From sebastian.bassi at ar.advantaseeds.com Fri Jan 2 09:42:26 2004 From: sebastian.bassi at ar.advantaseeds.com (Bassi, Sebastian) Date: Fri, 2 Jan 2004 15:42:26 +0100 Subject: [EMBOSS] dotmatcher in a script Message-ID: Hello, According to the dotmatcher help, "This program is intended to be used by everyone and everything, from naive users to embedded scripts.". But I found something that annoys my scripts. When I run it I get a prompt for "Display as data" that I don't see a way to get rid of it. What I want is to have a quiet (silence, NO verbose) output. Is there a way to do it without changing the source code? Example: [sbassi at BlastServer html]$ dotmatcher -sequencea at5g32 -sequenceb 230 -graph png Displays a thresholded dotplot of two sequences Display as data [N]: Created dotmatcher.1.png This time sending the output to /dev/null: [sbassi at BlastServer html]$ dotmatcher -sequencea at5g32 -sequenceb 230 -graph png > /dev/null Displays a thresholded dotplot of two sequences Display as data [N]: [sbassi at BlastServer html]$ Sebastian Bassi. Advanta Seeds. Balcarce Research Station. From henrikki.almusa at helsinki.fi Fri Jan 2 10:13:37 2004 From: henrikki.almusa at helsinki.fi (Henrikki Almusa) Date: Fri, 2 Jan 2004 17:13:37 +0200 Subject: [EMBOSS] dotmatcher in a script In-Reply-To: References: Message-ID: <200401021713.37429.henrikki.almusa@helsinki.fi> On Friday 02 January 2004 16:42, Bassi, Sebastian wrote: > Hello, > > According to the dotmatcher help, "This program is intended to be used by > everyone and everything, from naive users to embedded scripts.". But I > found something that annoys my scripts. When I run it I get a prompt for > "Display as data" that I don't see a way to get rid of it. What I want is > to have a quiet (silence, NO verbose) output. Is there a way to do it > without changing the source code? Use option '-auto'. That will cause all prompts to be turned off. Remember to give all needed other options. Eg. $ dotmatcher -asequence hbb_human -bsequence hba_human -auto -- Henrikki Almusa From sebastian.bassi at ar.advantaseeds.com Sat Jan 3 08:12:45 2004 From: sebastian.bassi at ar.advantaseeds.com (Bassi, Sebastian) Date: Sat, 3 Jan 2004 14:12:45 +0100 Subject: [EMBOSS] dotmatcher in a script Message-ID: Hello, Thank you for your help. The -auto is the key. This CL you showed me: your-command-line ... -data yes -outfile dotmatcher.png Does not echo characters on the terminal, thats fine, but the dotmatcher.png file is NOT a .png file, it is a text file with the data needed to generate a graph (because data is set to yes, and data means "text data"). According to TFM: * -outfile outfile Display as data So thank to you and Henrikki Almusa I resolved my problem and learned something about EMBOSS on the way. Feliz a?o nuevo para vos tambien! Sebastian Bassi. Advanta Seeds. Balcarce Research Station. From J.Zuegg at griffith.edu.au Wed Jan 7 20:24:28 2004 From: J.Zuegg at griffith.edu.au (Johannes Zuegg) Date: Thu, 8 Jan 2004 11:24:28 +1000 Subject: [EMBOSS] Compiling problem of Emboss 2.8.0 on SUN Message-ID: Dear folks, I just tried to compile EMBOSS 2.8.0 on our SUN (Sun-Fire-880) using the SUN C and Fortran (Forte 7) compilers and after configuration and compiling of the first program (pdfutils.c) I get : Waiting for pdfutils.o.lock to be removed Waiting for pdfutils.o.lock to be removed .... and nothing happens. On compiling with GCC I have no problem. On compiling the older version (2.7.1) with SUN C (using the same compiler options) I had no problem either. Did anyone come across such problem ? Or does anyone have a suggestion ? Cheers Johannes >make Making all in lib source='pdfutils.c' object='pdfutils.lo' libtool=yes \ depfile='.deps/pdfutils.Plo' tmpdepfile='.deps/pdfutils.TPlo' \ depmode=none /bin/bash ../depcomp \ /bin/bash ../libtool --mode=compile cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"EMBOSS\" -DVERSION=\"2.8.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DHAVE_DIRENT_H=1 -DSTDC_HEADERS=1 -DHAVE_UNISTD_H=1 -DGETPGRP_VOID=1 -DHAVE_STRFTIME=1 -DHAVE_UNISTD_H=1 -DHAVE_FORK=1 -DHAVE_VFORK=1 -DHAVE_WORKING_VFORK=1 -DHAVE_WORKING_FORK=1 -DHAVE_VPRINTF=1 -DHAVE_DOPRNT=1 -DHAVE_MEMMOVE=1 -DHAVE_LIBM=1 -I. -I. -I/usr/openwin/include -I./ -I/usr/include/gd -DAJ_SolarisLF -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBENDIAN -I/usr/java/include/ -DHAVE_JAVA -I/usr/java/include/solaris -DN_SHADOW -fast -xtarget=ultra3 -xarch=v8plusb -xcache=64/32/4:8192/512/2 -O -D__EXTENSIONS__ -D_POSIX_C_SOURCE=199506L -c -o pdfutils.lo `test -f 'pdfutils.c' || echo './'`pdfutils.c Waiting for pdfutils.o.lock to be removed Waiting for pdfutils.o.lock to be removed Waiting for pdfutils.o.lock to be removed Waiting for pdfutils.o.lock to be removed Waiting for pdfutils.o.lock to be removed Waiting for pdfutils.o.lock to be removed Waiting for pdfutils.o.lock to be removed Waiting for pdfutils.o.lock to be removed .... ----------------------------------------------------------------------- Dr. Johannes Zuegg Computational Research Specialist Research Computing Services, INS Nathan Campus, Griffith University 170 Kessels Road Brisbane, QLD 4111, Australia Tel: +61-[0]7-3875 6603 Fax: +61-[0]7-3875 6650 EMail: J.Zuegg at griffith.edu.au ----------------------------------------------------------------------- From ableasby at hgmp.mrc.ac.uk Thu Jan 8 03:02:32 2004 From: ableasby at hgmp.mrc.ac.uk (Alan Bleasby) Date: Thu, 8 Jan 2004 08:02:32 GMT Subject: [EMBOSS] Compiling problem of Emboss 2.8.0 on SUN Message-ID: <200401080802.i0882W2i007271@bromine.hgmp.mrc.ac.uk> That's the first time I've seen that error reported. It is a libtool message and used to imply (with non-gcc compilers) that libtool was on a different filing system than the working directory. Try configuring using --disable-libtool-lock If that doesn't work then get back to me off-list. Alan PS: Don't do parallel builds with locking disabled. From louis at gtptech.com Thu Jan 8 12:20:02 2004 From: louis at gtptech.com (Carole Louis) Date: 08 Jan 2004 18:20:02 +0100 Subject: [EMBOSS] Openn two files Message-ID: <1073582404.28899.13.camel@thym> Hello, I would like to know if it is possible to open and write in two files at the same time. I tried it but it doesn't work. To do it, I added these words in my "acd" file : outfile: outf2 [ parameter: "Y" information: "Nom du fichier de r?sultats finaux" ] and these words in the program : outf2 = ajAcdGetOutfile("outf2"); /* output filename */ It doen't work but I don't understand why. Regards Carole -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.open-bio.org/pipermail/emboss/attachments/20040108/0aadd15d/attachment.html From sbassi at asalup.org Sun Jan 11 21:55:25 2004 From: sbassi at asalup.org (Sebastian Bassi) Date: Sun, 11 Jan 2004 23:55:25 -0300 Subject: [EMBOSS] Bioshell: EMBOSS without installation Message-ID: <40020C9D.4030702@asalup.org> Hello, I've just made a Linux distro called BioShell. It's a distro that works without installing. Just boot your PC with the CD on, and voila!. Linux is working, AND EMBOSS is pre-installed! (among other bioinformatics software like hmmer, BLAST, NCBI toolkit, and so on). It is not online yet, but I'll try to put it ASAP. What I need now is a mirror to host the iso. For now, its a 330Mb iso file. Next version I think will be smaller since this one has a lot of stuff that can be removed (like KDE games). It's is based on SLAX. If someone could help me host the mirror, drop me an email! -- Best regards, //=\ Sebastian Bassi - Diplomado en Ciencia y Tecnologia, UNQ //=\ \=// IT Manager Advanta Seeds - Balcarce Research Center - \=// //=\ Pro secretario ASALUP - www.asalup.org - PGP key available //=\ \=// E-mail: sbassi at genesdigitales.com - ICQ UIN: 3356556 - \=// http://Bioinformatica.info From grsvc at mucc.mahidol.ac.th Mon Jan 12 20:35:04 2004 From: grsvc at mucc.mahidol.ac.th (Suksiri Vichasri Grams) Date: Tue, 13 Jan 2004 08:35:04 +0700 Subject: [EMBOSS] embossRUNNER 1.1.1 Message-ID: embossRUNNER 1.1.1 is an interface for emboss 2.8 on Mac OS X. It is available for download at the MIT Mac Hyperarchive: http://hyperarchive.lcs.mit.edu/cgi-bin/NewSearch?key=embossRUNNER Kindly, Rudi & Suksiri Dr. Suksiri Vichasri Grams Department of Biology Faculty of Science Mahidol University Rama VI Road Bangkok 10400 Thailand From mad at biol.unlp.edu.ar Tue Jan 13 08:31:37 2004 From: mad at biol.unlp.edu.ar (=?ISO-8859-1?Q?Mart=EDn_Sarachu?