From mad at biol.unlp.edu.ar Fri Mar 1 02:18:25 2002 From: mad at biol.unlp.edu.ar (Martin Sarachu) Date: Fri, 01 Mar 2002 10:18:25 +0300 Subject: Jemboss Message-ID: <3C7F2B41.DAFA33F8@biol.unlp.edu.ar> now I'm getting this when doing %java $EMBOSS_ROOT/share/EMBOSS/jemboss/org/emboss/jemboss/Jemboss & > Exception in thread "main" java.lang.NoClassDefFoundError: /usr/local/EMBOSS/share/EMBOSS/jemboss/org/emboss/jemboss/Jemboss > > [3]+ Exit 1 the previous problem was of missing files, any idea now? martin -- Martin Sarachu ICQ: 123797358 EMBnet Argentina: http://www.ar.embnet.org From axel.klenk at morphochem.ch Fri Mar 1 08:41:14 2002 From: axel.klenk at morphochem.ch (axel klenk) Date: Fri, 1 Mar 2002 14:41:14 +0100 Subject: db url access via proxy? Message-ID: <01C1C12F.242FCA60.axel.klenk@morphochem.ch> Hi, I apologize if this has been discussed before, but I couldn't find it in the documentation: can I and how can I set up database access method URL to use a proxy with authorization (e.g. wget uses an environment variable: http_proxy="http://user:passwd at proxy/")? Is there something comparable for EMBOSS? Thanks in advance, - axel ---------------------------------------- axel klenk morphochem AG wro-1055 schwarzwaldallee 215 4058 basel tel. ++41-61-6952104 fax ++41-61-6952122 axel.klenk at morphochem.ch http://www.morphochem.ch From mad at biol.unlp.edu.ar Fri Mar 1 04:21:26 2002 From: mad at biol.unlp.edu.ar (Martin Sarachu) Date: Fri, 01 Mar 2002 12:21:26 +0300 Subject: Jemboss (almost there) Message-ID: <3C7F4816.F8F76389@biol.unlp.edu.ar> Thanks Tim for all your help, hope this is the last issue. When starting the client (either form console or web), Jemboss loads the login screen but stops the "progress bar" on the message "EMBOSS applications found" and the programs menu never shows up. martin -- Martin Sarachu ICQ: 123797358 EMBnet Argentina: http://www.ar.embnet.org From saleh at tc.cornell.edu Sun Mar 3 18:03:18 2002 From: saleh at tc.cornell.edu (M. A. Saleh Elmohamed) Date: Sun, 03 Mar 2002 18:03:18 -0500 Subject: questions/comments reg Emboss on ms windows ... Message-ID: <5.1.0.14.2.20020303175020.026e38c8@theory.tc.cornell.edu> Hi there, I'd like to get in touch with anyone succeeded in installing EMBOSS-2.2.0 on an MS-windows env under Cygwin. Furthermore, I also would really like to hear from those who tried and succeeded porting it to MS Visual Studio 6 env. Please feel free to respond so I can send my questions and comments. Thank you. -Saleh From ableasby at hgmp.mrc.ac.uk Tue Mar 5 17:27:32 2002 From: ableasby at hgmp.mrc.ac.uk (ableasby at hgmp.mrc.ac.uk) Date: Tue, 5 Mar 2002 22:27:32 GMT Subject: EMBOSS 2.3.0 released Message-ID: <200203052227.WAA23282@bromine.hgmp.mrc.ac.uk> This version of EMBOSS contains two new programs (whichdb and interface) Problems addressed include wildcard database searches failing under some circumstances. Also, missing files in file-list queries no longer cause termination of the programs. The new program 'jembossctl' should not be run by typical users. It is a slave program for a forthcoming Jemboss server. This will hopefully be announced soon. Alan From battaile at post.its.mcw.edu Tue Mar 5 18:14:05 2002 From: battaile at post.its.mcw.edu (battaile at post.its.mcw.edu) Date: Tue, 5 Mar 2002 17:14:05 -0600 (CST) Subject: mse Message-ID: <6109.141.106.40.27.1015370045.squirrel@post.its.mcw.edu> I am trying to use mse like I would use lineup in gcg. I want to create a manual alignment, that I can reload at later dates to make adjustments/add new sequences/etc... Lineup in gcg allows this by saving the alignment to a file. I have tried this in mse and can't seem to get anything to work. The only thing I can figure is that I could write out each sequence individually to a separate file. Personally, I would rather not have to write out 15 sequences separately every time I end a session. I have tried... write: this works fine, but as I said above, I would rather not have to write out each individual sequence every time I quit. hardcopy: this also seems to work, but I can't read the multisequence alignment back in (mse -msf sequence-file gives a can't read error). exit [filename]: this doesn't work at all. If I am inserting gaps (which is 99% of the job) the sequences aren't recognized as being changed. If I type in, then delete some residues, I get the message 'Sequences modified do you wish to continue exiting [N]'. If I choose the default [N], I get dumped back into the editor. If I choose 'Y', the program exits. Either way, no file gets written. Am I doing something completely backwards? Any suggestions? Thanks, Kevin Battaile From ableasby at hgmp.mrc.ac.uk Thu Mar 7 19:47:13 2002 From: ableasby at hgmp.mrc.ac.uk (ableasby at hgmp.mrc.ac.uk) Date: Fri, 8 Mar 2002 00:47:13 GMT Subject: EMBOSS 2.3.1 released Message-ID: <200203080047.AAA14371@bromine.hgmp.mrc.ac.uk> This is a bugfix release. The ChangeLog appears below. As usual, all errors are added to the quality control suite to ensure they don't recur. Version 2.3.1 est2genome fixed for large alignments (over 40Mbase for est * genomic sequence length) sequence reading for ABI files fixed (and selex files tested) genbank feature input working pepinfo PNG output larger to make the text readable (only affects PNG output) empty sequence file input fails gracefully empty sequence input fails gracefully (and only needs one ^D from stdin) Alan From mathog at mendel.bio.caltech.edu Fri Mar 8 11:12:35 2002 From: mathog at mendel.bio.caltech.edu (David Mathog) Date: Fri, 08 Mar 2002 08:12:35 -0800 Subject: transeq/fuzzpro on large sequences Message-ID: One user here tried to do the following (switches omitted for clarity): gunzip chr1.gz | transeq | fuzzpro where chr1 is the Ensembl golden path for Human chromosome 1. This does not work well because transeq tries to accept the entire input sequence before doing its translations. Since chr1 is very large transeq grows to an unacceptable size before emitting anything. In this case I worked around it by using my own program fasttrans ftp://saf.bio.caltech.edu/pub/software/molbio/fasttrans.c instead of transeq. fasttrans breaks large input sequences at 1 Mb intervals, translates that chunk in the desired frames, and then resumes input, etc. That would be a very useful option to add to transeq since it would let it run in 1 or 2 Mb instead of the 100's of Mb it now requires for large genomic sequences. That said, it might make even more sense in terms of performance, if not in terms of clean functional separation, if fuzzpro could translate for itself. It could then easily emit the DNA position of the match (which has to be calculated from fragment number and offset for fragmented input) And since it makes no sense for fuzzpro patterns to be much larger than a couple of thousand residues from one end to the other, the "bin size" of 1 Mb for fasttrans could be effectively reduced to 10kb or so, which should reduce the size of the various buffers so much that they would all fit inside cache memory, and greatly speed up the performance. Also with regards to fuzzpro the only way that I know of now to show surrounding sequence is to put X characters on both sides of the pattern (or indicate a gap of 100 and then an X). But either way that makes the regexp code run unneeded operations and this sort of logical hack is too complex for the average user. Far better if there were switches something like this: fuzzpro sequence -pattern=whatever -upstream=100 -downstream=200 Regards, David Mathog mathog at caltech.edu Manager, Sequence Analysis Facility, Biology Division, Caltech From ableasby at hgmp.mrc.ac.uk Fri Mar 8 11:22:08 2002 From: ableasby at hgmp.mrc.ac.uk (ableasby at hgmp.mrc.ac.uk) Date: Fri, 8 Mar 2002 16:22:08 GMT Subject: transeq/fuzzpro on large sequences Message-ID: <200203081622.QAA12891@bromine.hgmp.mrc.ac.uk> Thanks for the info/suggestions. Don't forget the program fuzztran which is a translation/fuzzpro in one. Alan From thomas.laurent at uk.lionbioscience.com Fri Mar 8 11:28:04 2002 From: thomas.laurent at uk.lionbioscience.com (Thomas Laurent) Date: Fri, 08 Mar 2002 16:28:04 +0000 Subject: transeq/fuzzpro on large sequences References: Message-ID: <3C88E694.EF432FEC@uk.lionbioscience.com> David Mathog wrote: > That said, it might make even more sense in terms of performance, if not > in terms of > clean functional separation, if fuzzpro could translate for itself. Hi David, I'm far from being an EMBOSS expert, and I perheaps misunderstood this part of your mail, but isn't Fuzztran doing that already ? I mean instead of piping transeq to fuzzpro, fuzztran translate the dna sequence then search for the pattern. It seems doing the same job. But, I perheaps missed something. Cheers, Thomas --------------------- Thomas Laurent LION Bioscience From mathog at mendel.bio.caltech.edu Fri Mar 8 12:41:30 2002 From: mathog at mendel.bio.caltech.edu (David Mathog) Date: Fri, 08 Mar 2002 09:41:30 -0800 Subject: transeq/fuzzpro on large sequences Message-ID: > Don't forget the > program fuzztran which is a translation/fuzzpro in one. Unfortunately fuzztran acts exactly like transeq+fuzzpro on large input sequences, growing very, very large before doing anything. David Mathog mathog at caltech.edu Manager, Sequence Analysis Facility, Biology Division, Caltech From duhaimj at ircm.qc.ca Mon Mar 11 12:41:43 2002 From: duhaimj at ircm.qc.ca (Johanne Duhaime) Date: Mon, 11 Mar 2002 12:41:43 -0500 Subject: Script for incremental update of databases Message-ID: <3C8CEC57.83253FF5@ircm.qc.ca> Hello We will start using Emboss. We want certain databases to reside locally (genbank and swissprot for example). Are they any scripts already available that would update the database each day for new sequences only. Thank you in advance. -- Johanne Duhaime IRCM 110 Ave des Pins O Montreal, Quebec 987-5556 (tel) 987-5644 (fax) Johanne_Duhaime at ircm.qc.ca http://www.ircm.qc.ca From duhaimj at ircm.qc.ca Mon Mar 11 13:14:56 2002 From: duhaimj at ircm.qc.ca (Johanne Duhaime) Date: Mon, 11 Mar 2002 13:14:56 -0500 Subject: Transfac database Message-ID: <3C8CF420.51B42EC2@ircm.qc.ca> Hello I looked for the Transfac database on the web. It seems that it is now "buyable" but it used to be free. Are you buying it to use with tfextract? Or is there any other way to get that database? Thank you in advance -- Johanne Duhaime IRCM 110 Ave des Pins O Montreal, Quebec 987-5556 (tel) 987-5644 (fax) Johanne_Duhaime at ircm.qc.ca http://www.ircm.qc.ca From jison at hgmp.mrc.ac.uk Tue Mar 12 03:40:31 2002 From: jison at hgmp.mrc.ac.uk (Dr J.C. Ison) Date: Tue, 12 Mar 2002 08:40:31 +0000 Subject: Script for incremental update of databases References: <3C8CEC57.83253FF5@ircm.qc.ca> Message-ID: <3C8DBEFF.6878CF91@hgmp.mrc.ac.uk> Johanne - If the database was made up lots of files then Mirror might help: http://www.freecode.com/projects/mirror1/ "Mirror was designed to duplicate a directory hierarchy between two machines. It avoids copying files unnecessarily by comparing the file time-stamps and file sizes before transferring" J. Johanne Duhaime wrote: > Hello > > We will start using Emboss. We want certain databases to reside locally > (genbank and swissprot for example). Are they any scripts already > available that would update the database each day for new sequences > only. > > Thank you in advance. > -- > Johanne Duhaime > IRCM > 110 Ave des Pins O > Montreal, Quebec > 987-5556 (tel) 987-5644 (fax) > Johanne_Duhaime at ircm.qc.ca > http://www.ircm.qc.ca -- Jon C. Ison, PhD Bioinformatics Applications Group UK MRC Human Genome Mapping Project Resource Centre Hinxton, Cambridge, CB10 1SB, UK E-mail : jison at hgmp.mrc.ac.uk Tel : 01223 49-4548 HGMP-RC: http://www.hgmp.mrc.ac.uk/ EMBOSS : http://www.hgmp.mrc.ac.uk/Software/EMBOSS/ CCP11 : http://www.hgmp.mrc.ac.uk/CCP11/ From jrvalverde at cnb.uam.es Tue Mar 12 09:36:01 2002 From: jrvalverde at cnb.uam.es (jrvalverde at cnb.uam.es) Date: Tue, 12 Mar 2002 15:36:01 +0100 (MET) Subject: Script for incremental update of databases In-Reply-To: <3C8DBEFF.6878CF91@hgmp.mrc.ac.uk> Message-ID: <200203121436.g2CEa2R3372244@embnet.cnb.uam.es> "Dr J.C. Ison" wrote: > Johanne - > > If the database was made up lots of files then Mirror > might help: > http://www.freecode.com/projects/mirror1/ > Not really that much simple, see > > We will start using Emboss. We