ba,wa,la) c c extract flag c do i = 1,4 flag(i:i) = array(i) end do c c extract instance c do i = 1,4 ca(i)=array(9-i) end do instance = la c c extract datatype and datasize c do i = 1,4 ca(i)=array(13-i) end do datatype=wa(2) datasize=wa(1) c c extract Nrecords c do i = 1,4 ca(i)=array(17-i) end do nrecords = la c c extract Nbytes c do i = 1,4 ca(i)=array(21-i) end do nbytes = la c c extract value - swap or not depend on SWAP c if(swap .eq. 1)then do i = 1,4 ca(i)=array(25 - i) end do else do i = 1,4 ca(i)=array(20+i) end do end if value = la c c extract spare c do i = 1,4 ca(i)=array(29-i) end do spare = la c return end subroutine getaction(flagtypes,num,flag,instance,action) implicit none integer*4 action,num,instance character*4 flag character*7 flagtypes(num) c integer*4 i,k c do i = 1,num k = index(flagtypes(i),flag) if(k .ne. 0)then action = ichar(flagtypes(i)(7:7)) - ichar('0') c c The SVER field is screwy, the first instance is IMMEDIATE MULTIPLE c and the second instance is INDIRECT MULTIPLE. Blame ABI c for some silly programming. c if(action .eq. 5)then if(instance .eq. 1)then action = 2 else action = 3 end if end if c c The SPAC field is screwy, the first instance is IMMEDIATE SINGLE c and the second instance is INDIRECT MULTIPLE with a completely c different data type, and the third is back to IMMEDIATE SINGLE c again. Blame ABI for some silly programming. c if(action .eq. 6)then if(instance .eq. 2)then action = 3 else action = 1 end if end if c return end if end do action = -1 c return end subroutine writefield(unit, array,action, offset 1 ,flag,instance,datatype,datasize,nrecords 1 ,nbytes,value,spare) implicit none c character*1 array(1) integer*4 unit,action,offset integer*4 instance,datatype,datasize integer*4 nrecords, nbytes integer*4 value,spare character*4 flag c real*4 rtemp integer*4 i,k,ipoint logical novel c character*1 ca(4) byte ba(4),btemp integer*2 wa(2) integer*4 la real*4 ra equivalence (ca,ba,wa,la,ra) c c perform the appropriate action. If action <=0 nothing happens c novel = .false. if(action .eq. 1)then !immediate single value la = value if(datatype .eq. 2)then write(unit,1002)flag,instance,value else if(datatype .eq. 4)then btemp=ba(2) ba(2)=ba(1) ba(1)=btemp write(unit,1004)flag,instance,wa(1) else if(datatype .eq. 7)then do i = 1,2 btemp = ba(5-i) ba(5-i) = ba(i) ba(i) = btemp end do write(unit,1007)flag,instance,ra else if(datatype .eq. 10)then btemp=ba(2) ba(2)=ba(1) ba(1)=btemp write(unit,1010)flag,instance,wa(1),ba(3),ba(4) else if(datatype .eq. 11)then write(unit,1011)flag,instance,ba(1),ba(2),ba(3) else if(datatype .eq. 18)then i = ichar(ca(1))+1 k = 2 write(unit,1018)flag,instance,(ba(k),k=2,i) else novel = .true. end if else if(action .eq. 2)then !immediate multiple value la = value if(datatype .eq. 2)then write(unit,1002)flag,instance,value else if(datatype .eq. 4)then do i = 1,2 btemp = ba(5-i) ba(5-i) = ba(i) ba(i) = btemp end do write(unit,2004)flag,instance,wa(1),wa(2) else if(datatype .eq. 13)then i = nbytes write(unit,2013)flag,instance,(ba(i),k=1,i) else if(datatype .eq. 18)then k = jiand('ff'x,value) la = value write(unit,3018)flag,instance,( ca(i),i=2,1+k) else novel = .true. end if else if(action .eq. 3)then !indirect multiple value la = value ! always an offset into the file do i = 1,2 btemp = ba(5-i) ba(5-i) = ba(i) ba(i) = btemp