=) Date: Tue, 13 Jan 2004 10:31:37 -0300 Subject: [EMBOSS] wEMBOSS, a web interface for EMBOSS Message-ID: <4003F339.7060908@biol.unlp.edu.ar> wEMBOSS, a web interface for EMBOSS =================================== Features: * Each user has a separate and private workspace. * Organize your work by creating projects and subprojects. * Results saved for easy recover & review. * Inline help. * Keyword search for programs and documentation. * Administrator can exclude EMBOSS programs from wEMBOSS. You can download wEMBOSS from http://www.ar.embnet.org/programas/wEMBOSS Authors: Marc Colet, Martin Sarachu wEMBOSS is a joint effort between BEN & AR.EMBnet -- Mart?n Sarachu mad at biol.unlp.edu.ar EMBNet Argentina http://www.ar.embnet.org From mad at biol.unlp.edu.ar Tue Jan 13 08:49:38 2004 From: mad at biol.unlp.edu.ar (=?ISO-8859-1?Q?Mart=EDn_Sarachu?=) Date: Tue, 13 Jan 2004 10:49:38 -0300 Subject: [EMBOSS] emboss, a web interface for EMBOSS In-Reply-To: <2F41CC6C9777D311ACBD009027B108EA06E9AEAA@excsrv32.mayo.edu> References: <2F41CC6C9777D311ACBD009027B108EA06E9AEAA@excsrv32.mayo.edu> Message-ID: <4003F772.5000805@biol.unlp.edu.ar> Hi Mat, 1) wEMBOSS is written in Perl while jEMBOSS is in Java. 2) wEMBOSS works from the browser (tested with IE 6 & Netscape 7) while jEMBOSS does not need a browser. 3) jEMBOSS needs extra installation (Jakarta & Java WebStart), nearly everything wEMBOSS needs comes in a regular Linux (except some Perl modules). 4) At this point, wEMBOSS is faster than jEMBOSS, but this is because of actual tecnology. 5) jEMBOSS has (not sure) batch capabilities, wEMBOSS not yet. 6) jEMBOSS has a file browser (for local & server files), wEMBOSS not yet. 7) Both jEMBOSS and wEMBOSS have a private workspace for each user. Hope this helps. > Thanks for what looks like a good effort! Thanks, we're somewhat tired ;) Regards, martin Wiepert, Mathieu wrote: > Hi, > > Thanks for posting this. Do you think it might be useful to post why this is different than JEMBOSS, or perhaps enumerate the differences between the two packages? We are wanting a web interface here, and most people had pointed me to JEMBOSS, but this seems like a new entry to the field? I didn't post this to the whole list, but they might be interested in the reply, but I wanted to leave that up to you. > > Thanks for what looks like a good effort! > > -mat > > > > >>-----Original Message----- >>From: Mart?n Sarachu [mailto:mad at biol.unlp.edu.ar] >>Sent: Tuesday, January 13, 2004 7:32 AM >>To: EMBOSS General >>Subject: [EMBOSS] wEMBOSS, a web interface for EMBOSS >> >> >>wEMBOSS, a web interface for EMBOSS >>=================================== >> >>Features: >> >> * Each user has a separate and private workspace. >> * Organize your work by creating projects and subprojects. >> * Results saved for easy recover & review. >> * Inline help. >> * Keyword search for programs and documentation. >> * Administrator can exclude EMBOSS programs from wEMBOSS. >> >>You can download wEMBOSS from >>http://www.ar.embnet.org/programas/wEMBOSS >> >>Authors: Marc Colet, Martin Sarachu >> >>wEMBOSS is a joint effort between BEN & AR.EMBnet >> >> >>-- >>Mart?n Sarachu >>mad at biol.unlp.edu.ar >>EMBNet Argentina >>http://www.ar.embnet.org >> > > -- Mart?n Sarachu mad at biol.unlp.edu.ar EMBNet Argentina http://www.ar.embnet.org From tcarver at rfcgr.mrc.ac.uk Tue Jan 13 09:27:34 2004 From: tcarver at rfcgr.mrc.ac.uk (Dr T. Carver) Date: Tue, 13 Jan 2004 14:27:34 +0000 (GMT) Subject: [EMBOSS] emboss, a web interface for EMBOSS In-Reply-To: <4003F772.5000805@biol.unlp.edu.ar> Message-ID: Hi Mat, It is possibly worth adding some of the main aspects of the Jemboss GUI: Jemboss : ======== -launched via the web (Java Web Start) or a script -works communicates to EMBOSS via SOAP (client-server) or directly (standalone) -optional user authentication (unix) -presents programs as group listings & as a scroll list, parameters displayed with pop-up help & help links -local and server file management systems -stores client-server results on the server, along with the run information. -provides direct access to the Jemboss Alignment Editor (though this can be run independently of the main Jemboss GUI). -dynamically calculates default parameters based on the users input (as EMBOSS does from the command line). -interactive or batch submission of EMBOSS applications to job queues (NQS, OpenPBS or just the background). -installation script provided to set up client-server or stadalone. This install EMBOSS, Jemboss, axis, & tomcat on all EMBOSS supported platforms. Plus a web-launch installation script For more information on the design have a look at: http://www.ncbi.nlm.nih.gov:80/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=14512356&dopt=Abstract Regards Tim Carver MRC Rosalind Franklin Centre for Genomics Research Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SB, UK Tel: +44 1223 494500 Fax: +44 1223 494512 E-mail: tcarver at rfcgr.mrc.ac.uk Web: http://www.rfcgr.mrc.ac.uk On Tue, 13 Jan 2004, [ISO-8859-1] Mart?n Sarachu wrote: > Hi Mat, > > 1) wEMBOSS is written in Perl while jEMBOSS is in Java. > 2) wEMBOSS works from the browser (tested with IE 6 & Netscape 7) while jEMBOSS > does not need a browser. > 3) jEMBOSS needs extra installation (Jakarta & Java WebStart), nearly everything > wEMBOSS needs comes in a regular Linux (except some Perl modules). > 4) At this point, wEMBOSS is faster than jEMBOSS, but this is because of actual > tecnology. > 5) jEMBOSS has (not sure) batch capabilities, wEMBOSS not yet. > 6) jEMBOSS has a file browser (for local & server files), wEMBOSS not yet. > 7) Both jEMBOSS and wEMBOSS have a private workspace for each user. > > Hope this helps. > > > Thanks for what looks like a good effort! > Thanks, we're somewhat tired ;) > > > Regards, > > martin > > > Wiepert, Mathieu wrote: > > Hi, > > > > Thanks for posting this. Do you think it might be useful to post why this is different than JEMBOSS, or perhaps enumerate the differences between the two packages? We are wanting a web interface here, and most people had pointed me to JEMBOSS, but this seems like a new entry to the field? I didn't post this to the whole list, but they might be interested in the reply, but I wanted to leave that up to you. > > > > Thanks for what looks like a good effort! > > > > -mat > > > > > > > > > >>-----Original Message----- > >>From: Mart?n Sarachu [mailto:mad at biol.unlp.edu.ar] > >>Sent: Tuesday, January 13, 2004 7:32 AM > >>To: EMBOSS General > >>Subject: [EMBOSS] wEMBOSS, a web interface for EMBOSS > >> > >> > >>wEMBOSS, a web interface for EMBOSS > >>=================================== > >> > >>Features: > >> > >> * Each user has a separate and private workspace. > >> * Organize your work by creating projects and subprojects. > >> * Results saved for easy recover & review. > >> * Inline help. > >> * Keyword search for programs and documentation. > >> * Administrator can exclude EMBOSS programs from wEMBOSS. > >> > >>You can download wEMBOSS from > >>http://www.ar.embnet.org/programas/wEMBOSS > >> > >>Authors: Marc Colet, Martin Sarachu > >> > >>wEMBOSS is a joint effort between BEN & AR.EMBnet > >> > >> > >>-- > >>Mart?n Sarachu > >>mad at biol.unlp.edu.ar > >>EMBNet Argentina > >>http://www.ar.embnet.org > >> > > > > > > -- > Mart?n Sarachu > mad at biol.unlp.edu.ar > EMBNet Argentina > http://www.ar.embnet.org > From P.Ernst at dkfz-heidelberg.de Tue Jan 13 12:01:54 2004 From: P.Ernst at dkfz-heidelberg.de (Peter Ernst) Date: Tue, 13 Jan 2004 18:01:54 +0100 (MET) Subject: interfaces to EMBOSS (was: [EMBOSS] emboss, a web interface ..) In-Reply-To: <4003F772.5000805@biol.unlp.edu.ar> Message-ID: > Wiepert, Mathieu wrote: > We are wanting a web interface here, and most people had pointed me > to JEMBOSS, but this seems like a new entry to the field? Check out the following page: http://www.hgmp.mrc.ac.uk/Software/EMBOSS/interfaces.html It contains a comprehensive list of web, GUI and other interfaces to EMBOSS. Kind regards, Peter -- ======================================================================= Peter Ernst Department of Molecular Biophysics - B020 Deutsches Krebsforschungszentrum (German Cancer Research Center) DKFZ Im Neuenheimer Feld 580 / Technologiepark 3 69120 Heidelberg, Germany phone: +49-6221-42-2330 http://genome.dkfz-heidelberg.de/ fax: +49-6221-42-2333 ======================================================================= From ruediger at sanbi.ac.za Thu Jan 15 07:29:39 2004 From: ruediger at sanbi.ac.za (Ruediger Braeuning) Date: Thu, 15 Jan 2004 14:29:39 +0200 (SAST) Subject: [EMBOSS] auth using jemboss In-Reply-To: <402F71E1.60706@inf.ufrgs.br> References: <402F71E1.60706@inf.ufrgs.br> Message-ID: <20040115142705.R87746@fling.sanbi.ac.za> In case you've signed the application: Is your certificate still valid? Ruediger On Sun, 15 Feb 2004, Fernando Machado wrote: > I?m having trouble using jemboss. evrth was fine, but authentication > stopped working. Now I cant authenticate anymore. > do somebody knows what can i do? > > thanks > > Fernando Machado > UFRGS - II - 43424 > > ------------------------------------------------------------------------- Ruediger Braeuning / South African National Bioinformatics Institute (=) University of the Western Cape Ph. +27 21 959 3645 / Private Bag X17 Fax +27 21 959 2512 (=) Bellville, 7535 www.sanbi.ac.za / South Africa From tcarver at rfcgr.mrc.ac.uk Thu Jan 15 08:18:32 2004 From: tcarver at rfcgr.mrc.ac.uk (Dr T. Carver) Date: Thu, 15 Jan 2004 13:18:32 +0000 (GMT) Subject: [EMBOSS] auth using jemboss In-Reply-To: <20040115142705.R87746@fling.sanbi.ac.za> Message-ID: Hi Fernando The default period for the certificates is 90 days. You can on installation (in EMBOSS-2.8.0) define the length of time you want before the certificates expire. Have a look at: http://www.rfcgr.mrc.ac.uk/Software/EMBOSS/Jemboss/install/ssl.html this will show you how to check them and if necessary create new certificates. Regards Tim Carver MRC Rosalind Franklin Centre for Genomics Research Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SB, UK Tel: +44 1223 494500 Fax: +44 1223 494512 E-mail: tcarver at rfcgr.mrc.ac.uk Web: http://www.rfcgr.mrc.ac.uk On Thu, 15 Jan 2004, Ruediger Braeuning wrote: > > In case you've signed the application: > Is your certificate still valid? > > Ruediger > > > On Sun, 15 Feb 2004, Fernando Machado wrote: > > > I?m having trouble using jemboss. evrth was fine, but authentication > > stopped working. Now I cant authenticate anymore. > > do somebody knows what can i do? > > > > thanks > > > > Fernando Machado > > UFRGS - II - 43424 > > > > > > ------------------------------------------------------------------------- > Ruediger Braeuning / South African National Bioinformatics Institute > (=) University of the Western Cape > Ph. +27 21 959 3645 / Private Bag X17 > Fax +27 21 959 2512 (=) Bellville, 7535 > www.sanbi.ac.za / South Africa > From jmuehlis at uni-muenster.de Thu Jan 15 10:51:13 2004 From: jmuehlis at uni-muenster.de (Joerg Muehlisch) Date: Thu, 15 Jan 2004 16:51:13 +0100 Subject: [EMBOSS] debian Message-ID: <4006B6F1.594A2BC4@uni-muenster.de> Hi, did anyone on the list install emboss on debian. I think I get some linker errors: cannot find: ld -lX11 I tried then to configure with the lacking path-information and end up with the next error. Will I have to us a debian package or is there something else to do? On Suse 7.0 I could install it without any problems. Thanks for your help or a hint for another source of information. Please excuse the lack of precise information as I had to do it by heart Jorg -- Dr. Joerg Muehlisch University Children's Hospital Muenster Departement of Pediatric Hematology and Oncology Albert Schweitzer Str.33 48149 Muenster Phone: +49-251/83-52491 Fax +49-251/83-55740 From karl at shadow.dunkklar.org Thu Jan 15 10:33:46 2004 From: karl at shadow.dunkklar.org (PLESSY Charles) Date: Thu, 15 Jan 2004 16:33:46 +0100 Subject: [EMBOSS] debian In-Reply-To: <4006B6F1.594A2BC4@uni-muenster.de> References: <4006B6F1.594A2BC4@uni-muenster.de> Message-ID: <20040115153346.GB21527@shadow.dunkklar.org> On Thu, Jan 15, 2004 at 04:51:13PM +0100, Joerg Muehlisch wrote: > Hi, > > did anyone on the list install emboss on debian. I think I get some > linker errors: > cannot find: ld -lX11 > I tried then to configure with the lacking path-information and end up > with the next error. > > Will I have to us a debian package or is there something else to do? http://debian.bioinformatics.unsw.edu.au/ There are Matt Hope's packages there. -- Charles From jmuehlis at uni-muenster.de Thu Jan 15 11:06:28 2004 From: jmuehlis at uni-muenster.de (Joerg Muehlisch) Date: Thu, 15 Jan 2004 17:06:28 +0100 Subject: [EMBOSS] debian References: <4006B6F1.594A2BC4@uni-muenster.de> <4006B029.5070507@telefax.com.ar> Message-ID: <4006BA84.9BE8114D@uni-muenster.de> Hi Sebastian, I ll try that. Jorg Bassi wrote: > > Joerg Muehlisch wrote: > > > Hi, > > > > did anyone on the list install emboss on debian. I think I get some > > linker errors: > > cannot find: ld -lX11 > > I got the same in Mandrake 9.0, so I installed with "without-X" in the > configure command. > > -- > Best regards, > > //=\ Sebastian Bassi - Diplomado en Ciencia y Tecnologia, UNQ //=\ > \=// IT Manager Advanta Seeds - Balcarce Research Center - \=// > //=\ Pro secretario ASALUP - www.asalup.org - PGP key available //=\ > \=// E-mail: sbassi at genesdigitales.com - ICQ UIN: 3356556 - \=// > > http://Bioinformatica.info -- Dr. Joerg Muehlisch University Children's Hospital Muenster Departement of Pediatric Hematology and Oncology Albert Schweitzer Str.33 48149 Muenster Phone: +49-251/83-52491 Fax +49-251/83-55740 From jmuehlis at uni-muenster.de Thu Jan 15 11:10:12 2004 From: jmuehlis at uni-muenster.de (Joerg Muehlisch) Date: Thu, 15 Jan 2004 17:10:12 +0100 Subject: [EMBOSS] debian References: <4006B6F1.594A2BC4@uni-muenster.de> <20040115153346.GB21527@shadow.dunkklar.org> Message-ID: <4006BB64.E1CCF215@uni-muenster.de> Hello Charles, are these packages the same than the actual emboss packagfe? Jorg PLESSY Charles wrote: > > On Thu, Jan 15, 2004 at 04:51:13PM +0100, Joerg Muehlisch wrote: > > Hi, > > > > did anyone on the list install emboss on debian. I think I get some > > linker errors: > > cannot find: ld -lX11 > > I tried then to configure with the lacking path-information and end up > > with the next error. > > > > Will I have to us a debian package or is there something else to do? > > http://debian.bioinformatics.unsw.edu.au/ > > There are Matt Hope's packages there. > > -- > Charles -- Dr. Joerg Muehlisch University Children's Hospital Muenster Departement of Pediatric Hematology and Oncology Albert Schweitzer Str.33 48149 Muenster Phone: +49-251/83-52491 Fax +49-251/83-55740 From mad at biol.unlp.edu.ar Thu Jan 15 10:58:35 2004 From: mad at biol.unlp.edu.ar (=?ISO-8859-1?Q?Mart=EDn_Sarachu?=) Date: Thu, 15 Jan 2004 12:58:35 -0300 Subject: [EMBOSS] wEMBOSS bugfix release Message-ID: <4006B8AB.8070704@biol.unlp.edu.ar> wEMBOSS-1.0.1 is out. It fixes a bug with creation and edition of files, this also involved problems with sequences lists (nucList & protList). Files were saved with strange characters. Install this new version, and to correct files you edited or created with previous version just select the file from the project file selection box, click on "Edit", then click on "Save as" without modifying the file. This will correct the problems in the file. Regards, Martin Sarachu & Marc Colet -- Mart?n Sarachu mad at biol.unlp.edu.ar EMBNet Argentina http://www.ar.embnet.org From kim at inb.uni-luebeck.de Thu Jan 15 11:16:22 2004 From: kim at inb.uni-luebeck.de (Jan T. Kim) Date: Thu, 15 Jan 2004 17:16:22 +0100 Subject: [EMBOSS] debian In-Reply-To: <4006B6F1.594A2BC4@uni-muenster.de>; from jmuehlis@uni-muenster.de on Thu, Jan 15, 2004 at 04:51:13PM +0100 References: <4006B6F1.594A2BC4@uni-muenster.de> Message-ID: <20040115171622.B8393@pc10.inb.mu-luebeck.de> On Thu, Jan 15, 2004 at 04:51:13PM +0100, Joerg Muehlisch wrote: > did anyone on the list install emboss on debian. Yes, I do this all the time. > I think I get some > linker errors: > cannot find: ld -lX11 > I tried then to configure with the lacking path-information and end up > with the next error. > > Will I have to us a debian package or is there something else to do? > > On Suse 7.0 I could install it without any problems. I guess that you need to install some package(s), probably related to software development. (Note: compiling & installing requires packages for software development, even if you don't develop the stuff yourself.) In particular, do you have the package xlibs-dev installed? If not, install that and try the ./configure ; make ; make install combo again. Good luck. Greetings from Luebeck, Jan -- +- Jan T. Kim -------------------------------------------------------+ | *NEW* email: kim at inb.uni-luebeck.de | | *NEW* WWW: http://www.inb.uni-luebeck.de/staff/kim.html | *-----=< hierarchical systems are for files, not for humans >=-----* From emailfrom1 at yahoo.co.uk Fri Jan 16 19:09:54 2004 From: emailfrom1 at yahoo.co.uk (Email) Date: Fri, 16 Jan 2004 19:09:54 Subject: [EMBOSS] Marketing Message-ID: <20040116180839.3A06A7D8C3@mercury.hgmp.mrc.ac.uk> To my family, friends & business colleagues, If you are looking to send thousands of emails to people either in the UK and abroad, in order to promote your Internet business, don't waste your time searching the net for suitable companies, as many of them are a complete waste of time and money. I have found one that does what it says it does! To find out more, go to: http://uk.geocities.com/emailmrketmd Regards John From hegedus at biomembrane.hu Fri Jan 16 17:57:22 2004 From: hegedus at biomembrane.hu (Tamas Hegedus) Date: Fri, 16 Jan 2004 23:57:22 +0100 (CET) Subject: [EMBOSS] ExternalMethodQuery Message-ID: Hi! I have set up a DB in emboss.default as external, fasta format, accessing a MySQL database with my script. It