want certain databases to reside locally > > (genbank and swissprot for example). Are they any scripts already > > available that would update the database each day for new sequences ^^^^^^^^^^^^^ > > only. ^^^^^ So the actual answer is that it depends on the bandwidth you have. If you have enough to transfer a full cumulative update by the end of a release period in less than one night, then mirror or wget might be OK. Simply get either "cumulative.dat" or "cum_*.dat". Otherwise the things get complicated. The reason is that, as far as I know, you can't assume the cumulative file only changes by addition (please, correct me if I'm wrong). If it were only appended data every day, then it would be trivial to use wget to append the appended new data to your local copy. But sometimes entries get changed, deleted or merged. There are daily updates you can get, but these have the same problem: if an entry has been modified, deleted, merged... and you simply append a daily update to your local copy, then you'll end up with duplicated entries. The solution: get the daily/weekly update and list files, then use SynCron to merge the new data with the old version you have on your disk. SynCron is available at EBI and fine mirror sites: ftp://ftp.ebi.ac.uk/pub/software/unix/SynCron/ But, of course, it is easier if instead of only downloading the daily changes you got the full cumulative changes files, where you have ALL changes occurred since last release already applied in one (set of) file(s). j From jrvalverde at cnb.uam.es Tue Mar 12 09:45:36 2002 From: jrvalverde at cnb.uam.es (jrvalverde at cnb.uam.es) Date: Tue, 12 Mar 2002 15:45:36 +0100 (MET) Subject: Transfac database In-Reply-To: <3C8CF420.51B42EC2@ircm.qc.ca> Message-ID: <200203121445.g2CEjaH7161488@embnet.cnb.uam.es> Johanne Duhaime wrote: > Hello > > I looked for the Transfac database on the web. It seems that it is now > "buyable" but it used to be free. Are you buying it to use with > tfextract? Or is there any other way to get that database? > > Thank you in advance > > >From TRANSFAC main page: Message-ID: <3C8E1FD8.82F87A97@ircm.qc.ca> Hello People at BIOBASE Biological Databases wrote me the following: A less maintained and data reduced TRANSFAC PUBLIC database system is available(only online) for non-commercial and academic organisations at ---------- www.gene-regulation.com. This service is free of charge. Since I want the database locally this is not a solution. They offer an academic price but still it is around $500. Thank you for your help jrvalverde at cnb.uam.es wrote: > Johanne Duhaime wrote: > > Hello > > > > I looked for the Transfac database on the web. It seems that it is now > > "buyable" but it used to be free. Are you buying it to use with > > tfextract? Or is there any other way to get that database? > > > > Thank you in advance > > > > > > >From TRANSFAC main page: > > > We are an academic, non-profit organization, therefore we do not need > to buy it. > > j > > -- > Jos? R. Valverde > EMBnet/CNB -- Johanne Duhaime IRCM 110 Ave des Pins O Montreal, Quebec 987-5556 (tel) 987-5644 (fax) Johanne_Duhaime at ircm.qc.ca http://www.ircm.qc.ca From David.Bauer at SCHERING.DE Wed Mar 13 04:57:27 2002 From: David.Bauer at SCHERING.DE (David.Bauer at SCHERING.DE) Date: Wed, 13 Mar 2002 10:57:27 +0100 Subject: hmmer threads Message-ID: If I try to compile hmmer with threads on Solaris 5.7 I get the folowing error messages: ehmmsearch.c: In function `worker_thread': ehmmsearch.c:1200: `seqall' undeclared (first use in this function) ehmmsearch.c:1200: (Each undeclared identifier is reported only once ehmmsearch.c:1200: for each function it appears in.) ehmmsearch.c:1201: parse error before `{' ehmmsearch.c:1237: continue statement not within a loop ehmmsearch.c: At top level: ehmmsearch.c:1294: parse error before `&' ehmmsearch.c:1294: conflicting types for `ajStrDel' ../../../ajax/ajstr.h:301: previous declaration of `ajStrDel' ehmmsearch.c:1294: warning: data definition has no type or storage class The hmmer compiles fine if I do not define HMMER_THREADS. Any Ideas? Thanks, David. From gbottu at black.vub.ac.be Wed Mar 13 13:24:05 2002 From: gbottu at black.vub.ac.be (Guy Bottu) Date: Wed, 13 Mar 2002 19:24:05 +0100 Subject: primer3_core ??? Message-ID: <20020313192405.A1550544@black.vub.ac.be> from : BEN Dear developers, A question : I have installed EMBOSS 2.3.1 and Primer 3.0.6. When I run the program eprimer3 I get an error message : EMBOSS An error in eprimer3.c at line 316: The program 'primer3_core' must be on the path. It is part of the 'primer3' package, available from the Whitehead Institute. See: http://www-genome.wi.mit.edu/ The package primer however does not contain an executable primer3_core. I installed on the public path a logical link from primer3_core to the Primer executable primer3, but this time I get a Segmentation fault when I try to run eprimer3. Do I miss something ? Sincerely, Guy Bottu From Jack.Leunissen at cmbi.kun.nl Wed Mar 13 18:53:41 2002 From: Jack.Leunissen at cmbi.kun.nl (Jack Leunissen) Date: Thu, 14 Mar 2002 00:53:41 +0100 Subject: primer3_core ??? In-Reply-To: <20020313192405.A1550544@black.vub.ac.be> Message-ID: Hello Guy, When you build primer3 in the "src" directory, it definitely creates the program as "primer3_core" in that directory. I have installed it locally under the name "primer3" too (via a link), as this is more obvious to commandline users. But the web interface calls it under its original name. Cheers, Jack Jack Leunissen Centre of Molecular and Biomolecular Informatics University of Nijmegen, NL > -----Original Message----- > From: owner-emboss at hgmp.mrc.ac.uk [mailto:owner-emboss at hgmp.mrc.ac.uk]On > Behalf Of Guy Bottu > Sent: Wednesday, 13 March, 2002 19:24 > To: emboss at embnet.org > Subject: primer3_core ??? > > > from : BEN > > Dear developers, > > A question : I have installed EMBOSS 2.3.1 and Primer 3.0.6. When I run > the program eprimer3 I get an error message : > > > EMBOSS An error in eprimer3.c at line 316: > The program 'primer3_core' must be on the path. > It is part of the 'primer3' package, > available from the Whitehead Institute. > See: http://www-genome.wi.mit.edu/ > > The package primer however does not contain an executable primer3_core. > I installed on the public path a logical link from primer3_core to the > Primer executable primer3, but this time I get a Segmentation fault when > I try to run eprimer3. Do I miss something ? > > Sincerely, > Guy Bottu > > From hauckl at mail.science.orst.edu Wed Mar 13 20:27:00 2002 From: hauckl at mail.science.orst.edu (Laura Hauck) Date: Wed, 13 Mar 2002 17:27:00 -0800 (PST) Subject: CAI Tables Message-ID: Greetings; My name is Laura Hauck and I am a pre-doctoral grad student at Oregon State University. I have recently been using your Emboss application to generate CAI values for several genes of interest that emerged from a symbiotic relationship. I find that my values are a bit odd. I have Codon Bias tables in Wisconsin Package format that I shifted the columns around to look like the appropriate format of .cut files. The program seems to accept that. The order of the codons, however, does not match the codon order of the .cut tables that you supply (no, my model organisms are not on the list...). Will this interfere with the analysis? What is a good 'HI' value? I generated a codon bias table with one gene, ran a CAI analysis with that table and that gene and got a value of 0.643. That seemed low, is it? The codons should have matched exactly, I was expecting a value of 1.0. Please let me know how to appropriately format my tables if this sounds like an error result, or let me know what you think may be wrong. Thank You, - Laura Hauck From piet at clondiag.com Thu Mar 14 04:03:12 2002 From: piet at clondiag.com (Peter Slickers) Date: Thu, 14 Mar 2002 10:03:12 +0100 Subject: primer3 and eprimer3 References: <20020313192405.A1550544@black.vub.ac.be> Message-ID: <3C906750.C9C03BDC@clondiag.com> After installing EMBOSS-2.3.1 I found the applications 'primer3' and 'eprimer3'. 'primer3' seems to be new with respect to my previous installation. Now I'm wondering what is the difference between these two programs. Their descriptions in 'doc/programs/html' are nearly identical, only the names 'primer3' and 'eprimer3' are interchanged. Peter ------------------------------------------------------------------- Peter Slickers piet at clondiag.com Clondiag Chip Technologies http://www.clondiag.com/ L?bstedter Str. 105 07749 Jena Germany Fon: 03641/5947-65 Fax: 03641/5947-20 ------------------------------------------------------------------- From gwilliam at hgmp.mrc.ac.uk Thu Mar 14 04:24:52 2002 From: gwilliam at hgmp.mrc.ac.uk (Gary Williams, Tel 01223 494522) Date: Thu, 14 Mar 2002 09:24:52 +0000 Subject: primer3_core ??? References: <20020313192405.A1550544@black.vub.ac.be> Message-ID: <3C906C64.F800BA93@hgmp.mrc.ac.uk> You need Whitehead primer3 version 3.0.9, not 3.0.6 >From the eprimer3 documentation: The Whitehead Institute program that is run by this program is available from: http://www-genome.wi.mit.edu/genome_software/other/primer3.html (Then see the link 'Get release 0.9') The version that is run by this program is 3.0.9 currently available from: http://www-genome.wi.mit.edu/ftp/distribution/software/primer3_0_9_test.tar.gz Gary Guy Bottu wrote: > > from : BEN > > Dear developers, > > A question : I have installed EMBOSS 2.3.1 and Primer 3.0.6. When I run > the program eprimer3 I get an error message : > > EMBOSS An error in eprimer3.c at line 316: > The program 'primer3_core' must be on the path. > It is part of the 'primer3' package, > available from the Whitehead Institute. > See: http://www-genome.wi.mit.edu/ > > The package primer however does not contain an executable primer3_core. > I installed on the public path a logical link from primer3_core to the > Primer executable primer3, but this time I get a Segmentation fault when > I try to run eprimer3. Do I miss something ? > > Sincerely, > Guy Bottu -- Gary Williams Tel: +44 1223 494522 Fax: +44 1223 494512 mailto:G.Williams at hgmp.mrc.ac.uk http://www.hgmp.mrc.ac.uk/ Bioinformatics,MRC HGMP Resource Centre,Hinxton,Cambridge, CB10 1SB,UK From peter.rice at uk.lionbioscience.com Thu Mar 14 05:45:26 2002 From: peter.rice at uk.lionbioscience.com (Peter Rice) Date: Thu, 14 Mar 2002 10:45:26 +0000 Subject: primer3 and eprimer3 References: <20020313192405.A1550544@black.vub.ac.be> <3C906750.C9C03BDC@clondiag.com> Message-ID: <3C907F46.D3A8787@uk.lionbioscience.com> Peter Slickers wrote: > > After installing EMBOSS-2.3.1 I found the > applications 'primer3' and 'eprimer3'. > 'primer3' seems to be new with respect to > my previous installation. > > Now I'm wondering what is the difference > between these two programs. > > Their descriptions in 'doc/programs/html' > are nearly identical, only the names > 'primer3' and 'eprimer3' are interchanged. primer3 was the old name. eprimer3 is the new name, to avoid a possible clash with sites that install primer3_core as "primer3". eprimer3 is a front-end to primer 3.0.9 and replaces the old "prima" program from early EMBOSS releases. There is a small problem with the documentation files primer3.html and primer3.txt which are still being installed. This will be corrected in a future release. -- ------------------------------------------------ Peter Rice, LION Bioscience Ltd, Cambridge, UK peter.rice at uk.lionbioscience.com +44 1223 224723 From ztu at msi.umn.edu Thu Mar 14 08:50:52 2002 From: ztu at msi.umn.edu (Zheng Jin Tu) Date: Thu, 14 Mar 2002 07:50:52 -0600 (CST) Subject: Compare EMBOSS vs GCG In-Reply-To: Message-ID: Is there any web site or article discuss about difference or strong/short pointscomparision between EMBOSS vs GCG? I know EMBOSS is free while GCG is commerical product of Accelrys Inc. Any information are really appreciated. Thanks, Tu /****************************************/ /* Zheng Jin Tu */ /* SuperComputing Institute */ /* University of Minnesota */ /* Minneapolis, MN 55455 */ /* ztu at msi.umn.edu */ /* Tel: 612-624-9504 */ /****************************************/ From w2hgcg at netscape.net Thu Mar 14 19:00:45 2002 From: w2hgcg at netscape.net (w2hgcg at netscape.net) Date: Thu, 14 Mar 2002 19:00:45 -0500 Subject: databases Message-ID: <506F2FC2.44557EBB.000665E2@netscape.net> I am trying