end do ipoint = la + offset !now we know where in the array c if(datatype .eq. 2)then if(ipoint .ne. offset)then write(unit,3002)flag,instance,(array(i),i=ipoint,ipoint+nbytes-1) else write(unit,1002)flag,instance,'NONE' end if else if(datatype .eq. 4)then wa(2)=0 if(ipoint .ne. offset)then write(unit,3004)flag,instance do i = 1, nrecords ca(2)=array(ipoint) ipoint = ipoint + 1 ca(1)=array(ipoint) ipoint = ipoint + 1 write(unit,30045)i,la end do else write(unit,1002)flag,instance,'NONE' endif else if(datatype .eq. 1004)then wa(2)=0 if(ipoint .ne. offset)then write(unit,3004)flag,instance do i = 1, nrecords ca(2)=array(ipoint) ipoint = ipoint + 1 ca(1)=array(ipoint) ipoint = ipoint + 1 rtemp = float(wa(1))/1000. write(unit,30046)i,rtemp end do else write(unit,1002)flag,instance,'NONE' endif else if(datatype .eq. 18)then if(ipoint .ne. offset)then write(unit,3018)flag,instance,(array(i),i=ipoint+1,ipoint+nbytes-1) else write(unit,1002)flag,instance,'NONE' end if else novel = .true. end if else if(action .eq. 4)then !indirect single value la = value ! always an offset into the file do i = 1,2 btemp = ba(5-i) ba(5-i) = ba(i) ba(i) = btemp end do ipoint = la + offset !now we know where in the array c if(datatype .eq. 12)then !THUM structures write(unit,4012)flag,instance,(ichar(array(i)),i=ipoint,ipoint+9) else novel = .true. end if end if c if(novel)then write(6,9000)flag,instance,datatype,datasize 1 ,nrecords,nbytes,value,spare end if 9000 format(' Novel FLAG structure encountered',/ 1 ' FLAG: ',a4,/ 1 ' instance ',i6,/ 1 ' datatype ',i6,/ 1 ' datasize ',i6,/ 1 ' nrecords ',i6,/ 1 ' nbytes ',i6,/ 1 ' value(hex) ',z8,/ 1 ' spare(hex) ',z8) 1002 format('>',a4,i6,' ',a4) 1004 format('>',a4,i6,' ',i6) 1007 format('>',a4,i6,' ',f9.3) 1010 format('>',a4,i6,' ',i6,'(y)',i3,'(m)',i3,'(d)') 1011 format('>',a4,i6,' ',i6,'(h)',i3,'(m)',i3,'(s)') 1018 format('>',a4,i6,' ',a4) 2004 format('>',a4,i6,2(' ',i6)) 2013 format('>',a4,i6,4(' ',z6)) 3002 format('>',a4,i6,' ',/,5000(50a,/)) 3004 format('>',a4,i6, '(Pos,Value)') 30045 format(' ',i6,',',i6) 30046 format(' ',i6,',',f7.3) 3018 format('>',a4,i6,' ',256a) 4012 format('>',a4,i6,' ',z2,9(',',z2)) return end *** datasniffer.for ************************************************************ c DataSniffer.FOR C 20-FEB-1997 David Mathog C C This program dumps data from a binary file in arbitrary C formats. It uses pointers in an awful way and is probably C extremely nonportable. C ***************************************************** c implicit none integer*4 MAXFILE parameter (MAXFILE=2**20) byte array(MAXFILE) !A 1Mb array to hold the file character*120 infile,search integer*4 irec,brec,istat,incount,inlen,numstrings,ipoint integer*4 begin,length,step,swap,slen integer*4 inlenarray(10) integer*4 lastbyte byte sbyte(80,10) logical ok c c c write(6,*)'DataSniffer' write(6,*)' This program examines the data in a binary file' c write(6,*)' ' write(6,*)'Input the name of the file to process' read(5,'(q,a)')inlen,infile(1:inlen) c open(unit=10 1 ,file=infile(1:inlen) 1 ,form='UNFORMATTED',status='OLD' 1 ,ORGANIZATION='SEQUENTIAL' 1 ,RECORDTYPE='FIXED' 1 ,READONLY,iostat=istat) if(istat.ne.0)stop 'Fatal error, something wrong with that file' c inquire(10,RECL=irec) !longwords, because unformmated if(irec.lt.0)then !error... stop '