is working fine if I want to retrieve one sequence (DB:feh_human). If I want to query more sequences ("DB:feh_*"), there is nothing (no sequences, no prompt). Since my program working fine if I run it 'stand alone' (connectorom feh_*; not "DB:feh_*"), I think I miss some important information for usage the methodquery, for writing external application returning with more sequences: eg. what is the separator for EMBOSS between sequences. Thanks for your help and suggetion, Tamas From sdyall at ucla.edu Fri Jan 16 23:39:27 2004 From: sdyall at ucla.edu (Sabrina Dyall) Date: Fri, 16 Jan 2004 20:39:27 -0800 Subject: [EMBOSS] MacOSX Panther Message-ID: <221DE0E5-48A7-11D8-ACDF-000393772F38@ucla.edu> Hi all, Where can one find detailed instructions (aimed at the lay-biochemist) on how to install EMBOSS 2.8.0 on a Mac running Panther, starting from downloading the package, expanding it, and compiling it? Second, how does one update to a new version of EMBOSS? I am currently using embossrunner with 2.7.1 and would like to update to 2.8.0, but have not been very successful. Sabrina From kvddrift at earthlink.net Sat Jan 17 07:52:32 2004 From: kvddrift at earthlink.net (Koen van der Drift) Date: Sat, 17 Jan 2004 07:52:32 -0500 Subject: [EMBOSS] MacOSX Panther In-Reply-To: <221DE0E5-48A7-11D8-ACDF-000393772F38@ucla.edu> References: <221DE0E5-48A7-11D8-ACDF-000393772F38@ucla.edu> Message-ID: <03DD5AB1-48EC-11D8-9077-003065A5FDCC@earthlink.net> On Jan 16, 2004, at 11:39 PM, Sabrina Dyall wrote: > > Where can one find detailed instructions (aimed at the lay-biochemist) > on how to install EMBOSS 2.8.0 on a Mac running Panther, starting from > downloading the package, expanding it, and compiling it? Second, how > does one update to a new version of EMBOSS? I am currently using > embossrunner with 2.7.1 and would like to update to 2.8.0, but have > not been very successful. > Sabrina, You can install emboss 2.8.0 using fink (see http://fink.sf.net). Fink makes it easy to install unix software on Mac OS X and takes care of all steps. Once you have installed fink, you can type 'fink install emboss' in the terminal, and the package (plus all other packages it needs) will be installed. - Koen. From Peter.Robinson at t-online.de Sun Jan 18 12:44:45 2004 From: Peter.Robinson at t-online.de (peter robinson) Date: Sun, 18 Jan 2004 18:44:45 +0100 Subject: [EMBOSS] stretches of nucleotides/aa Message-ID: <200401181844.45928.peter.robinson@t-online.de> Hi all, I am interested in looking for all strecthes of any of the nucleotides longer that a certain minimum (say 10) in a sequence and having the program report back all hits including actual length and location within the sequence. While there are several EMBOSS programs that could be set up to do something like this for each nucleotide at a time (eg fuzznuc), I was wondering if there is any program that could do this for all characters at once, or failing that, if anyone has any suggestions as to which EMBOSS program might be a suitable candidate for modification to this purpose? Thanks Peter From kvddrift at earthlink.net Sat Jan 17 11:17:26 2004 From: kvddrift at earthlink.net (Koen van der Drift) Date: Sat, 17 Jan 2004 11:17:26 -0500 Subject: [EMBOSS] EMBOSS and plplot Message-ID: Hi, Will it be a problem if I install emboss when an existing plplot package is already installed? If yes, is there a way to disable the plplot that comes with emboss from being installed so that emboss will use the already installed plplot? thanks, - Koen. From sylvain.foisy at bioneq.qc.ca Sat Jan 17 12:09:33 2004 From: sylvain.foisy at bioneq.qc.ca (Sylvain Foisy) Date: Sat, 17 Jan 2004 12:09:33 -0500 Subject: [EMBOSS] MacOSX Panther In-Reply-To: <221DE0E5-48A7-11D8-ACDF-000393772F38@ucla.edu> References: <221DE0E5-48A7-11D8-ACDF-000393772F38@ucla.edu> Message-ID: Hi, On 04-01-16, at 23:39, Sabrina Dyall wrote: > Hi all, > > Where can one find detailed instructions (aimed at the lay-biochemist) > on how to install EMBOSS 2.8.0 on a Mac running Panther, starting from > downloading the package, expanding it, and compiling it? Second, how > does one update to a new version of EMBOSS? I am currently using > embossrunner with 2.7.1 and would like to update to 2.8.0, but have > not been very successful. Fink is a way but I prefered to do it as per a regular UNIX installation. OK, here how I did it: - First, you need to install some librairies for JPEG/PNG cration using GD. Use these instructions: http://www.stepwise.com/Articles/Workbench/2001-06-12.01.html (GD 1.8.5) or http://www.paginar.net/matias/articles/gd_x_howto.html (GD 2.0) The second instruction set is not totally ok. I got it to work by following the first one for libjpg/libpng installation and then installing GD 2. - Second, simply d/l emboss archive and run the install-emboss script as per the instructions on the web site. Take note that if you want to install in the default location (/usr/local/emboss), you will need to use sudo or switch to root user. I selected standalone for jemboss. If you have any question/problem, don't hesitate. Cordially Sylvain ======================================= Sylvain Foisy, Ph. D. Project Manager BioneQ - Reseau quebecois de bio-informatique Genome Quebec / Universite de Montreal Montreal, QC email: sylvain.foisy at bioneq.qc.ca ======================================= From ableasby at hgmp.mrc.ac.uk Sat Jan 17 13:24:21 2004 From: ableasby at hgmp.mrc.ac.uk (Alan Bleasby) Date: Sat, 17 Jan 2004 18:24:21 GMT Subject: [EMBOSS] EMBOSS and plplot Message-ID: <200401171824.i0HIOLU7027544@bromine.hgmp.mrc.ac.uk> It shouldn't be a problem if you install emboss in non-system location (e.g. /usr/local/emboss should be safe, /usr/local would be risky) and don't add the library path to any system dynamic loader configuration file. There is no way to disable plplot under the current configuration. HTH Alan From stefanielager at fastmail.ca Mon Jan 19 01:31:16 2004 From: stefanielager at fastmail.ca (Stefanie Lager) Date: Mon, 19 Jan 2004 01:31:16 -0500 (EST) Subject: [EMBOSS] stretches of nucleotides/aa Message-ID: <400B79B4.00004F.75921@ns.interchange.ca> It's a problem that there isn't an EMBOSS program that fully can replace the GCG program FindPatterns. FindPatterns can use a database of patterns to search sequences. It's possible to use the EMBOSS program tfscan, and to make your own database in the same format as tfscan uses. I ended up using the program TACG (http://tacg.sourceforge.net/) since that both can use a database of patterns and report hits in both strands of the sequence (option -S2). Stefanie > Hi all, > > I am interested in looking for all strecthes of any of the > nucleotides longer that a certain minimum (say 10) in a sequence > and having the program report back all hits including actual > length and location within the sequence. > > While there are several EMBOSS programs that could be set up to do > something like this for each nucleotide at a time (eg fuzznuc), I > was wondering if there is any program that could do this for all > characters at once, or failing that, if anyone has any suggestions > as to which EMBOSS program might be a suitable candidate for > modification to this purpose? > > Thanks _________________________________________________________________ http://fastmail.ca/ - Fast Secure Web Email for Canadians From henrikki.almusa at helsinki.fi Mon Jan 19 02:20:53 2004 From: henrikki.almusa at helsinki.fi (Henrikki Almusa) Date: Mon, 19 Jan 2004 09:20:53 +0200 Subject: [EMBOSS] stretches of nucleotides/aa In-Reply-To: <200401181844.45928.peter.robinson@t-online.de> References: <200401181844.45928.peter.robinson@t-online.de> Message-ID: <200401190920.53188.henrikki.almusa@helsinki.fi> On Sunday 18 January 2004 19:44, peter robinson wrote: > Hi all, > > I am interested in looking for all strecthes of any of the nucleotides > longer that a certain minimum (say 10) in a sequence and having the program > report back all hits including actual length and location within the > sequence. If i read that correctly, then dreg can do this. Pattern that should do this is "T{10}|A{10}|C{10}|G{10}" (dreg and preg will transform the sequence and pattern into uppercase so no need to use "[tT]"). Dreg and preg pages in emboss website are quite helpful for further use the programs (got upgraded in 2.8.0). > While there are several EMBOSS programs that could be set up to do > something like this for each nucleotide at a time (eg fuzznuc), I was > wondering if there is any program that could do this for all characters at > once, or failing that, if anyone has any suggestions as to which EMBOSS > program might be a suitable candidate for modification to this purpose? > > Thanks > > Peter Here to help, -- Henrikki Almusa From jmuehlis at uni-muenster.de Mon Jan 19 04:16:06 2004 From: jmuehlis