to learn how to set up emboss on my pc,I am running linux suse 7.3, and have some space on my HD, I would like to know from where can I download a little database (no matter what this DB be about) so I can use it to learn to implement the emboss pack, I do not really care about what the DB be about because I only want it for learning how to set the emboss up, and see it runing on my pc, just one little thing I would need a not so big DB, let say for example some between 5 to 10 megs, or something like so, well thanks a lot in advance. bye :-) -- __________________________________________________________________ Your favorite stores, helpful shopping tools and great gift ideas. Experience the convenience of buying online with Shop at Netscape! http://shopnow.netscape.com/ Get your own FREE, personal Netscape Mail account today at http://webmail.netscape.com/ From haruna at sgi.com Fri Mar 15 00:12:52 2002 From: haruna at sgi.com (Haruna Cofer) Date: Fri, 15 Mar 2002 00:12:52 -0500 Subject: EMBOSS/Jemboss 2.3.1 on SGI Message-ID: <3C9182D4.F70552BF@sgi.com> Hello there -- I have updated my porting notes for both EMBOSS and Jemboss 2.3.1 on SGI systems, and they are available from here: http://www.sgi.com/solutions/sciences/chembio/resources/emboss/ Many thanks to Tim Carver for helping me get Jemboss up and running, and many thanks to Alan Bleasby, Peter Tribble, Guido Steiner, and several others for helping me refine my porting notes. Please do let me know if you have any questions or problems building EMBOSS/Jemboss on SGI. Thanks! -- Haruna :) -- Haruna N. Cofer SGI ChemPharm Applications From heme at postmark.net Fri Mar 15 04:08:53 2002 From: heme at postmark.net (Per Johansson) Date: Fri, 15 Mar 2002 09:08:53 +0000 Subject: Compare EMBOSS vs GCG Message-ID: <20020315090853.13997.qmail@venus.postmark.net> Not discussion but a comparison table: http://www.no.embnet.org/Programs/SAL/EMBOSS/fromGCG.php3 This i GCG centered, but EMBOSS also supply many functions NOT available in GCG, and EMBOSS is ALIVE and new algorithms are included. Zheng Jin Tu wrote: > Is there any web site or article discuss about difference or > strong/short pointscomparision between EMBOSS vs GCG? I know > EMBOSS is free while GCG is commerical product of Accelrys Inc. > > Any information are really appreciated. > > Thanks, > > Tu > > /****************************************/ > /* Zheng Jin Tu */ > /* SuperComputing Institute */ > /* University of Minnesota */ > /* Minneapolis, MN 55455 */ > /* ztu at msi.umn.edu */ > /* Tel: 612-624-9504 */ > /****************************************/ > From peter.rice at uk.lionbioscience.com Fri Mar 15 04:36:13 2002 From: peter.rice at uk.lionbioscience.com (Peter Rice) Date: Fri, 15 Mar 2002 09:36:13 +0000 Subject: databases References: <506F2FC2.44557EBB.000665E2@netscape.net> Message-ID: <3C91C08D.F165FF44@uk.lionbioscience.com> w2hgcg at netscape.net wrote: > > I am trying to learn how to set up emboss on my pc, >I am running linux suse 7.3, and have some space on my HD, > I would like to know from where can I download a little database > (no matter what this DB be about) so I can use it to learn to > implement the emboss pack, I do not really care about what the > DB be about because I only want it for learning how to set the > emboss up, and see it runing on my pc, just one little thing I > would need a not so big DB, let say for example some between > 5 to 10 megs, or something like so, well thanks a lot in advance. There are small databases included in EMBOSS in the test directory after you unpack the release. The EMBOSS developers use them to test database indexing and sequence reading. See directories: test/data (emrod (DNA) and swnew (protein) are in blast format) test/embl (*.dat for EMBL format, *.ref and *.seq for gcg format) test/pir (*.ref and *.seq for nbrf format) test/swiss (*.dat for swissprot format, 1 file) test/swnew (*.dat for swissprot format, 3 files) test/wormpep (wormpep is in fasta and blast format) If you use the emboss/emboss.default.template file to create your own emboss.default file, change the definition of emboss_tempdata at the top to point to your test directory and you can use the test databases as "tembl", "tsw" and so on. The databases contain the sequences in the program examples (see the web pages, or run the "tfm" program to see the documentation). You can also reindex these files yourself to test the dbi* programs and to test writing your own DB definitions for emboss.default. regards, Peter -- ------------------------------------------------ Peter Rice, LION Bioscience Ltd, Cambridge, UK peter.rice at uk.lionbioscience.com +44 1223 224723 From w2hgcg at netscape.net Sat Mar 16 14:22:09 2002 From: w2hgcg at netscape.net (w2hgcg at netscape.net) Date: Sat, 16 Mar 2002 14:22:09 -0500 Subject: emboss/newuser Message-ID: <77CCD894.6A7B0C25.000665E2@netscape.net> ok, so I downloaded the pack, I gunziped it, then tar -xvf (following the instructions) I installed it on /usr/local/httpd/htdocs/emboss I did not change any default value during installation, I followed the instrucions and my compilation was successful, then I got the the part where I was suppouse to start with the postcompilation setup, I am unsing linux suse 7.3, I checked the etc dir and checked the files bash.bashrc and profile, well on profile I found the paths values, and the I tryed to add the path stated on the manual page 13, point 2.3.4 but I do not see any lib directory not at /usr/local/emboss (where acording to the manual there should be) nor at the place where I unpacked the emboss and runned ./configure and then make, /usr/local/httpd/htdocs/emboss the thing is that anyway I tested the emboss with wossname /auto|more and it successed, runned ok, and when I type wossname and as keyword give it protein it gives me a list of programs with a short description .. so... did I do something wrong? is my emboss running now? thanks a lot in advance, sorry to be asking so many things but ... -- __________________________________________________________________ Your favorite stores, helpful shopping tools and great gift ideas. Experience the convenience of buying online with Shop at Netscape! http://shopnow.netscape.com/ Get your own FREE, personal Netscape Mail account today at http://webmail.netscape.com/ From battaile at post.its.mcw.edu Sat Mar 16 14:49:58 2002 From: battaile at post.its.mcw.edu (battaile at post.its.mcw.edu) Date: Sat, 16 Mar 2002 13:49:58 -0600 (CST) Subject: topo error message Message-ID: <1794.141.106.40.116.1016308198.squirrel@post.its.mcw.edu> Hi, I am trying to run topo and get the following error message while it is making the plot: topo: relocation error: /usr/local/lib/libajaxg.so.0: undefined symbol: c_plfileinfo It won't draw an X-window plot (it dies part way through), and when it makes a postscript file many of the residues overlap and it generally looks mangled. FWIW, I am running Red Hat 7.2. Any suggestions would be appreciated. Thanks, Kevin From inagy at abc.hu Sun Mar 17 02:57:37 2002 From: inagy at abc.hu (inagy at abc.hu) Date: Sun, 17 Mar 2002 08:57:37 +0100 (CET) Subject: primer3_core ??? In-Reply-To: <3C906C64.F800BA93@hgmp.mrc.ac.uk> Message-ID: The executable is called "primer3" in Primer 3.0.6 and "primer3_core" in Primer 3.0.9. If you rename "primer3" to "primer3_core" (or make a symbolic link), you can use Primer 3.0.6 es well. Istvan On 14-Mar-2002 Gary Williams, Tel 01223 494522 wrote: > > You need Whitehead primer3 version 3.0.9, not 3.0.6 > >>From the eprimer3 documentation: > > The Whitehead Institute program that is run by this program is available > from: > http://www-genome.wi.mit.edu/genome_software/other/primer3.html > (Then see the link 'Get release 0.9') > > The version that is run by this program is 3.0.9 currently available > from: > http://www-genome.wi.mit.edu/ftp/distribution/software/primer3_0_9_test.tar.gz > > Gary > > Guy Bottu wrote: >> >> from : BEN >> >> Dear developers, >> >> A question : I have installed EMBOSS 2.3.1 and Primer 3.0.6. When I run >> the program eprimer3 I get an error message : >> >> EMBOSS An error in eprimer3.c at line 316: >> The program 'primer3_core' must be on the path. >> It is part of the 'primer3' package, >> available from the Whitehead Institute. >> See: http://www-genome.wi.mit.edu/ >> >> The package primer however does not contain an executable primer3_core. >> I installed on the public path a logical link from primer3_core to the >> Primer executable primer3, but this time I get a Segmentation fault when >> I try to run eprimer3. Do I miss something ? >> >> Sincerely, >> Guy Bottu > > -- > Gary Williams Tel: +44 1223 494522 Fax: +44 1223 494512 > mailto:G.Williams at hgmp.mrc.ac.uk http://www.hgmp.mrc.ac.uk/ > Bioinformatics,MRC HGMP Resource Centre,Hinxton,Cambridge, CB10 1SB,UK From gbottu at ben.vub.ac.be Mon Mar 18 04:02:04 2002 From: gbottu at ben.vub.ac.be (Guy Bottu) Date: Mon, 18 Mar 2002 10:02:04 +0100 (CET) Subject: primer3_core ??? Message-ID: <200203180902.KAA0001244123@ben.vub.ac.be> from : BEN > From inagy at abc.hu Mon Mar 18 08:51:16 2002 > > The executable is called "primer3" in Primer 3.0.6 and "primer3_core" in Primer > 3.0.9. If you rename "primer3" to "primer3_core" (or make a symbolic link), you > can use Primer 3.0.6 es well. > > Istvan Well, I had already tried that and got a segmentation fault. But it is maybe operating system depemdant. I have a CompaqTru64. I finally installed Primer 3.0.9 and this does work fine. Guy Bottu From sgmd at genetik.fu-berlin.de Mon Mar 18 10:02:21 2002 From: sgmd at genetik.fu-berlin.de (Thomas Siegmund) Date: Mon, 18 Mar 2002 16:02:21 +0100 Subject: EMBOSS.kaptn - X11/KDE GUI for EMBOSS finished Message-ID: <200203181602.21544.sgmd@genetik.fu-berlin.de> Dear list, I have completed my graphical user interface for EMBOSS. It now supports the complete set of command line options of 160 applications of EMBOSS 2.3. You will find a compressed tar archive for download, additional information, and a few screenshots at http://userpage.fu-berlin.de/~sgmd . Please check it out. EMBOSS.kaptn needs - kdelibs 2.0 - 2.2.2 - kaptain 0.6 - nedit 5.0 - 5.2 Questions, comments and suggestions are always welcome. Best regards, Thomas -- Thomas Siegmund Freie Universit?t Berlin Institut f?r Genetik Arnimallee 7 14195 Berlin Germany http://userpage.fu-berlin.de/~sgmd From cquijano at iib.uam.es Fri Mar 22 07:39:13 2002 From: cquijano at iib.uam.es (Carlos Quijano) Date: Fri, 22 Mar 2002 13:39:13 +0100 Subject: Problems displaying graphics whith Emboss+W2H Message-ID: <3C9B25F1.3060505@iib.uam.es> Greetings; I have Emboss + w2h installed and running on a Linux RedHat, but when it has to show graphics (dotplots, etc) it doesn't work. Using the w2h "show as data" option, everything goes rigth. When you expect to see a graphic somewhere, it does not appear. How works the program w2h with the graphics? I mean; Are shown in the window or another window? Where can I found what fails? If there is a way to set debug mode to a higher level than default, how can I do it? A file called "xxxxxxx.hp2png" is saved in my working directory with another called same name different extension "xxxxxxx.outfile" which has 0 size. Nothing more happens. hp2xx-3.20-png is working well (or it seems to) My versions are: w2h 4.0 Emboss 2.0.1 Thak you all. From David.Bauer at SCHERING.DE Tue Mar 26 03:59:15 2002 From: David.Bauer at SCHERING.DE (David.Bauer at SCHERING.DE) Date: Tue, 26 Mar 2002 09:59:15 +0100 Subject: prosite Message-ID: Hi, I compared outputs from ps_scan.pl with that from patmatmotifs. This shows that the emboss prosite applications (prosextract, patmatmotifs) make only use of the PATTERN entries in prosite. There are also MATRIX entries, which are silently ignored, i.e. they are not included in prosite.lines. OK, a matrix is not a line, I know :-) Are there any plans to extend patmatmotifs with another algorithm which would make use of the matrix entries ? Ciao, David. From richard at seqbio.com Tue Mar 26 14:18:40 2002 From: richard at seqbio.com (Richard Cote) Date: Tue, 26 Mar 2002 14:18:40 -0500 Subject: Seqret and GIs Message-ID: <3CA0C990.1020805@seqbio.com> Hello. Is there a way to retrieve entries from genbank flatfiles and blast formatted databases based on the GI using seqret? A typical entry in my emboss.defaults file is DB blastnr [ type: P method: blast format: ncbi dir: /databases/blast/ file: "nr" release: "1" comment: "BLAST nr database" ] If I use seqret blastnr:NP_005047.1 (a typical AC entry), it will return a fasta file without a problem. If I use seqret blastnr:4826968 (the GI corresponding to the same AC as above), it complains that it cannot find the entry... The reason why I need to access records through their GI and not their AC is that the standalone www blast server only returns a GI in the html output and not a AC. Can anyone help? Thank you, Rc -- ========================================================== Richard Cote, M.Sc. richard at seqbio.com Senior Bioinformatician http://www.seqbio.com Sequence Bioinformatics 1-877-SEQUENCE 1410 Stanley St. Suite 704 (tel) 514-842-5356 Montreal, QC H3A 1P8 (fax) 514-842-7230 ========================================================== From peter.rice at uk.lionbioscience.com Wed Mar 27 04:19:41 2002 From: peter.rice at uk.lionbioscience.com (Peter Rice) Date: Wed, 27 Mar 2002 09:19:41 +0000 Subject: Seqret and GIs References: <3CA0C990.1020805@seqbio.com> Message-ID: <3CA18EAD.43F51272@uk.lionbioscience.com> Richard Cote wrote: > Is there a way to retrieve entries from genbank flatfiles and blast > formatted databases based on the GI using seqret? > > If I use seqret blastnr:NP_005047.1 (a typical AC entry), it will return > a fasta file without a problem. If I use seqret blastnr:4826968 (the GI > corresponding to the same AC as above), it complains that it cannot find > the entry... > > The reason why I need to access records through their GI and not their > AC is that the standalone www blast server only returns a GI in the html > output and not a AC. > > Can anyone help? Well ... You can write a script to query the database by GI (or ID or ACC) using some other NCBI utility, and use that as "methodentry". That will work with the present EMBOSS release. But also ... Coming soon (in EMBOSS 2.4, but some work is needed before we have the index fields for dbiblast indexed databases) is the ability to query by additional fields, including for example "SV" for the sequence version (AA123456.1 for example). It is easy to extend this to include GI (the USA would be expanded to "BLASTNR-GI:4826968"), but this would be limited to databases that include a GI number, for example GenBank but not EMBL. (Aside: Why don't NCBI use the sequence version so entries can be tracked by accession number as well??? AA123456.1 is so much more useful than 1681491). For EMBOSS is is not a problem if only a few databases include a field, because the database definition includes the list of fields that can be queried (you add "fields: sv" to the database definition to query by SeqVersion) so GI can be limited to NCBI format blast databases. The fields added so far are (in addition to ID and ACC already supported) : SV (EMBL/GenBank sequence version) DES (words in description) KEY (complete keywords) ORG (taxonomy levels) These work (because they are part of the query language) through SRS, and for querying simple file input. We are looking at how best to build indices for them with dbiflat, dbifasta, dbiblast and dbigcg. The index file format and the source code to query the indices will be essentially the same as the existing code for accession numbers. Are there other fields that would be useful? regards, Peter Rice -- ------------------------------------------------ Peter Rice, LION Bioscience Ltd, Cambridge, UK peter.rice at uk.lionbioscience.com +44 1223 224723 From francis at cmmt.ubc.ca Wed Mar 27 04:39:12 2002 From: francis at cmmt.ubc.ca (Francis Ouellette) Date: Wed, 27 Mar 2002 01:39:12 -0800 (PST) Subject: Seqret and GIs In-Reply-To: <3CA18EAD.43F51272@uk.lionbioscience.com> Message-ID: > (Aside: Why don't NCBI use the sequence version so entries can be > tracked by accession number as well??? AA123456.1 is so much more > useful than 1681491). Peter, the simple reason for that is historical, and software updating. As you know NCBI was using gi's many years before DDBJ and EMBL saw the wisdom of tracking sequence vbersion numbers -- now that they are all doing it, it does make much more sense to use SV, but historically, nobody wanted to know about gi's -- but that was the backbone (and still is) of all sequence tracking within the NCBI. As far as tools and databases are concerned -- a gi and a SV number are exactly the same -- it's just the human brain which finds the SV more esthetically pleasing :-) cheers, f. (ex-NCBIer) -- | B.F. Francis Ouellette francis at cmmt.ubc.ca | | Director, Bioinformatics Core Facility Tel: (604) 875-3815 | | Centre for Molecular Medicine & Therapeutics Fax: (425) 740-6978 | | Vancouver, BC Canada http://www.cmmt.ubc.ca/ouellette | On Wed, 27 Mar 2002, Peter Rice wrote: > Date: Wed, 27 Mar 2002 09:19:41 +0000 > From: Peter Rice > To: Richard Cote > Cc: emboss at embnet.org > Subject: Re: Seqret and GIs > > > Richard Cote wrote: > > Is there a way to retrieve entries from genbank flatfiles and blast > > formatted databases based on the GI using seqret? > > > > If I use seqret blastnr:NP_005047.1 (a typical AC entry), it will return > > a fasta file without a problem. If I use seqret blastnr:4826968 (the GI > > corresponding to the same AC as above), it complains that it cannot find > > the entry... > > > > The reason why I need to access records through their GI and not their > > AC is that the standalone www blast server only returns a GI in the html > > output and not a AC. > > > > Can anyone help? > > Well ... You can write a script to query the database by GI (or ID or ACC) > using some other NCBI utility, and use that as "methodentry". That will > work with the present EMBOSS release. But also ... > > Coming soon (in EMBOSS 2.4, but some work is needed before we have the > index fields for dbiblast indexed databases) is the ability to query by > additional fields, including for example "SV" for the sequence version > (AA123456.1 for example). > > It is easy to extend this to include GI (the USA would be expanded to > "BLASTNR-GI:4826968"), but this would be limited to databases that include > a GI number, for example GenBank but not EMBL. (Aside: Why don't NCBI use > the sequence version so entries can be tracked by accession number as > well??? AA123456.1 is so much more useful than 1681491). > > For EMBOSS is is not a problem if only a few databases include a field, > because the database definition includes the list of fields that can be > queried (you add "fields: sv" to the database definition to query by > SeqVersion) so GI can be limited to NCBI format blast databases. > > The fields added so far are (in addition to ID and ACC already supported) : > > SV (EMBL/GenBank sequence version) > DES (words in description) > KEY (complete keywords) > ORG (taxonomy levels) > > These work (because they are part of the query language) through SRS, and > for querying simple file input. We are looking at how best to build indices > for them with dbiflat, dbifasta, dbiblast and dbigcg. The index file format > and the source code to query the indices will be essentially the same as > the existing code for accession numbers. > > Are there other fields that would be useful? > > regards, > > Peter Rice > > -- | B.F. Francis Ouellette francis at cmmt.ubc.ca | | Director, Bioinformatics Core Facility Tel: (604) 875-3815 | | Centre for Molecular Medicine & Therapeutics Fax: (425) 740-6978 | | Vancouver, BC Canada http://www.cmmt.ubc.ca/ouellette | From peter.rice at uk.lionbioscience.com Wed Mar 27 05:27:18 2002 From: peter.rice at uk.lionbioscience.com (Peter Rice) Date: Wed, 27 Mar 2002 10:27:18 +0000 Subject: Seqret and GIs References: Message-ID: <3CA19E86.CD757D8B@uk.lionbioscience.com> Bonjour Francis!!! (or is that bon nuit, at 2am in Vancouver?) > the simple reason for that is historical, and software updating. As > you know NCBI was using gi's many years before DDBJ and EMBL saw the > wisdom of tracking sequence vbersion numbers -- now that they are all > doing it, it does make much more sense to use SV, but historically, > nobody wanted to know about gi's -- but that was the backbone (and > still is) of all sequence tracking within the NCBI. As far as tools > and databases are concerned -- a gi and a SV number are exactly the > same -- it's just the human brain which finds the SV more esthetically > pleasing :-) Ah yes, I remember the backbone database too. GIs were long before SVs but, I seem to recall, were not so easy to synchronize between GenBank, EMBL and DDBJ and so SVs were invented. I like SVs because it makes it possible to find the current version of any sequence and to guess the SV of all previous versions. Something similar happened with pid/protein_id. EMBOSS will be able to read the GI from a GenBank entry, but it is lost in the EMBL equivalent. At the moment, the development EMBOSS code is writing GenBank VERSION lines without the GI, so it makes sense to include it in the data structure. Do you happen to know if there is a need to include a GI in a GenBank VERSION line, and if so what number should EMBOSS 'invent' (0 would be the obvious choice, although 999999999 would also be possible)? SVs are tricky too. The SRS parser indexes "AA123456.1" as "1" which is not very useful for database searching. EBI have changed their SRS server to index the SV as a complete string, and that is a requirement to use SV in EMBOSS 2.4 (of course, you can point to the EBI's SRS server with the new srswww access method ... oops, another preannouncement :-) Peter -- ------------------------------------------------ Peter Rice, LION Bioscience Ltd, Cambridge, UK peter.rice at uk.lionbioscience.com +44 1223 224723 From francis at cmmt.ubc.ca Thu Mar 28 00:14:03 2002 From: francis at cmmt.ubc.ca (Francis Ouellette) Date: Wed, 27 Mar 2002 21:14:03 -0800 (PST) Subject: Seqret and GIs In-Reply-To: <3CA19E86.CD757D8B@uk.lionbioscience.com> Message-ID: On Wed, 27 Mar 2002, Peter Rice wrote: > Bonjour Francis!!! Bonjour Peter! > I like SVs because it makes it possible to > find the current version of any sequence and to guess the SV of all > previous versions. Be carefull, that may be a false sense of security! In February 1999, everything in DDBJ/EMBL/GenBank got version 1, even if it was the 1st or 10 version for a given sequence. For example, AC000003 shows version 1 (and to show non-partisanship, here it is in EMBL format:) ID HSAC00003 standard; DNA; HUM; 122228 BP. XX AC AC000003; XX SV AC000003.1 XX DT 01-OCT-1996 (Rel. 49, Created) DT 07-MAR-2000 (Rel. 63, Last updated, Version 6) but is really the third sequence version (3rd gi) for that record. See: http://www.ncbi.nlm.nih.gov:80/entrez/sutils/girevhist.cgi?val=AC000003 (and of course, the Version on the DT line has nothing to do with the sequence version (SV or or VERSION lines -- that would be too simple :-). But you are right, if after Feb 1999 I would have updated the sequence of the AC000003, then that new one would be version 2 (AC000003.2) and it is a *lot* easier for a human to track sequence version changes when you see the incremental increase -- but (my point here) is that just because you are looking at VS X00001.1 it doesn't mean you have the first version the databases (DDBJ/EMBL/GenBank) have ever seen. cheers from the west coast, f. -- | B.F. Francis Ouellette francis at cmmt.ubc.ca | | Director, Bioinformatics Core Facility Tel: (604) 875-3815 | | Centre for Molecular Medicine & Therapeutics Fax: (425) 740-6978 | | Vancouver, BC Canada http://www.cmmt.ubc.ca/ouellette | From magellanstocks at excite.com Fri Mar 29 22:32:40 2002 From: magellanstocks at excite.com (magellanstocks at excite.com) Date: Fri, 29 Mar 2002 16:32:40 -1100 Subject: Public shell available for reverse merger Message-ID: <001d16a77d7b$2422d7b1$0db13aa0@qocfli> Public shell available for reverse merger I have a public shell company seeking a reverse merger with a suitable private company. I will deliver control of the public company, provide all legal and accounting services including SEC filings, and a Bulletin Board listing for $150,000. The entire project can be accomplished in four months. I also have a trading shell available at a higher price. Please reply to this email for more information or click on the link below. mailto:magellanstocks at excite.com?subject=INFO If you feel you have received this message in error please reply with "noshell" in the subject line OR mailto:somefun777 at excite.com?subject=NOSHELL Thank you 3787EFcp8-995jrqr6775DZlv0-511LSUA2877HiUD5-027zLnSl48 From mad at biol.unlp.edu.ar Fri Mar 1 07:18:25 2002 From: mad at biol.unlp.edu.ar (Martin Sarachu) Date: Fri, 01 Mar 2002 10:18:25 +0300 Subject: Jemboss Message-ID: <3C7F2B41.DAFA33F8@biol.unlp.edu.ar> now I'm getting this when doing %java $EMBOSS_ROOT/share/EMBOSS/jemboss/org/emboss/jemboss/Jemboss & > Exception in thread "main" java.lang.NoClassDefFoundError: /usr/local/EMBOSS/share/EMBOSS/jemboss/org/emboss/jemboss/Jemboss > > [3]+ Exit 1 the previous problem was of missing files, any idea now? martin -- Martin Sarachu ICQ: 123797358 EMBnet Argentina: http://www.ar.embnet.org From axel.klenk at morphochem.ch Fri Mar 1 13:41:14 2002 From: axel.klenk at morphochem.ch (axel klenk) Date: Fri, 1 Mar 2002 14:41:14 +0100 Subject: db url access via proxy? Message-ID: <01C1C12F.242FCA60.axel.klenk@morphochem.ch> Hi, I apologize if this has been discussed before, but I couldn't find it in the documentation: can I and how can I set up database access method URL to use a proxy with authorization (e.g. wget uses an environment variable: http_proxy="http://user:passwd at proxy/")? Is there something comparable for EMBOSS? Thanks in advance, - axel ---------------------------------------- axel klenk morphochem AG wro-1055 schwarzwaldallee 215 4058 basel tel. ++41-61-6952104 fax ++41-61-6952122 axel.klenk at morphochem.ch http://www.morphochem.ch From mad at biol.unlp.edu.ar Fri Mar 1 09:21:26 2002 From: mad at biol.unlp.edu.ar (Martin Sarachu) Date: Fri, 01 Mar 2002 12:21:26 +0300 Subject: Jemboss (almost there) Message-ID: <3C7F4816.F8F76389@biol.unlp.edu.ar> Thanks Tim for all your help, hope this is the last issue. When starting the client (either form console or web), Jemboss loads the login screen but stops the "progress bar" on the message "EMBOSS applications found" and the programs menu never shows up. martin -- Martin Sarachu ICQ: 123797358 EMBnet Argentina: http://www.ar.embnet.org From saleh at tc.cornell.edu Sun Mar 3 23:03:18 2002 From: saleh at tc.cornell.edu (M. A. Saleh Elmohamed) Date: Sun, 03 Mar 2002 18:03:18 -0500 Subject: questions/comments reg Emboss on ms windows ... Message-ID: <5.1.0.14.2.20020303175020.026e38c8@theory.tc.cornell.edu> Hi there, I'd like to get in touch with anyone succeeded in installing EMBOSS-2.2.0 on an MS-windows env under Cygwin. Furthermore, I also would really like to hear from those who tried and succeeded porting it to MS Visual Studio 6 env. Please feel free to respond so I can send my questions and comments. Thank you. -Saleh From ableasby at hgmp.mrc.ac.uk Tue Mar 5 22:27:32 2002 From: ableasby at hgmp.mrc.ac.uk (ableasby at hgmp.mrc.ac.uk) Date: Tue, 5 Mar 2002 22:27:32 GMT Subject: EMBOSS 2.3.0 released Message-ID: <200203052227.WAA23282@bromine.hgmp.mrc.ac.uk> This version of EMBOSS contains two new programs (whichdb and interface) Problems addressed include wildcard database searches failing under some circumstances. Also, missing files in file-list queries no longer cause termination of the programs. The new program 'jembossctl' should not be run by typical users. It is a slave program for a forthcoming Jemboss server. This will hopefully be announced soon. Alan From battaile at post.its.mcw.edu Tue Mar 5 23:14:05 2002 From: battaile at post.its.mcw.edu (battaile at post.its.mcw.edu) Date: Tue, 5 Mar 2002 17:14:05 -0600 (CST) Subject: mse Message-ID: <6109.141.106.40.27.1015370045.squirrel@post.its.mcw.edu> I am trying to use mse like I would use lineup in gcg. I want to create a manual alignment, that I can reload at later dates to make adjustments/add new sequences/etc... Lineup in gcg allows this by saving the alignment to a file. I have tried this in mse and can't seem to get anything to work. The only thing I can figure is that I could write out each sequence individually to a separate file. Personally, I would rather not have to write out 15 sequences separately every time I end a session. I have tried... write: this works fine, but as I said above, I would rather not have to write out each individual sequence every time I quit. hardcopy: this also seems to work, but I can't read the multisequence alignment back in (mse -msf sequence-file gives a can't read error). exit [filename]: this doesn't work at all. If I am inserting gaps (which is 99% of the job) the sequences aren't recognized as being changed. If I type in, then delete some residues, I get the message 'Sequences modified do you wish to continue exiting [N]'. If I choose the default [N], I get dumped back into the editor. If I choose 'Y', the program exits. Either way, no file gets written. Am I doing something completely backwards? Any suggestions? Thanks, Kevin Battaile From ableasby at hgmp.mrc.ac.uk Fri Mar 8 00:47:13 2002 From: ableasby at hgmp.mrc.ac.uk (ableasby at hgmp.mrc.ac.uk) Date: Fri, 8 Mar 2002 00:47:13 GMT Subject: EMBOSS 2.3.1 released Message-ID: <200203080047.AAA14371@bromine.hgmp.mrc.ac.uk> This is a bugfix release. The ChangeLog appears below. As usual, all errors are added to the quality control suite to ensure they don't recur. Version 2.3.1 est2genome fixed for large alignments (over 40Mbase for est * genomic sequence length) sequence reading for ABI files fixed (and selex files tested) genbank feature input working pepinfo PNG output larger to make the text readable (only affects PNG output) empty sequence file input fails gracefully empty sequence input fails gracefully (and only needs one ^D from stdin) Alan From mathog at mendel.bio.caltech.edu Fri Mar 8 16:12:35 2002 From: mathog at mendel.bio.caltech.edu (David Mathog) Date: Fri, 08 Mar 2002 08:12:35 -0800 Subject: transeq/fuzzpro on large sequences Message-ID: One user here tried to do the following (switches omitted for clarity): gunzip chr1.gz | transeq | fuzzpro where chr1 is the Ensembl golden path for Human chromosome 1. This does not work well because transeq tries to accept the entire input sequence before doing its translations. Since chr1 is very large transeq grows to an unacceptable size before emitting anything. In this case I worked around it by using my own program fasttrans ftp://saf.bio.caltech.edu/pub/software/molbio/fasttrans.c instead of transeq. fasttrans breaks large input sequences at 1 Mb intervals, translates that chunk in the desired frames, and then resumes input, etc. That would be a very useful option to add to transeq since it would let it run in 1 or 2 Mb instead of the 100's of Mb it now requires for large genomic sequences. That said, it might make even more sense in terms of performance, if not in terms of clean functional separation, if fuzzpro could translate for itself. It could then easily emit the DNA position of the match (which has to be calculated from fragment number and offset for fragmented input) And since it makes no sense for fuzzpro patterns to be much larger than a couple of thousand residues from one end to the other, the "bin size" of 1 Mb for fasttrans could be effectively reduced to 10kb or so, which should reduce the size of the various buffers so much that they would all fit inside cache memory, and greatly speed up the performance. Also with regards to fuzzpro the only way that I know of now to show surrounding sequence is to put X characters on both sides of the pattern (or indicate a gap of 100 and then an X). But either way that makes the regexp code run unneeded operations and this sort of logical hack is too complex for the average user. Far better if there were switches something like this: fuzzpro sequence -pattern=whatever -upstream=100 -downstream=200 Regards, David Mathog mathog at caltech.edu Manager, Sequence Analysis Facility, Biology Division, Caltech From ableasby at hgmp.mrc.ac.uk Fri Mar 8 16:22:08 2002 From: ableasby at hgmp.mrc.ac.uk (ableasby at hgmp.mrc.ac.uk) Date: Fri, 8 Mar 2002 16:22:08 GMT Subject: transeq/fuzzpro on large sequences Message-ID: <200203081622.QAA12891@bromine.hgmp.mrc.ac.uk> Thanks for the info/suggestions. Don't forget the program fuzztran which is a translation/fuzzpro in one. Alan From thomas.laurent at uk.lionbioscience.com Fri Mar 8 16:28:04 2002 From: thomas.laurent at uk.lionbioscience.com (Thomas Laurent) Date: Fri, 08 Mar 2002 16:28:04 +0000 Subject: transeq/fuzzpro on large sequences References: Message-ID: <3C88E694.EF432FEC@uk.lionbioscience.com> David Mathog wrote: > That said, it might make even more sense in terms of performance, if not > in terms of > clean functional separation, if fuzzpro could translate for itself. Hi David, I'm far from being an EMBOSS expert, and I perheaps misunderstood this part of your mail, but isn't Fuzztran doing that already ? I mean instead of piping transeq to fuzzpro, fuzztran translate the dna sequence then search for the pattern. It seems doing the same job. But, I perheaps missed something. Cheers, Thomas --------------------- Thomas Laurent LION Bioscience From mathog at mendel.bio.caltech.edu Fri Mar 8 17:41:30 2002 From: mathog at mendel.bio.caltech.edu (David Mathog) Date: Fri, 08 Mar 2002 09:41:30 -0800 Subject: transeq/fuzzpro on large sequences Message-ID: > Don't forget the > program fuzztran which is a translation/fuzzpro in one. Unfortunately fuzztran acts exactly like transeq+fuzzpro on large input sequences, growing very, very large before doing anything. David Mathog mathog at caltech.edu Manager, Sequence Analysis Facility, Biology Division, Caltech From duhaimj at ircm.qc.ca Mon Mar 11 17:41:43 2002 From: duhaimj at ircm.qc.ca (Johanne Duhaime) Date: Mon, 11 Mar 2002 12:41:43 -0500 Subject: Script for incremental update of databases Message-ID: <3C8CEC57.83253FF5@ircm.qc.ca> Hello We will start using Emboss. We want certain databases to reside locally (genbank and swissprot for example). Are they any scripts already available that would update the database each day for new sequences only. Thank you in advance. -- Johanne Duhaime IRCM 110 Ave des Pins O Montreal, Quebec 987-5556 (tel) 987-5644 (fax) Johanne_Duhaime at ircm.qc.ca http://www.ircm.qc.ca From duhaimj at ircm.qc.ca Mon Mar 11 18:14:56 2002 From: duhaimj at ircm.qc.ca (Johanne Duhaime) Date: Mon, 11 Mar 2002 13:14:56 -0500 Subject: Transfac database Message-ID: <3C8CF420.51B42EC2@ircm.qc.ca> Hello I looked for the Transfac database on the web. It seems that it is now "buyable" but it used to be free. Are you buying it to use with tfextract? Or is there any other way to get that database? Thank you in advance -- Johanne Duhaime IRCM 110 Ave des Pins O Montreal, Quebec 987-5556 (tel) 987-5644 (fax) Johanne_Duhaime at ircm.qc.ca http://www.ircm.qc.ca From jison at hgmp.mrc.ac.uk Tue Mar 12 08:40:31 2002 From: jison at hgmp.mrc.ac.uk (Dr J.C. Ison) Date: Tue, 12 Mar 2002 08:40:31 +0000 Subject: Script for incremental update of databases References: <3C8CEC57.83253FF5@ircm.qc.ca> Message-ID: <3C8DBEFF.6878CF91@hgmp.mrc.ac.uk> Johanne - If the database was made up lots of files then Mirror might help: http://www.freecode.com/projects/mirror1/ "Mirror was designed to duplicate a directory hierarchy between two machines. It avoids copying files unnecessarily by comparing the file time-stamps and file sizes before transferring" J. Johanne Duhaime wrote: > Hello > > We will start using Emboss. We want certain databases to reside locally > (genbank and swissprot for example). Are they any scripts already > available that would update the database each day for new sequences > only. > > Thank you in advance. > -- > Johanne Duhaime > IRCM > 110 Ave des Pins O > Montreal, Quebec > 987-5556 (tel) 987-5644 (fax) > Johanne_Duhaime at ircm.qc.ca > http://www.ircm.qc.ca -- Jon C. Ison, PhD Bioinformatics Applications Group UK MRC Human Genome Mapping Project Resource Centre Hinxton, Cambridge, CB10 1SB, UK E-mail : jison at hgmp.mrc.ac.uk Tel : 01223 49-4548 HGMP-RC: http://www.hgmp.mrc.ac.uk/ EMBOSS : http://www.hgmp.mrc.ac.uk/Software/EMBOSS/ CCP11 : http://www.hgmp.mrc.ac.uk/CCP11/ From jrvalverde at cnb.uam.es Tue Mar 12 14:36:01 2002 From: jrvalverde at cnb.uam.es (jrvalverde at cnb.uam.es) Date: Tue, 12 Mar 2002 15:36:01 +0100 (MET) Subject: Script for incremental update of databases In-Reply-To: <3C8DBEFF.6878CF91@hgmp.mrc.ac.uk> Message-ID: <200203121436.g2CEa2R3372244@embnet.cnb.uam.es> "Dr J.C. Ison" wrote: > Johanne - > > If the database was made up lots of files then Mirror > might help: > http://www.freecode.com/projects/mirror1/ > Not really that much simple, see > > We will start using Emboss. We want certain databases to reside locally > > (genbank and swissprot for example). Are they any scripts already > > available that would update the database each day for new sequences ^^^^^^^^^^^^^ > > only. ^^^^^ So the actual answer is that it depends on the bandwidth you have. If you have enough to transfer a full cumulative update by the end of a release period in less than one night, then mirror or wget might be OK. Simply get either "cumulative.dat" or "cum_*.dat". Otherwise the things get complicated. The reason is that, as far as I know, you can't assume the cumulative file only changes by addition (please, correct me if I'm wrong). If it were only appended data every day, then it would be trivial to use wget to append the appended new data to your local copy. But sometimes entries get changed, deleted or merged. There are daily updates you can get, but these have the same problem: if an entry has been modified, deleted, merged... and you simply append a daily update to your local copy, then you'll end up with duplicated entries. The solution: get the daily/weekly update and list files, then use SynCron to merge the new data with the old version you have on your disk. SynCron is available at EBI and fine mirror sites: ftp://ftp.ebi.ac.uk/pub/software/unix/SynCron/ But, of course, it is easier if instead of only downloading the daily changes you got the full cumulative changes files, where you have ALL changes occurred since last release already applied in one (set of) file(s). j From jrvalverde at cnb.uam.es Tue Mar 12 14:45:36 2002 From: jrvalverde at cnb.uam.es (jrvalverde at cnb.uam.es) Date: Tue, 12 Mar 2002 15:45:36 +0100 (MET) Subject: Transfac database In-Reply-To: <3C8CF420.51B42EC2@ircm.qc.ca> Message-ID: <200203121445.g2CEjaH7161488@embnet.cnb.uam.es> Johanne Duhaime wrote: > Hello > > I looked for the Transfac database on the web. It seems that it is now > "buyable" but it used to be free. Are you buying it to use with > tfextract? Or is there any other way to get that database? > > Thank you in advance > > >From TRANSFAC main page: Message-ID: <3C8E1FD8.82F87A97@ircm.qc.ca> Hello People at BIOBASE Biological Databases wrote me the following: A less maintained and data reduced TRANSFAC PUBLIC database system is available(only online) for non-commercial and academic organisations at ---------- www.gene-regulation.com. This service is free of charge. Since I want the database locally this is not a solution. They offer an academic price but still it is around $500. Thank you for your help jrvalverde at cnb.uam.es wrote: > Johanne Duhaime wrote: > > Hello > > > > I looked for the Transfac database on the web. It seems that it is now > > "buyable" but it used to be free. Are you buying it to use with > > tfextract? Or is there any other way to get that database? > > > > Thank you in advance > > > > > > >From TRANSFAC main page: > > > We are an academic, non-profit organization, therefore we do not need > to buy it. > > j > > -- > Jos? R. Valverde > EMBnet/CNB -- Johanne Duhaime IRCM 110 Ave des Pins O Montreal, Quebec 987-5556 (tel) 987-5644 (fax) Johanne_Duhaime at ircm.qc.ca http://www.ircm.qc.ca From David.Bauer at SCHERING.DE Wed Mar 13 09:57:27 2002 From: David.Bauer at SCHERING.DE (David.Bauer at SCHERING.DE) Date: Wed, 13 Mar 2002 10:57:27 +0100 Subject: hmmer threads Message-ID: If I try to compile hmmer with threads on Solaris 5.7 I get the folowing error messages: ehmmsearch.c: In function `worker_thread': ehmmsearch.c:1200: `seqall' undeclared (first use in this function) ehmmsearch.c:1200: (Each undeclared identifier is reported only once ehmmsearch.c:1200: for each function it appears in.) ehmmsearch.c:1201: parse error before `{' ehmmsearch.c:1237: continue statement not within a loop ehmmsearch.c: At top level: ehmmsearch.c:1294: parse error before `&' ehmmsearch.c:1294: conflicting types for `ajStrDel' ../../../ajax/ajstr.h:301: previous declaration of `ajStrDel' ehmmsearch.c:1294: warning: data definition has no type or storage class The hmmer compiles fine if I do not define HMMER_THREADS. Any Ideas? Thanks, David. From gbottu at black.vub.ac.be Wed Mar 13 18:24:05 2002 From: gbottu at black.vub.ac.be (Guy Bottu) Date: Wed, 13 Mar 2002 19:24:05 +0100 Subject: primer3_core ??? Message-ID: <20020313192405.A1550544@black.vub.ac.be> from : BEN Dear developers, A question : I have installed EMBOSS 2.3.1 and Primer 3.0.6. When I run the program eprimer3 I get an error message : EMBOSS An error in eprimer3.c at line 316: The program 'primer3_core' must be on the path. It is part of the 'primer3' package, available from the Whitehead Institute. See: http://www-genome.wi.mit.edu/ The package primer however does not contain an executable primer3_core. I installed on the public path a logical link from primer3_core to the Primer executable primer3, but this time I get a Segmentation fault when I try to run eprimer3. Do I miss something ? Sincerely, Guy Bottu From Jack.Leunissen at cmbi.kun.nl Wed Mar 13 23:53:41 2002 From: Jack.Leunissen at cmbi.kun.nl (Jack Leunissen) Date: Thu, 14 Mar 2002 00:53:41 +0100 Subject: primer3_core ??? In-Reply-To: <20020313192405.A1550544@black.vub.ac.be> Message-ID: Hello Guy, When you build primer3 in the "src" directory, it definitely creates the program as "primer3_core" in that directory. I have installed it locally under the name "primer3" too (via a link), as this is more obvious to commandline users. But the web interface calls it under its original name. Cheers, Jack Jack Leunissen Centre of Molecular and Biomolecular Informatics University of Nijmegen, NL > -----Original Message----- > From: owner-emboss at hgmp.mrc.ac.uk [mailto:owner-emboss at hgmp.mrc.ac.uk]On > Behalf Of Guy Bottu > Sent: Wednesday, 13 March, 2002 19:24 > To: emboss at embnet.org > Subject: primer3_core ??? > > > from : BEN > > Dear developers, > > A question : I have installed EMBOSS 2.3.1 and Primer 3.0.6. When I run > the program eprimer3 I get an error message : > > > EMBOSS An error in eprimer3.c at line 316: > The program 'primer3_core' must be on the path. > It is part of the 'primer3' package, > available from the Whitehead Institute. > See: http://www-genome.wi.mit.edu/ > > The package primer however does not contain an executable primer3_core. > I installed on the public path a logical link from primer3_core to the > Primer executable primer3, but this time I get a Segmentation fault when > I try to run eprimer3. Do I miss something ? > > Sincerely, > Guy Bottu > > From hauckl at mail.science.orst.edu Thu Mar 14 01:27:00 2002 From: hauckl at mail.science.orst.edu (Laura Hauck) Date: Wed, 13 Mar 2002 17:27:00 -0800 (PST) Subject: CAI Tables Message-ID: Greetings; My name is Laura Hauck and I am a pre-doctoral grad student at Oregon State University. I have recently been using your Emboss application to generate CAI values for several genes of interest that emerged from a symbiotic relationship. I find that my values are a bit odd. I have Codon Bias tables in Wisconsin Package format that I shifted the columns around to look like the appropriate format of .cut files. The program seems to accept that. The order of the codons, however, does not match the codon order of the .cut tables that you supply (no, my model organisms are not on the list...). Will this interfere with the analysis? What is a good 'HI' value? I generated a codon bias table with one gene, ran a CAI analysis with that table and that gene and got a value of 0.643. That seemed low, is it? The codons should have matched exactly, I was expecting a value of 1.0. Please let me know how to appropriately format my tables if this sounds like an error result, or let me know what you think may be wrong. Thank You, - Laura Hauck From piet at clondiag.com Thu Mar 14 09:03:12 2002 From: piet at clondiag.com (Peter Slickers) Date: Thu, 14 Mar 2002 10:03:12 +0100 Subject: primer3 and eprimer3 References: <20020313192405.A1550544@black.vub.ac.be> Message-ID: <3C906750.C9C03BDC@clondiag.com> After installing EMBOSS-2.3.1 I found the applications 'primer3' and 'eprimer3'. 'primer3' seems to be new with respect to my previous installation. Now I'm wondering what is the difference between these two programs. Their descriptions in 'doc/programs/html' are nearly identical, only the names 'primer3' and 'eprimer3' are interchanged. Peter ------------------------------------------------------------------- Peter Slickers piet at clondiag.com Clondiag Chip Technologies http://www.clondiag.com/ L?bstedter Str. 105 07749 Jena Germany Fon: 03641/5947-65 Fax: 03641/5947-20 ------------------------------------------------------------------- From gwilliam at hgmp.mrc.ac.uk Thu Mar 14 09:24:52 2002 From: gwilliam at hgmp.mrc.ac.uk (Gary Williams, Tel 01223 494522) Date: Thu, 14 Mar 2002 09:24:52 +0000 Subject: primer3_core ??? References: <20020313192405.A1550544@black.vub.ac.be> Message-ID: <3C906C64.F800BA93@hgmp.mrc.ac.uk> You need Whitehead primer3 version 3.0.9, not 3.0.6 >From the eprimer3 documentation: The Whitehead Institute program that is run by this program is available from: http://www-genome.wi.mit.edu/genome_software/other/primer3.html (Then see the link 'Get release 0.9') The version that is run by this program is 3.0.9 currently available from: http://www-genome.wi.mit.edu/ftp/distribution/software/primer3_0_9_test.tar.gz Gary Guy Bottu wrote: > > from : BEN > > Dear developers, > > A question : I have installed EMBOSS 2.3.1 and Primer 3.0.6. When I run > the program eprimer3 I get an error message : > > EMBOSS An error in eprimer3.c at line 316: > The program 'primer3_core' must be on the path. > It is part of the 'primer3' package, > available from the Whitehead Institute. > See: http://www-genome.wi.mit.edu/ > > The package primer however does not contain an executable primer3_core. > I installed on the public path a logical link from primer3_core to the > Primer executable primer3, but this time I get a Segmentation fault when > I try to run eprimer3. Do I miss something ? > > Sincerely, > Guy Bottu -- Gary Williams Tel: +44 1223 494522 Fax: +44 1223 494512 mailto:G.Williams at hgmp.mrc.ac.uk http://www.hgmp.mrc.ac.uk/ Bioinformatics,MRC HGMP Resource Centre,Hinxton,Cambridge, CB10 1SB,UK From peter.rice at uk.lionbioscience.com Thu Mar 14 10:45:26 2002 From: peter.rice at uk.lionbioscience.com (Peter Rice) Date: Thu, 14 Mar 2002 10:45:26 +0000 Subject: primer3 and eprimer3 References: <20020313192405.A1550544@black.vub.ac.be> <3C906750.C9C03BDC@clondiag.com> Message-ID: <3C907F46.D3A8787@uk.lionbioscience.com> Peter Slickers wrote: > > After installing EMBOSS-2.3.1 I found the > applications 'primer3' and 'eprimer3'. > 'primer3' seems to be new with respect to > my previous installation. > > Now I'm wondering what is the difference > between these two programs. > > Their descriptions in 'doc/programs/html' > are nearly identical, only the names > 'primer3' and 'eprimer3' are interchanged. primer3 was the old name. eprimer3 is the new name, to avoid a possible clash with sites that install primer3_core as "primer3". eprimer3 is a front-end to primer 3.0.9 and replaces the old "prima" program from early EMBOSS releases. There is a small problem with the documentation files primer3.html and primer3.txt which are still being installed. This will be corrected in a future release. -- ------------------------------------------------ Peter Rice, LION Bioscience Ltd, Cambridge, UK peter.rice at uk.lionbioscience.com +44 1223 224723 From ztu at msi.umn.edu Thu Mar 14 13:50:52 2002 From: ztu at msi.umn.edu (Zheng Jin Tu) Date: Thu, 14 Mar 2002 07:50:52 -0600 (CST) Subject: Compare EMBOSS vs GCG In-Reply-To: Message-ID: Is there any web site or article discuss about difference or strong/short pointscomparision between EMBOSS vs GCG? I know EMBOSS is free while GCG is commerical product of Accelrys Inc. Any information are really appreciated. Thanks, Tu /****************************************/ /* Zheng Jin Tu */ /* SuperComputing Institute */ /* University of Minnesota */ /* Minneapolis, MN 55455 */ /* ztu at msi.umn.edu */ /* Tel: 612-624-9504 */ /****************************************/ From w2hgcg at netscape.net Fri Mar 15 00:00:45 2002 From: w2hgcg at netscape.net (w2hgcg