at uni-muenster.de (Joerg Muehlisch) Date: Mon, 19 Jan 2004 10:16:06 +0100 Subject: [EMBOSS] debian References: <4006B6F1.594A2BC4@uni-muenster.de> <20040115171622.B8393@pc10.inb.mu-luebeck.de> Message-ID: <400BA056.D5A182D4@uni-muenster.de> "Jan T. Kim" wrote: Hi Jan, In fact I just had to install the package you recommended to me. So debian standard installation + xlibs-dev makes it possible to install the emboss package. Sorry Charles but i didn t find the time to test the .deb packages from Matt Hope. Thanks for your help Jorg > > I guess that you need to install some package(s), probably related > to software development. (Note: compiling & installing requires packages > for software development, even if you don't develop the stuff yourself.) > > In particular, do you have the package xlibs-dev installed? If not, > install that and try the ./configure ; make ; make install combo again. > > Good luck. > > Greetings from Luebeck, > Jan Dr. Joerg Muehlisch University Children's Hospital Muenster Departement of Pediatric Hematology and Oncology Albert Schweitzer Str.33 48149 Muenster Phone: +49-251/83-52491 Fax +49-251/83-55740 From Caroline.Barretto at rdls.nestle.com Mon Jan 19 06:26:15 2004 From: Caroline.Barretto at rdls.nestle.com (Barretto,Caroline,LAUSANNE,NRC/BAS) Date: Mon, 19 Jan 2004 12:26:15 +0100 Subject: [EMBOSS] problem to retrieve sequences with seqret after indexing the data base Message-ID: Dear all, I have indexed a database with "dbifasta" and modified the ".embossrc" file: When I use the seqret command to retrieve the sequence, here is the error I got: $ seqret Database:NC_005126 Reads and writes (returns) sequences Error: Database Entry 'NC_005126' not found Error: Unable to read sequence 'Database:NC_005126' Died: seqret terminated: Bad value for option [sequence] and no prompt But this sequence is present in the database file... Do you know why I cannot find it ? Thank you very much for your help... Best regards Caroline. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.open-bio.org/pipermail/emboss/attachments/20040119/77bcb4f0/attachment.html From stefanielager at fastmail.ca Tue Jan 20 07:45:40 2004 From: stefanielager at fastmail.ca (Stefanie Lager) Date: Tue, 20 Jan 2004 07:45:40 -0500 (EST) Subject: [EMBOSS] Nexus format Message-ID: <400D22F4.00022B.54281@ns.interchange.ca> When i use seqret and output protein alignments in Nexus format it says "datatype=DNA missing=N" . Is it possible to make it recognice that the sequence is a protein sequence and not a DNA sequence? Stefanie _________________________________________________________________ http://fastmail.ca/ - Fast Secure Web Email for Canadians From J.Zuegg at griffith.edu.au Tue Jan 20 21:27:03 2004 From: J.Zuegg at griffith.edu.au (Johannes Zuegg) Date: Wed, 21 Jan 2004 12:27:03 +1000 Subject: [EMBOSS] JEmboss on AFS Message-ID: Dear folks, Does someone have a patch or solution to make JEmboss able to access a AFS directories ? Or at least know the best place to look at (besides openAFS), to include a corresponding AFS-token code into jembossctl.c Cheers Johannes ----------------------------------------------------------------------- Dr. Johannes Zuegg Computational Research Specialist Research Computing Services, INS Nathan Campus, Griffith University 170 Kessels Road Brisbane, QLD 4111, Australia Tel: +61-[0]7-3875 6603 Fax: +61-[0]7-3875 6650 EMail: J.Zuegg at griffith.edu.au ----------------------------------------------------------------------- From simon.andrews at bbsrc.ac.uk Wed Jan 21 04:13:51 2004 From: simon.andrews at bbsrc.ac.uk (simon andrews (BI)) Date: Wed, 21 Jan 2004 09:13:51 -0000 Subject: [EMBOSS] Making Jemboss available to all Message-ID: <2DC41140A89ED411989D00508BDCD9ED01E28C7E@bi-exsrv1.iapc.bbsrc.ac.uk> I'm trying to install the Jemboss client in such a way that it's accessible to everyone on our site. For other applications I've done this by installing them on a network share which is visible to everyone and then getting them to run them from there. I can't get this to work with Jemboss though. The problem seems to be that I need to refer to the program location using a windows UNC path (\\server\share\Jemboss\run_jemboss.bat), rather than by using a mapped drive (X:\Jemboss\run_jemboss.bat). The latter method works fine, but this isn't an option when I've got to make this accessible to everyone. Using a UNC path seems to mess up the classpath so that Jemboss can't find the modules it needs. Having asked about this in a Java newsgroup it appears there may be an internal java function to locate the initial directory of the java application, rather than the current method of defining a classpath. Is there any way this could be implemented in Jemboss to allow for this kind of installation? The relevant thread can be found here: http://groups.google.com/groups?threadm=bujmqf%24k8t%241%40south.jnrs.ja.net Cheers Simon. -- Simon Andrews PhD Bioinformatics Dept The Babraham Institute simon.andrews at bbsrc.ac.uk +44 (0)1223 496463 From tcarver at rfcgr.mrc.ac.uk Wed Jan 21 09:31:36 2004 From: tcarver at rfcgr.mrc.ac.uk (Dr T. Carver) Date: Wed, 21 Jan 2004 14:31:36 +0000 (GMT) Subject: [EMBOSS] Making Jemboss available to all In-Reply-To: <2DC41140A89ED411989D00508BDCD9ED01E28C7E@bi-exsrv1.iapc.bbsrc.ac.uk> Message-ID: Hi Simon This isn't a problem I have encountered before. It may be useful if you provided the script. An alternative of course is just to set up a web launch page: http://www.rfcgr.mrc.ac.uk/Software/EMBOSS/Jemboss/install/deploy.html Regards Tim Carver MRC Rosalind Franklin Centre for Genomics Research Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SB, UK Tel: +44 1223 494500 Fax: +44 1223 494512 E-mail: tcarver at rfcgr.mrc.ac.uk Web: http://www.rfcgr.mrc.ac.uk On Wed, 21 Jan 2004, simon andrews (BI) wrote: > I'm trying to install the Jemboss client in such a way that it's accessible to everyone on our site. For other applications I've done this by installing them on a network share which is visible to everyone and then getting them to run them from there. I can't get this to work with Jemboss though. > > The problem seems to be that I need to refer to the program location using a windows UNC path (\\server\share\Jemboss\run_jemboss.bat), rather than by using a mapped drive (X:\Jemboss\run_jemboss.bat). The latter method works fine, but this isn't an option when I've got to make this accessible to everyone. Using a UNC path seems to mess up the classpath so that Jemboss can't find the modules it needs. > > Having asked about this in a Java newsgroup it appears there may be an internal java function to locate the initial directory of the java application, rather than the current method of defining a classpath. Is there any way this could be implemented in Jemboss to allow for this kind of installation? The relevant thread can be found here: > > http://groups.google.com/groups?threadm=bujmqf%24k8t%241%40south.jnrs.ja.net > > Cheers > > Simon. > > -- > Simon Andrews PhD > Bioinformatics Dept > The Babraham Institute > > simon.andrews at bbsrc.ac.uk > +44 (0)1223 496463 > From simon.andrews at bbsrc.ac.uk Wed Jan 21 10:01:34 2004 From: simon.andrews at bbsrc.ac.uk (simon andrews (BI)) Date: Wed, 21 Jan 2004 15:01:34 -0000 Subject: [EMBOSS] Making Jemboss available to all Message-ID: <2DC41140A89ED411989D00508BDCD9ED01E28C81@bi-exsrv1.iapc.bbsrc.ac.uk> > -----Original Message----- > From: Dr T. Carver [mailto:tcarver at rfcgr.mrc.ac.uk] > Subject: Re: [EMBOSS] Making Jemboss available to all > Tim - thanks for the reply. > This isn't a problem I have encountered before. > It may be useful if you provided the script. The launch script I'm using is just the standard jemboss.bat launch script which is included in the Jemboss download package. I'm linking to this script using a windows shortcut. The reason this doesn't just work is that when you create the shortcut it asks for a target and a "start in" directory. The target is no problem, but I can't use a UNC path as the directory to start in. This appears to be a limitation of the MS cmd shell: C:\>cd \\server\share '\\server\share' CMD does not support UNC paths as current directories. This then causes the jemboss.bat to fail as it includes the line: start javaw -classpath .;Jemboss.jar;JembossAlignment.jar;etc... Because the Jemboss directory isn't the same as ".", the classpath statement fails and Jemboss with the error "Program could not find the main class. Program will exit" I've tried substituting the . in the classpath for the full UNC path, and whilst this doesn't itself throw an error I still get the same error message as before when I try to run it. From the little information I've found it appears that the JRE itself doesn't allow UNC paths in a classpath statement (I'm not 100% sure about this though). As