at netscape.net) Date: Thu, 14 Mar 2002 19:00:45 -0500 Subject: databases Message-ID: <506F2FC2.44557EBB.000665E2@netscape.net> I am trying to learn how to set up emboss on my pc,I am running linux suse 7.3, and have some space on my HD, I would like to know from where can I download a little database (no matter what this DB be about) so I can use it to learn to implement the emboss pack, I do not really care about what the DB be about because I only want it for learning how to set the emboss up, and see it runing on my pc, just one little thing I would need a not so big DB, let say for example some between 5 to 10 megs, or something like so, well thanks a lot in advance. bye :-) -- __________________________________________________________________ Your favorite stores, helpful shopping tools and great gift ideas. Experience the convenience of buying online with Shop at Netscape! http://shopnow.netscape.com/ Get your own FREE, personal Netscape Mail account today at http://webmail.netscape.com/ From haruna at sgi.com Fri Mar 15 05:12:52 2002 From: haruna at sgi.com (Haruna Cofer) Date: Fri, 15 Mar 2002 00:12:52 -0500 Subject: EMBOSS/Jemboss 2.3.1 on SGI Message-ID: <3C9182D4.F70552BF@sgi.com> Hello there -- I have updated my porting notes for both EMBOSS and Jemboss 2.3.1 on SGI systems, and they are available from here: http://www.sgi.com/solutions/sciences/chembio/resources/emboss/ Many thanks to Tim Carver for helping me get Jemboss up and running, and many thanks to Alan Bleasby, Peter Tribble, Guido Steiner, and several others for helping me refine my porting notes. Please do let me know if you have any questions or problems building EMBOSS/Jemboss on SGI. Thanks! -- Haruna :) -- Haruna N. Cofer SGI ChemPharm Applications From heme at postmark.net Fri Mar 15 09:08:53 2002 From: heme at postmark.net (Per Johansson) Date: Fri, 15 Mar 2002 09:08:53 +0000 Subject: Compare EMBOSS vs GCG Message-ID: <20020315090853.13997.qmail@venus.postmark.net> Not discussion but a comparison table: http://www.no.embnet.org/Programs/SAL/EMBOSS/fromGCG.php3 This i GCG centered, but EMBOSS also supply many functions NOT available in GCG, and EMBOSS is ALIVE and new algorithms are included. Zheng Jin Tu wrote: > Is there any web site or article discuss about difference or > strong/short pointscomparision between EMBOSS vs GCG? I know > EMBOSS is free while GCG is commerical product of Accelrys Inc. > > Any information are really appreciated. > > Thanks, > > Tu > > /****************************************/ > /* Zheng Jin Tu */ > /* SuperComputing Institute */ > /* University of Minnesota */ > /* Minneapolis, MN 55455 */ > /* ztu at msi.umn.edu */ > /* Tel: 612-624-9504 */ > /****************************************/ > From peter.rice at uk.lionbioscience.com Fri Mar 15 09:36:13 2002 From: peter.rice at uk.lionbioscience.com (Peter Rice) Date: Fri, 15 Mar 2002 09:36:13 +0000 Subject: databases References: <506F2FC2.44557EBB.000665E2@netscape.net> Message-ID: <3C91C08D.F165FF44@uk.lionbioscience.com> w2hgcg at netscape.net wrote: > > I am trying to learn how to set up emboss on my pc, >I am running linux suse 7.3, and have some space on my HD, > I would like to know from where can I download a little database > (no matter what this DB be about) so I can use it to learn to > implement the emboss pack, I do not really care about what the > DB be about because I only want it for learning how to set the > emboss up, and see it runing on my pc, just one little thing I > would need a not so big DB, let say for example some between > 5 to 10 megs, or something like so, well thanks a lot in advance. There are small databases included in EMBOSS in the test directory after you unpack the release. The EMBOSS developers use them to test database indexing and sequence reading. See directories: test/data (emrod (DNA) and swnew (protein) are in blast format) test/embl (*.dat for EMBL format, *.ref and *.seq for gcg format) test/pir (*.ref and *.seq for nbrf format) test/swiss (*.dat for swissprot format, 1 file) test/swnew (*.dat for swissprot format, 3 files) test/wormpep (wormpep is in fasta and blast format) If you use the emboss/emboss.default.template file to create your own emboss.default file, change the definition of emboss_tempdata at the top to point to your test directory and you can use the test databases as "tembl", "tsw" and so on. The databases contain the sequences in the program examples (see the web pages, or run the "tfm" program to see the documentation). You can also reindex these files yourself to test the dbi* programs and to test writing your own DB definitions for emboss.default. regards, Peter -- ------------------------------------------------ Peter Rice, LION Bioscience Ltd, Cambridge, UK peter.rice at uk.lionbioscience.com +44 1223 224723 From w2hgcg at netscape.net Sat Mar 16 19:22:09 2002 From: w2hgcg at netscape.net (w2hgcg at netscape.net) Date: Sat, 16 Mar 2002 14:22:09 -0500 Subject: emboss/newuser Message-ID: <77CCD894.6A7B0C25.000665E2@netscape.net> ok, so I downloaded the pack, I gunziped it, then tar -xvf (following the instructions) I installed it on /usr/local/httpd/htdocs/emboss I did not change any default value during installation, I followed the instrucions and my compilation was successful, then I got the the part where I was suppouse to start with the postcompilation setup, I am unsing linux suse 7.3, I checked the etc dir and checked the files bash.bashrc and profile, well on profile I found the paths values, and the I tryed to add the path stated on the manual page 13, point 2.3.4 but I do not see any lib directory not at /usr/local/emboss (where acording to the manual there should be) nor at the place where I unpacked the emboss and runned ./configure and then make, /usr/local/httpd/htdocs/emboss the thing is that anyway I tested the emboss with wossname /auto|more and it successed, runned ok, and when I type wossname and as keyword give it protein it gives me a list of programs with a short description .. so... did I do something wrong? is my emboss running now? thanks a lot in advance, sorry to be asking so many things but ... -- __________________________________________________________________ Your favorite stores, helpful shopping tools and great gift ideas. Experience the convenience of buying online with Shop at Netscape! http://shopnow.netscape.com/ Get your own FREE, personal Netscape Mail account today at http://webmail.netscape.com/ From battaile at post.its.mcw.edu Sat Mar 16 19:49:58 2002 From: battaile at post.its.mcw.edu (battaile at post.its.mcw.edu) Date: Sat, 16 Mar 2002 13:49:58 -0600 (CST) Subject: topo error message Message-ID: <1794.141.106.40.116.1016308198.squirrel@post.its.mcw.edu> Hi, I am trying to run topo and get the following error message while it is making the plot: topo: relocation error: /usr/local/lib/libajaxg.so.0: undefined symbol: c_plfileinfo It won't draw an X-window plot (it dies part way through), and when it makes a postscript file many of the residues overlap and it generally looks mangled. FWIW, I am running Red Hat 7.2. Any suggestions would be appreciated. Thanks, Kevin From inagy at abc.hu Sun Mar 17 07:57:37 2002 From: inagy at abc.hu (inagy at abc.hu) Date: Sun, 17 Mar 2002 08:57:37 +0100 (CET) Subject: primer3_core ??? In-Reply-To: <3C906C64.F800BA93@hgmp.mrc.ac.uk> Message-ID: The executable is called "primer3" in Primer 3.0.6 and "primer3_core" in Primer 3.0.9. If you rename "primer3" to "primer3_core" (or make a symbolic link), you can use Primer 3.0.6 es well. Istvan On 14-Mar-2002 Gary Williams, Tel 01223 494522 wrote: > > You need Whitehead primer3 version 3.0.9, not 3.0.6 > >>From the eprimer3 documentation: > > The Whitehead Institute program that is run by this program is available > from: > http://www-genome.wi.mit.edu/genome_software/other/primer3.html > (Then see the link 'Get release 0.9') > > The version that is run by this program is 3.0.9 currently available > from: > http://www-genome.wi.mit.edu/ftp/distribution/software/primer3_0_9_test.tar.gz > > Gary > > Guy Bottu wrote: >> >> from : BEN >> >> Dear developers, >> >> A question : I have installed EMBOSS 2.3.1 and Primer 3.0.6. When I run >> the program eprimer3 I get an error message : >> >> EMBOSS An error in eprimer3.c at line 316: >> The program 'primer3_core' must be on the path. >> It is part of the 'primer3' package, >> available from the Whitehead Institute. >> See: http://www-genome.wi.mit.edu/ >> >> The package primer however does not contain an executable primer3_core. >> I installed on the public path a logical link from primer3_core to the >> Primer executable primer3, but this time I get a Segmentation fault when >> I try to run eprimer3. Do I miss something ? >> >> Sincerely, >> Guy Bottu > > -- > Gary Williams Tel: +44 1223 494522 Fax: +44 1223 494512 > mailto:G.Williams at hgmp.mrc.ac.uk http://www.hgmp.mrc.ac.uk/ > Bioinformatics,MRC HGMP Resource Centre,Hinxton,Cambridge, CB10 1SB,UK From gbottu at ben.vub.ac.be Mon Mar 18 09:02:04 2002 From: gbottu at ben.vub.ac.be (Guy Bottu) Date: Mon, 18 Mar 2002 10:02:04 +0100 (CET) Subject: primer3_core ??? Message-ID: <200203180902.KAA0001244123@ben.vub.ac.be> from : BEN > From inagy at abc.hu Mon Mar 18 08:51:16 2002 > > The executable is called "primer3" in Primer 3.0.6 and "primer3_core" in Primer > 3.0.9. If you rename "primer3" to "primer3_core" (or make a symbolic link), you > can use Primer 3.0.6 es well. > > Istvan Well, I had already tried that and got a segmentation fault. But it is maybe operating system depemdant. I have a CompaqTru64. I finally installed Primer 3.0.9 and this does work fine. Guy Bottu From sgmd at genetik.fu-berlin.de Mon Mar 18 15:02:21 2002 From: sgmd at genetik.fu-berlin.de (Thomas Siegmund) Date: Mon, 18 Mar 2002 16:02:21 +0100 Subject: EMBOSS.kaptn - X11/KDE GUI for EMBOSS finished Message-ID: <200203181602.21544.sgmd@genetik.fu-berlin.de> Dear list, I have completed my graphical user interface for EMBOSS. It now supports the complete set of command line options of 160 applications of EMBOSS 2.3. You will find a compressed tar archive for download, additional information, and a few screenshots at http://userpage.fu-berlin.de/~sgmd . Please check it out. EMBOSS.kaptn needs - kdelibs 2.0 - 2.2.2 - kaptain 0.6 - nedit 5.0 - 5.2 Questions, comments and suggestions are always welcome. Best regards, Thomas -- Thomas Siegmund Freie Universit?t Berlin Institut f?r Genetik Arnimallee 7 14195 Berlin Germany http://userpage.fu-berlin.de/~sgmd From cquijano at iib.uam.es Fri Mar 22 12:39:13 2002 From: cquijano at iib.uam.es (Carlos Quijano) Date: Fri, 22 Mar 2002 13:39:13 +0100 Subject: Problems displaying graphics whith Emboss+W2H Message-ID: <3C9B25F1.3060505@iib.uam.es> Greetings; I have Emboss + w2h installed and running on a Linux RedHat, but when it has to show graphics (dotplots, etc) it doesn't work. Using the w2h "show as data" option, everything goes rigth. When you expect to see a graphic somewhere, it does not appear. How works the program w2h with the graphics? I mean; Are shown in the window or another window? Where can I found what fails? If there is a way to set debug mode to a higher level than default, how can I do it? A file called "xxxxxxx.hp2png" is saved in my working directory with another called same name different extension "xxxxxxx.outfile" which has 0 size. Nothing more happens. hp2xx-3.20-png is working well (or it seems to) My versions are: w2h 4.0 Emboss 2.0.1 Thak you all. From David.Bauer at SCHERING.DE Tue Mar 26 08:59:15 2002 From: David.Bauer at SCHERING.DE (David.Bauer at SCHERING.DE) Date: Tue, 26 Mar 2002 09:59:15 +0100 Subject: prosite Message-ID: Hi, I compared outputs from ps_scan.pl with that from patmatmotifs. This shows that the emboss prosite applications (prosextract, patmatmotifs) make only use of the PATTERN entries in prosite. There are also MATRIX entries, which are silently ignored, i.e. they are not included in prosite.lines. OK, a matrix is not a line, I know :-) Are there any plans to extend patmatmotifs with another algorithm which would make use of the matrix entries ? Ciao, David. From richard at seqbio.com Tue Mar 26 19:18:40 2002 From: richard at seqbio.com (Richard Cote) Date: Tue, 26 Mar 2002 14:18:40 -0500 Subject: Seqret and GIs Message-ID: <3CA0C990.1020805@seqbio.com> Hello. Is there a way to retrieve entries from genbank