I said before, if I map \\server\share to X: then I can successfully run Jemboss either from a shortcut directly, or indirectly using X:\Jemboss\ in the classpath. This isn't an option sitewide though as there isn't a drive letter I can guarantee will be free. > An alternative of course is just to set up a web launch page: I've looked at that and that seems to be one way around this. The problem with this is that our site standard image currently doesn't include Java Web Start so I'd have to get that installed first. It would also mean that Jemboss wouldn't appear with all the other applications we've got set up. From emailfrom1 at yahoo.co.uk Wed Jan 21 19:16:07 2004 From: emailfrom1 at yahoo.co.uk (Email) Date: Wed, 21 Jan 2004 19:16:07 Subject: [EMBOSS] Addresses Message-ID: <20040121181527.42ABE7D898@mercury.hgmp.mrc.ac.uk> To my family, friends & business colleagues, If you are looking to send thousands of emails to people either in the UK and abroad, in order to promote your Internet business, don't waste your time searching the net for suitable companies, as many of them are a complete waste of time and money. I have found one that does what it says it does! To find out more, go to: http://uk.geocities.com/emailbusiness1 Regards John From maoj at mail.nih.gov Wed Jan 21 14:50:21 2004 From: maoj at mail.nih.gov (Jean Mao) Date: Wed, 21 Jan 2004 14:50:21 -0500 Subject: [EMBOSS] about trasfac database Message-ID: <11b701c3e057$cdb20b40$494de780@CIT.NIH.GOV> Does anyone know where I can download an older version of transfac db for free? Thanks. Jean From R-6-721447-21420248-2-9873-US2-8552FB77 at xmr3.com Thu Jan 22 00:07:53 2004 From: R-6-721447-21420248-2-9873-US2-8552FB77 at xmr3.com (International Scientific Communications, Inc.) Date: Thu, 22 Jan 2004 00:07:53 -0500 Subject: [EMBOSS] Laboratory Instrumentation News - January 2004 Message-ID: An HTML attachment was scrubbed... URL: http://lists.open-bio.org/pipermail/emboss/attachments/20040122/98f23847/attachment.html From simon.andrews at bbsrc.ac.uk Thu Jan 22 05:01:45 2004 From: simon.andrews at bbsrc.ac.uk (simon andrews (BI)) Date: Thu, 22 Jan 2004 10:01:45 -0000 Subject: [EMBOSS] Solved: Making Jemboss available to all Message-ID: <2DC41140A89ED411989D00508BDCD9ED01E28C86@bi-exsrv1.iapc.bbsrc.ac.uk> Following a series of helpful emails from Tim Carver at RFCGR I've now managed to set up the Jemboss client so that it's accessible to a whole site from a Windows network share. If anyone is interested in doing this in the future I thought I'd summarise how I did it. These instructions detail how you would install Jemboss onto \\server\share First, download the Jemboss client from: ftp://ftp.rfcgr.mrc.ac.uk/pub/EMBOSS/Jemboss/Jemboss-current.zip Create the directory \\server\share\Jemboss and unzip the downloaded file into there. Open \\server\share\Jemboss\jemboss.bat in a text editor You need to edit the line which starts: start javaw -classpath .;Jemboss.jar;JembossAlignment.jar;axis.jar... You need to change the initial . to \\server\share\Jemboss and then prefix each of the xxxx.jar entries with \\server\share\Jemboss\ . The only entry you don't need to prefix is the very last one which defines the first class to launch. You will end up with a very long command which looks something like this: start javaw -classpath \\server\share\Jemboss;\\server\share\Jemboss\Jemboss.jar; ..snip.. \\server\share\Jemboss\grout.jar org.emboss.jemboss.Jemboss You now need to make the directory \\server\share\Jemboss\resources and copy into it an appropriate jemboss.properties file to connect to your Jemboss server. Details of how to construct the jemboss.properties file can be found here: http://www.rfcgr.mrc.ac.uk/Software/EMBOSS/Jemboss/install/properties.html Finally, to run the program easily you can create a shortcut to the jemboss.bat file. It's also a good idea when creating the shortcut to go into its properties and under the Shortcut tab change the Run variable to "Minimised". If you don't do this you get a brief flash of a DOS window when you launch Jemboss, and then a wait until the first jemboss window appears. We found that our users got impatient in this time and clicked the link again. From matovue at hotmail.com Thu Jan 22 06:00:58 2004 From: matovue at hotmail.com (Enock Matovu) Date: Thu, 22 Jan 2004 11:00:58 +0000 Subject: [EMBOSS] Problem with emboss Message-ID: An HTML attachment was scrubbed... URL: http://lists.open-bio.org/pipermail/emboss/attachments/20040122/1b2489f2/attachment.html From idrummon at receptor.mgh.harvard.edu Thu Jan 22 08:11:56 2004 From: idrummon at receptor.mgh.harvard.edu (Iain Drummond) Date: Thu, 22 Jan 2004 08:11:56 -0500 Subject: [EMBOSS] Problem with emboss In-Reply-To: Message-ID: you might need to install the libraries themselves if they are not in /usr/local/lib or something like that. look at the library requirements for emboss: http://www.hgmp.mrc.ac.uk/Software/EMBOSS/Doc/Admin_guide/adminguide/node3.h tml#SECTION00330000000000000000 Also try looking at your login profile and be sure that you have defined the environmental variables that tells emboss where to find the library: i'm using tcsh on mac os x setenv PLPLOT_LIB "/usr/local/lib" its different for other unix shells it is also suggested to set the LD_LIBRARY_PATH environmental variable in your login file. one of these steps might help. good luck -- Iain Drummond, Ph.D. Assistant Professor Department of Medicine, Harvard Medical School and Renal Unit, Massachusetts General Hospital idrummond at partners.org idrummon at receptor.mgh.harvard.edu Lab Home Page: http://danio.mgh.harvard.edu > From: "Enock Matovu" > Date: Thu, 22 Jan 2004 11:00:58 +0000 > To: emboss at embnet.org > Subject: [EMBOSS] Problem with emboss > > we have installed emboss. But when we type in any command such as wossname, he > replies wossname: error while loading shared libraries: libnuclesu.so.0: > cannot > > open shared object file: no such file or directory > > What shall we do to overcome this? We are real amateurs with linux and all > stuff > > Regards > > > Enock Matovu, > Livestock Health Research Institute > P. O. Box 96 Tororo > Uganda > +256 77 550 226 > > > The new MSN 8: smart spam protection and > 2 months FREE* From Sean.Maceachern at dpi.vic.gov.au Fri Jan 23 00:42:12 2004 From: Sean.Maceachern at dpi.vic.gov.au (Sean.Maceachern at dpi.vic.gov.au) Date: Fri, 23 Jan 2004 16:42:12 +1100 Subject: [EMBOSS] Coderet Message-ID: Hello, I am trying to use coderet to extract cds from some genbank flat files. I am running into a problem regarding the desriptor line in the output fasta files. eg) >nm_000367_cds_1 ATGGATGGTACAAGAACTTCACTTGACATTGAAGAGTACTCGGATACTGAGGTACAGAAA AACCAAGTACTAACTCTGGAAGAATGGCAAGACAAGTGGGTGAACGGCAAGACTGCTTTT I was hoping someone would be able to tell me how I can change the descriptor line from the generic output above (nm_000367_cds_1) to include the GI : ID form the flat file? I also think it would be a good idea if the id could be followed by a definition line to make the output more closely resemble the output from NCBI. eg) >gi|4507652 Homo sapiens thiopurine S-methyltransferase (TPMT), mRNA ATGGATGGTACAAGAACTTCACTTGACATTGAAGAGTACTCGGATACTGAGGTACAGAAA AACCAAGTACTAACTCTGGAAGAATGGCAAGACAAGTGGGTGAACGGCAAGACTGCTTTT Is there anyway to currently do this using the existing options? I am mostly interested in changing the output from the (nm _ ID) to the (gi | ID) but I think the deffinition line would also be useful. I'm assuming that it shouldn't be too hard as all of this information exists in the flat file, which looks fairly easy to parse. If there is no way to currently do this I would appreciate it if someone could suggest where and if I could modify the existing script to complete the above. Thanks, Sean MacEachern From henrikki.almusa at helsinki.fi Fri Jan 23 01:36:54 2004 From: henrikki.almusa at helsinki.fi (Henrikki Almusa) Date: Fri, 23 Jan 2004 08:36:54 +0200 Subject: [EMBOSS] Coderet In-Reply-To: References: Message-ID: <200401230836.54223.henrikki.almusa@helsinki.fi> On Friday 23 January 2004 07:42, Sean.Maceachern at dpi.vic.gov.au wrote: > Hello, > > I am trying to use coderet to extract cds from some genbank flat files. I > am running into a problem regarding the desriptor line in the output fasta > files. > > eg) > > >nm_000367_cds_1 > ATGGATGGTACAAGAACTTCACTTGACATTGAAGAGTACTCGGATACTGAGGTACAGAAA > AACCAAGTACTAACTCTGGAAGAATGGCAAGACAAGTGGGTGAACGGCAAGACTGCTTTT > > I was hoping someone would be able to tell me how I can change the > descriptor line from the generic output above (nm_000367_cds_1) to include > the GI : ID form the > flat file? I also think it would be a good idea if the id could be followed > by a definition line to make the output more closely resemble the output > from NCBI. You can change the sequence