flatfiles and blast formatted databases based on the GI using seqret? A typical entry in my emboss.defaults file is DB blastnr [ type: P method: blast format: ncbi dir: /databases/blast/ file: "nr" release: "1" comment: "BLAST nr database" ] If I use seqret blastnr:NP_005047.1 (a typical AC entry), it will return a fasta file without a problem. If I use seqret blastnr:4826968 (the GI corresponding to the same AC as above), it complains that it cannot find the entry... The reason why I need to access records through their GI and not their AC is that the standalone www blast server only returns a GI in the html output and not a AC. Can anyone help? Thank you, Rc -- ========================================================== Richard Cote, M.Sc. richard at seqbio.com Senior Bioinformatician http://www.seqbio.com Sequence Bioinformatics 1-877-SEQUENCE 1410 Stanley St. Suite 704 (tel) 514-842-5356 Montreal, QC H3A 1P8 (fax) 514-842-7230 ========================================================== From peter.rice at uk.lionbioscience.com Wed Mar 27 09:19:41 2002 From: peter.rice at uk.lionbioscience.com (Peter Rice) Date: Wed, 27 Mar 2002 09:19:41 +0000 Subject: Seqret and GIs References: <3CA0C990.1020805@seqbio.com> Message-ID: <3CA18EAD.43F51272@uk.lionbioscience.com> Richard Cote wrote: > Is there a way to retrieve entries from genbank flatfiles and blast > formatted databases based on the GI using seqret? > > If I use seqret blastnr:NP_005047.1 (a typical AC entry), it will return > a fasta file without a problem. If I use seqret blastnr:4826968 (the GI > corresponding to the same AC as above), it complains that it cannot find > the entry... > > The reason why I need to access records through their GI and not their > AC is that the standalone www blast server only returns a GI in the html > output and not a AC. > > Can anyone help? Well ... You can write a script to query the database by GI (or ID or ACC) using some other NCBI utility, and use that as "methodentry". That will work with the present EMBOSS release. But also ... Coming soon (in EMBOSS 2.4, but some work is needed before we have the index fields for dbiblast indexed databases) is the ability to query by additional fields, including for example "SV" for the sequence version (AA123456.1 for example). It is easy to extend this to include GI (the USA would be expanded to "BLASTNR-GI:4826968"), but this would be limited to databases that include a GI number, for example GenBank but not EMBL. (Aside: Why don't NCBI use the sequence version so entries can be tracked by accession number as well??? AA123456.1 is so much more useful than 1681491). For EMBOSS is is not a problem if only a few databases include a field, because the database definition includes the list of fields that can be queried (you add "fields: sv" to the database definition to query by SeqVersion) so GI can be limited to NCBI format blast databases. The fields added so far are (in addition to ID and ACC already supported) : SV (EMBL/GenBank sequence version) DES (words in description) KEY (complete keywords) ORG (taxonomy levels) These work (because they are part of the query language) through SRS, and for querying simple file input. We are looking at how best to build indices for them with dbiflat, dbifasta, dbiblast and dbigcg. The index file format and the source code to query the indices will be essentially the same as the existing code for accession numbers. Are there other fields that would be useful? regards, Peter Rice -- ------------------------------------------------ Peter Rice, LION Bioscience Ltd, Cambridge, UK peter.rice at uk.lionbioscience.com +44 1223 224723 From francis at cmmt.ubc.ca Wed Mar 27 09:39:12 2002 From: francis at cmmt.ubc.ca (Francis Ouellette) Date: Wed, 27 Mar 2002 01:39:12 -0800 (PST) Subject: Seqret and GIs In-Reply-To: <3CA18EAD.43F51272@uk.lionbioscience.com> Message-ID: > (Aside: Why don't NCBI use the sequence version so entries can be > tracked by accession number as well??? AA123456.1 is so much more > useful than 1681491). Peter, the simple reason for that is historical, and software updating. As you know NCBI was using gi's many years before DDBJ and EMBL saw the wisdom of tracking sequence vbersion numbers -- now that they are all doing it, it does make much more sense to use SV, but historically, nobody wanted to know about gi's -- but that was the backbone (and still is) of all sequence tracking within the NCBI. As far as tools and databases are concerned -- a gi and a SV number are exactly the same -- it's just the human brain which finds the SV more esthetically pleasing :-) cheers, f. (ex-NCBIer) -- | B.F. Francis Ouellette francis at cmmt.ubc.ca | | Director, Bioinformatics Core Facility Tel: (604) 875-3815 | | Centre for Molecular Medicine & Therapeutics Fax: (425) 740-6978 | | Vancouver, BC Canada http://www.cmmt.ubc.ca/ouellette | On Wed, 27 Mar 2002, Peter Rice wrote: > Date: Wed, 27 Mar 2002 09:19:41 +0000 > From: Peter Rice > To: Richard Cote > Cc: emboss at embnet.org > Subject: Re: Seqret and GIs > > > Richard Cote wrote: > > Is there a way to retrieve entries from genbank flatfiles and blast > > formatted databases based on the GI using seqret? > > > > If I use seqret blastnr:NP_005047.1 (a typical AC entry), it will return > > a fasta file without a problem. If I use seqret blastnr:4826968 (the GI > > corresponding to the same AC as above), it complains that it cannot find > > the entry... > > > > The reason why I need to access records through their GI and not their > > AC is that the standalone www blast server only returns a GI in the html > > output and not a AC. > > > > Can anyone help? > > Well ... You can write a script to query the database by GI (or ID or ACC) > using some other NCBI utility, and use that as "methodentry". That will > work with the present EMBOSS release. But also ... > > Coming soon (in EMBOSS 2.4, but some work is needed before we have the > index fields for dbiblast indexed databases) is the ability to query by > additional fields, including for example "SV" for the sequence version > (AA123456.1 for example). > > It is easy to extend this to include GI (the USA would be expanded to > "BLASTNR-GI:4826968"), but this would be limited to databases that include > a GI number, for example GenBank but not EMBL. (Aside: Why don't NCBI use > the sequence version so entries can be tracked by accession number as > well??? AA123456.1 is so much more useful than 1681491). > > For EMBOSS is is not a problem if only a few databases include a field, > because the database definition includes the list of fields that can be > queried (you add "fields: sv" to the database definition to query by > SeqVersion) so GI can be limited to NCBI format blast databases. > > The fields added so far are (in addition to ID and ACC already supported) : > > SV (EMBL/GenBank sequence version) > DES (words in description) > KEY (complete keywords) > ORG (taxonomy levels) > > These work (because they are part of the query language) through SRS, and > for querying simple file input. We are looking at how best to build indices > for them with dbiflat, dbifasta, dbiblast and dbigcg. The index file format > and the source code to query the indices will be essentially the same as > the existing code for accession numbers. > > Are there other fields that would be useful? > > regards, > > Peter Rice > > -- | B.F. Francis Ouellette francis at cmmt.ubc.ca | | Director, Bioinformatics Core Facility Tel: (604) 875-3815 | | Centre for Molecular Medicine & Therapeutics Fax: (425) 740-6978 | | Vancouver, BC Canada http://www.cmmt.ubc.ca/ouellette | From peter.rice at uk.lionbioscience.com Wed Mar 27 10:27:18 2002 From: peter.rice at uk.lionbioscience.com (Peter Rice) Date: Wed, 27 Mar 2002 10:27:18 +0000 Subject: Seqret and GIs References: Message-ID: <3CA19E86.CD757D8B@uk.lionbioscience.com> Bonjour Francis!!! (or is that bon nuit, at 2am in Vancouver?) > the simple reason for that is historical, and software updating. As > you know NCBI was using gi's many years before DDBJ and EMBL saw the > wisdom of tracking sequence vbersion numbers -- now that they are all > doing it, it does make much more sense to use SV, but historically, > nobody wanted to know about gi's -- but that was the backbone (and > still is) of all sequence tracking within the NCBI. As far as tools > and databases are concerned -- a gi and a SV number are exactly the > same -- it's just the human brain which finds the SV more esthetically > pleasing :-) Ah yes, I remember the backbone database too. GIs were long before SVs but, I seem to recall, were not so easy to synchronize between GenBank, EMBL and DDBJ and so SVs were invented. I like SVs because it makes it possible to find the current version of any sequence and to guess the SV of all previous versions. Something similar happened with pid/protein_id. EMBOSS will be able to read the GI from a GenBank entry, but it is lost in the EMBL equivalent. At the moment, the development EMBOSS code is writing GenBank VERSION lines without the GI, so it makes sense to include it in the data structure. Do you happen to know if there is a need to include a GI in a GenBank VERSION line, and if so what number should EMBOSS 'invent' (0 would be the obvious choice, although 999999999 would also be possible)? SVs are tricky too. The SRS parser indexes "AA123456.1" as "1" which is not very useful for database searching. EBI have changed their SRS server to index the SV as a complete string, and that is a requirement to use SV in EMBOSS 2.4 (of course, you can point to the EBI's SRS server with the new srswww access method ... oops, another preannouncement :-) Peter -- ------------------------------------------------ Peter Rice, LION Bioscience Ltd, Cambridge, UK peter.rice at uk.lionbioscience.com +44 1223 224723 From francis at cmmt.ubc.ca Thu Mar 28 05:14:03 2002 From: francis at cmmt.ubc.ca (Francis Ouellette) Date: Wed, 27 Mar 2002 21:14:03 -0800 (PST) Subject: Seqret and GIs In-Reply-To: <3CA19E86.CD757D8B@uk.lionbioscience.com> Message-ID: On Wed, 27 Mar 2002, Peter Rice wrote: > Bonjour Francis!!! Bonjour Peter! > I like SVs because it makes it possible to > find the current version of any sequence and to guess the SV of all > previous versions. Be carefull, that may be a false sense of security! In February 1999, everything in DDBJ/EMBL/GenBank got version 1, even if it was the 1st or 10 version for a given sequence. For example, AC000003 shows version 1 (and to show non-partisanship, here it is in EMBL format:) ID HSAC00003 standard; DNA; HUM; 122228 BP. XX AC AC000003; XX SV AC000003.1 XX DT 01-OCT-1996 (Rel. 49, Created) DT 07-MAR-2000 (Rel. 63, Last updated, Version 6) but is really the third sequence version (3rd gi) for that record. See: http://www.ncbi.nlm.nih.gov:80/entrez/sutils/girevhist.cgi?val=AC000003 (and of course, the Version on the DT line has nothing to do with the sequence version (SV or or VERSION lines -- that would be too simple :-). But you are right, if after Feb 1999 I would have updated the sequence of the AC000003, then that new one would be version 2 (AC000003.2) and it is a *lot* easier for a human to track sequence version changes when you see the incremental increase -- but (my point here) is that just because you are looking at VS X00001.1 it doesn't mean you have the first version the databases (DDBJ/EMBL/GenBank) have ever seen. cheers from the west coast, f. -- | B.F. Francis Ouellette francis at cmmt.ubc.ca | | Director, Bioinformatics Core Facility Tel: (604) 875-3815 | | Centre for Molecular Medicine & Therapeutics Fax: (425) 740-6978 | | Vancouver, BC Canada http://www.cmmt.ubc.ca/ouellette | From magellanstocks at excite.com Sat Mar 30 03:32:40 2002 From: magellanstocks at excite.com (magellanstocks at excite.com) Date: Fri, 29 Mar 2002 16:32:40 -1100 Subject: Public shell available for reverse merger Message-ID: <001d16a77d7b$2422d7b1$0db13aa0@qocfli> Public shell available for reverse merger I have a public shell company seeking a reverse merger with a suitable private company. I will deliver control of the public company, provide all legal and accounting services including SEC filings, and a Bulletin Board listing for $150,000. The entire project can be accomplished in four months. I also have a trading shell available at a higher price. 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