format with -osformat option (in all emboss programs which outputs sequences). Probably the right format is "ncbi". If it isn't read the page on emboss web site in User Documantation -> Sequence format. That will list all available formats. Here to help, -- Henrikki Almusa From David.Bauer at SCHERING.DE Fri Jan 23 02:16:00 2004 From: David.Bauer at SCHERING.DE (David.Bauer at SCHERING.DE) Date: Fri, 23 Jan 2004 08:16:00 +0100 Subject: [EMBOSS] Coderet Message-ID: Hi, the problem is that -osformat ncbi with coderet creates the NCBI pipe notation but it does not parse the GI number from the CDS feature. I think it's a good idea to transfer more tags from the CDS feature into the ID line of coderet. I'm not sure if /gene, /protein_id and /product are mandatory for CDS. But if they are there it would be nice to transfer them into the description of the extracted cds and/or mRNA sequence. David. Henrikki Almusa An: Sean.Maceachern at dpi.vic.gov.au Gesendet von: Kopie: emboss at embnet.org owner-emboss at hgmp. Thema: Re: [EMBOSS] Coderet mrc.ac.uk 23.01.04 07:36 On Friday 23 January 2004 07:42, Sean.Maceachern at dpi.vic.gov.au wrote: > Hello, > > I am trying to use coderet to extract cds from some genbank flat files. I > am running into a problem regarding the desriptor line in the output fasta > files. > > eg) > > >nm_000367_cds_1 > ATGGATGGTACAAGAACTTCACTTGACATTGAAGAGTACTCGGATACTGAGGTACAGAAA > AACCAAGTACTAACTCTGGAAGAATGGCAAGACAAGTGGGTGAACGGCAAGACTGCTTTT > > I was hoping someone would be able to tell me how I can change the > descriptor line from the generic output above (nm_000367_cds_1) to include > the GI : ID form the > flat file? I also think it would be a good idea if the id could be followed > by a definition line to make the output more closely resemble the output > from NCBI. You can change the sequence format with -osformat option (in all emboss programs which outputs sequences). Probably the right format is "ncbi". If it isn't read the page on emboss web site in User Documantation -> Sequence format. That will list all available formats. Here to help, -- Henrikki Almusa From sinnottj at cs.man.ac.uk Mon Jan 26 10:24:33 2004 From: sinnottj at cs.man.ac.uk (James Sinnott) Date: Mon, 26 Jan 2004 15:24:33 +0000 Subject: [EMBOSS] Problems converting sequences with seqret Message-ID: <200401261524.33620.sinnottj@cs.man.ac.uk> Hi, I'm building an application that should allow the user to work with a set of sequences in an arbitrary format (e.g. FastA) regardless of the formats the sequences may actually be stored in (clustal, nexus, msf, etc.) I need to be able to convert sequences to and back-from the users' desired format behind the scenes, and seqret seems to be the most suitable tool for this. However, I've found a problem in that seqret seems to output some sequence formats that it cannot subsequently re-read! As an example, I converted a set of FastaA files into clustal, phylip, msf, & nexus formats and then tried to re-convert the files back into FastA format. The clustal & phylip files all worked OK, but several of the msf and all of the nexus files were found to be unreadable by seqret when trying to re-convert them. Am I doing anything wrong? Is this a common issue with seqret? Any help would be gratefully accepted! Best regards, James Sinnott. From simon.andrews at bbsrc.ac.uk Mon Jan 26 11:03:44 2004 From: simon.andrews at bbsrc.ac.uk (simon andrews (BI)) Date: Mon, 26 Jan 2004 16:03:44 -0000 Subject: [EMBOSS] Problems converting sequences with seqret Message-ID: <2DC41140A89ED411989D00508BDCD9ED01E28C8D@bi-exsrv1.iapc.bbsrc.ac.uk> > -----Original Message----- > From: James Sinnott [mailto:sinnottj at cs.man.ac.uk] > Sent: 26 January 2004 15:25 > To: emboss at embnet.org > Subject: [EMBOSS] Problems converting sequences with seqret > > > However, I've found a problem in that seqret seems to output > some sequence formats that it cannot subsequently re-read! > > several of the msf and all of the nexus files were found > to be unreadable by seqret when trying to re-convert them. There looks to be a bug in seqret. I can't reproduce this with msf files (may just be the data I was using), but certainly there's something wrong with the nexus parser. If you use the dna.msf file included with EMBOSS as a test case $ uname -sr Linux 2.4.22-1.2149.nptlsmp $ embossversion Writes the current EMBOSS version number 2.8.0 $ seqret /usr/local/share/EMBOSS/test/data/dna.msf nexus::nexus.txt Reads and writes (returns) sequences $ seqret nexus::nexus.txt fasta::stdout Reads and writes (returns) sequences Segmentation fault Running a debug on the second process doesn't show much. The matrix seems to be read OK, but then it segfaults. An strace on the process doesn't show any system calls going awry so I'm not sure what's going wrong. Certainly something to look at... Simon. -- Simon Andrews PhD Bioinformatics Dept The Babraham Institute simon.andrews at bbsrc.ac.uk +44 (0)1223 496463 From Sean.Maceachern at dpi.vic.gov.au Mon Jan 26 20:17:37 2004 From: Sean.Maceachern at dpi.vic.gov.au (Sean.Maceachern at dpi.vic.gov.au) Date: Tue, 27 Jan 2004 12:17:37 +1100 Subject: [EMBOSS] Coderet Message-ID: Thanks for the replies, I have tried a number of the -osformat options before I posted my original request. What I was hoping to find out was how to replicate the NCBI output. The current -osformat ncbi option seems to replicate NCBI's cds output in fasta format only and does not replicate the descriptor line very well. I was thinking that as the file usually comes from an NCBI flat file that it would be good if the output resembled the NCBI output that is provided on the web (cds links and eutils) to allow sequences from both the net and coderet to be combined in the same fasta file. I have not done any programming in c++ so I was hoping that someone might be able how to suggest how I can get the output from coderet to resemble that of NCBI's I think it could be done by parsing the sections in BOLD from the first few lines of the feature table. LOCUS NM_000367 2742 bp mRNA linear PRI 31-OCT-2000 DEFINITION Homo sapiens thiopurine S-methyltransferase (TPMT), mRNA. ACCESSION NM_000367 VERSION NM_000367.1 GI:4507652 KEYWORDS . SOURCE Homo sapiens (human) ie) >gi|4507652 Homo sapiens thiopurine S-methyltransferase (TPMT), mRNA ATGGATGGTACAAGAACTTCACTTGACATTGAAGAGTACTCGGATACTGAGGTACAGAAA AACCAAGTACTAACTCTGGAAGAATGGCAAGACAAGTGGGTGAACGGCAAGACTGCTTTT Does anyone know if this already exists in a coderet option or how I would be able to modfiy this in the original script? Thanks Sean MacEachern David.Bauer at SCHERING.DE on 23/01/2004 06:16:00 PM To: henrikki.almusa at helsinki.fi cc: emboss at embnet.org, Sean.Maceachern at dpi.vic.gov.au Subject: Re: [EMBOSS] Coderet Hi, the problem is that -osformat ncbi with coderet creates the NCBI pipe notation but it does not parse the GI number from the CDS feature. I think it's a good idea to transfer more tags from the CDS feature into the ID line of coderet. I'm not sure if /gene, /protein_id and /product are mandatory for CDS. But if they are there it would be nice to transfer them into the description of the extracted cds and/or mRNA sequence. David. Henrikki Almusa An: Sean.Maceachern at dpi.vic.gov.au Gesendet von: Kopie: emboss at embnet.org owner-emboss at hgmp. Thema: Re: [EMBOSS] Coderet mrc.ac.uk 23.01.04 07:36 On Friday 23 January 2004 07:42, Sean.Maceachern at dpi.vic.gov.au wrote: > Hello, > > I am trying to use coderet to extract cds from some genbank flat files. I > am running into a problem regarding the desriptor line in the output fasta > files. > > eg) > > >nm_000367_cds_1 > ATGGATGGTACAAGAACTTCACTTGACATTGAAGAGTACTCGGATACTGAGGTACAGAAA > AACCAAGTACTAACTCTGGAAGAATGGCAAGACAAGTGGGTGAACGGCAAGACTGCTTTT > > I was hoping someone would be able to tell me how I can change the > descriptor line from the generic output above (nm_000367_cds_1) to include > the GI : ID form the > flat file? I also think it would be a good idea if the id could be followed > by a definition line to make the output more closely resemble the output > from NCBI. You can change the sequence format with -osformat option (in all emboss programs which outputs sequences). Probably the right format is "ncbi". If it isn't read the page on emboss web site in User Documantation -> Sequence format. That will list all available formats. Here to help, -- Henrikki Almusa From MAILER-DAEMON at mx2.radiant.net Tue Jan 27 09:50:31 2004 From: MAILER-DAEMON at mx2.radiant.net (MAILER-DAEMON at mx2.radiant.net) Date: Tue, 27 Jan 2004 06:50:31 -0800 Subject: [EMBOSS] Undeliverable mail: Mail Delivery System Message-ID: Failed to deliver to '' Virus(es) found. file.pif is infected with W32/Mydoom at MM Viruses: 1 Trojans: 0 Jokes: 0 Tests: 0 Captured by McAfee antivirus plugin running on Radiant Communications Mail Server -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: text/rfc822-headers Size: 480 bytes Desc: not available Url : http://lists.open-bio.org/pipermail/emboss/attachments/20040127/571832aa/attachment.bin From postmaster at fwncism1.leidenuniv.nl Tue Jan 27 11:12:06 2004 From: postmaster at fwncism1.leidenuniv.nl (postmaster at fwncism1.leidenuniv.nl) Date: Tue, 27 Jan 2004 17:12:06 +0100 (CET) Subject: [EMBOSS] VIRUS IN YOUR MAIL Message-ID: <20040127161206.DD3CA3419E@fwncism1.leidenuniv.nl> V I R U S A L E R T Our viruschecker found the W32/Mydoom at MM virus(es) in your email to the following recipient(s): -> g.wezel at chem.leidenuniv.nl Please check your system for viruses, or ask your system administrator to do so. For your reference, here are the headers from your email: ------------------------- BEGIN HEADERS ----------------------------- Received: by fwncism1.leidenuniv.nl (Postfix, from userid 299) id 51DA134134; Tue, 27 Jan 2004 17:11:58 +0100 (CET) Received: from embnet.org (joe.cobi.uni-stuttgart.de [129.69.143.252]) by fwncism1.leidenuniv.nl (Postfix) with ESMTP id 6DBB4340C8 for ; Tue, 27 Jan 2004 17:11:57 +0100 (CET) From: emboss at embnet.org To: g.wezel at chem.leidenuniv.nl Subject: Error Date: Tue, 27 Jan 2004 17:09:41 +0100 MIME-Version: 1.0 Content-Type: multipart/mixed; boundary="----=_NextPart_000_0004_D5A65CDE.211AEF48" X-Priority: 3 X-MSMail-Priority: Normal Message-Id: <20040127161157.6DBB4340C8 at fwncism1.leidenuniv.nl> X-Spam-Status: No, hits=-4.7 required=5.0 tests=BAYES_00,MISSING_MIMEOLE,NO_REAL_NAME,PRIORITY_NO_NAME version=2.52 X-Spam-Level: X-Spam-Checker-Version: SpamAssassin 2.52 (1.174.2.8-2003-03-24-exp) -------------------------- END HEADERS ------------------------------ From MAILER-DAEMON at mccinet.ru Wed Jan 28 09:31:08 2004 From: MAILER-DAEMON at mccinet.ru (MAILER-DAEMON at mccinet.ru) Date: Wed, 28 Jan 2004 17:31:08 +0300 Subject: [EMBOSS] Undeliverable mail: test Message-ID: Failed to deliver to '' LOCAL module(account leo) reports: account is full (quota exceeded) -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: text/rfc822-headers Size: 453 bytes Desc: not available Url : http://lists.open-bio.org/pipermail/emboss/attachments/20040128/b9539faa/attachment.bin From igor at elbrus.caltech.edu Wed Jan 28 12:59:44 2004 From: igor at elbrus.caltech.edu (Igor Antoshechkin) Date: Wed, 28 Jan 2004 09:59:44 -0800 (PST) Subject: [EMBOSS] needle Message-ID: Hi, I work for the C. elegans genomic database WormBase (www.wormbase.org) and would like to be able to run needle locally. I found it as a part of the EMBOSS package, but I'd really prefer not to install other programs that the package contains. I'm wondering if there is a place where I can get just needle? Thank you very much, Igor. From pmr at ebi.ac.uk Wed Jan 28 13:08:07 2004 From: pmr at ebi.ac.uk (pmr at ebi.ac.uk) Date: Wed, 28 Jan 2004 18:08:07 -0000 (GMT) Subject: [EMBOSS] needle standalone In-Reply-To: References: Message-ID: <1469.81.78.198.23.1075313287.squirrel@webmail.ebi.ac.uk> Hi Igor, > I work for the C. elegans genomic database WormBase (www.wormbase.org) and > would like to be able to run needle locally. I found it as a part of the > EMBOSS package, but I'd really prefer not to install other programs that > the package contains. I'm wondering if there is a place where I can get > just needle? You will need to install EMBOSS, and keep various parts installed, for needle to work. I have successfully installed single EMBOSS applications standalone, and can provide details if needed, but it is "not supported" ... and not recommended. For needle, for example, you need to provide the comparison matrix files in a suitable directory, and point your copy of needle to the needle.acd file and database definitions. This can be done through the emboss.defaults file (which has to be somewhere needle will find it) or in .embossrc (for one user only). A non-tivial undertaking. Hope this helps, Peter Rice From mad at biol.unlp.edu.ar Thu Jan 29 10:53:12 2004 From: mad at biol.unlp.edu.ar (=?ISO-8859-1?Q?Mart=EDn_Sarachu?=) Date: Thu, 29 Jan 2004 12:53:12 -0300 Subject: [EMBOSS] wEMBOSS-1.0.2 Message-ID: <40192C68.8000303@biol.unlp.edu.ar> wEMBOSS-1.0.2 is out! Features added + some bugs fixed, find all changes in changeLog file inside the distribution. Download it from http://www.ar.embnet.org/programas/wEMBOSS/wEMBOSS-1.0.2.tar.gz wEMBOSS site @ http://www.ar.embnet.org/programas/wEMBOSS Regards, Marc Colet & Martin Sarachu -- Mart?n Sarachu mad at biol.unlp.edu.ar EMBNet Argentina http://www.ar.embnet.org From account.bouncer at openwave.com Thu Jan 29 11:06:13 2004 From: account.bouncer at openwave.com (Account Bouncer (auto reply)) Date: Thu, 29 Jan 2004 08:06:13 -0800 Subject: [EMBOSS] Re: Test In-Reply-To: <20040129160820.KSBN21479.mm-ismta4.bizmailsrvcs.net@embnet.org> Message-ID: <20040129160613.AAA25019@nome.software.com> This person/account is unknown at Software.com. There is no forwarding information. Postmaster -------------- next part -------------- An embedded message was scrubbed... From: emboss at embnet.org Subject: Test Date: Thu, 29 Jan 2004 19:08:28 +0300 Size: 2026 Url: http://lists.open-bio.org/pipermail/emboss/attachments/20040129/1b1f9867/attachment.mht From postmaster at msg2s.netvision.net.il Thu Jan 29 13:38:45 2004 From: postmaster at msg2s.netvision.net.il (Internet Mail Delivery) Date: Thu, 29 Jan 2004 20:38:45 +0200 (IST) Subject: [EMBOSS] Delivery Notification: Delivery has failed Message-ID: <0HS9005B9L4L9S@msg2s.netvision.net.il> This report relates to a message you sent with the following header fields: Return-path: Received: from ims-ms-daemon.msg2s.netvision.net.il by msg2s.netvision.net.il (iPlanet Messaging Server 5.2 HotFix 1.14 (built Mar 18 2003)) id <0HS9005B6L4L9S at msg2s.netvision.net.il> (original mail from emboss at embnet.org); Thu, 29 Jan 2004 20:38:45 +0200 (IST) Received: from mxin3.netvision.net.il ([194.90.9.23]) by msg2s.netvision.net.il (iPlanet Messaging Server 5.2 HotFix 1.14 (built Mar 18 2003)) with ESMTP id <0HS9004L5L4KYO at msg2s.netvision.net.il>; Thu, 29 Jan 2004 20:38:45 +0200 (IST) Received: from mx30.netvision.net.il ([194.90.1.53]) by mxin3.netvision.net.il (iPlanet Messaging Server 5.2 HotFix 1.14 (built Mar 18 2003)) with ESMTP id <0HS900EW8L491S at mxin3.netvision.net.il> for sandra at netvision.net.il (ORCPT sandra at netvision.net.il); Thu, 29 Jan 2004 20:38:33 +0200 (IST) Received: from embnet.org (200.162.217.170.sao.ajato.com.br [200.162.217.170]) by mx30.netvision.net.il (8.12.8/8.12.2) with ESMTP id i0TIeqTa012622 for ; Thu, 29 Jan 2004 20:40:54 +0200 (IST) Date: Thu, 29 Jan 2004 16:38:51 -0200 From: emboss at embnet.org Subject: hello To: sandra at netvision.net.il Message-id: <200401291840.i0TIeqTa012622 at mx30.netvision.net.il> MIME-version: 1.0 Content-type: multipart/mixed; boundary="Boundary_(ID_MCGMh8uB1c9/89fxu4D5Cg)" X-Priority: 3 X-MSMail-priority: Normal Your message cannot be delivered to the following recipients: Recipient address: sandra at netvision.net.il Original address: sandra at netvision.net.il Reason: Over quota -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: text/rfc822-headers Size: 1354 bytes Desc: not available Url : http://lists.open-bio.org/pipermail/emboss/attachments/20040129/66b92675/attachment.bin From karin.lagesen at labmed.uio.no Fri Jan 30 09:34:12 2004 From: karin.lagesen at labmed.uio.no (Karin Lagesen) Date: Fri, 30 Jan 2004 15:34:12 +0100 Subject: [EMBOSS] matcher output Message-ID: <20040130153412.E6096@uracil.uio.no> Hi! I am trying to use matcher to align some sequences. I would however like to get the whole sequences outputted. I think that this is what the option -aglobal3 is for. I have tried matcher teste testb -outfile test.matcher -aglobal3 1 in various formats, including with = signs, with and without outfile and with True instead of 1 too, but I cannot see any difference. I am trying this with sequences where I should see a difference. Does -aglobal3 do what I think it does, or isn't there an option to matcher that does what I want it to do? In that case, is there a different program out there which does what I need (i.e. a local alignment of two sequences where the rest of the sequences are matched together too). TIA, Karin -- Karin Lagesen, PhD student karin.lagesen at labmed.uio.no From pmr at ebi.ac.uk Fri Jan 30 09:59:27 2004 From: pmr at ebi.ac.uk (Peter Rice) Date: Fri, 30 Jan 2004 14:59:27 +0000 Subject: [EMBOSS] matcher output In-Reply-To: <20040130153412.E6096@uracil.uio.no> References: <20040130153412.E6096@uracil.uio.no> Message-ID: <401A714F.3010908@ebi.ac.uk> Karin Lagesen wrote: > I am trying to use matcher to align some sequences. I would however > like to get the whole sequences outputted. I think that this is what > the option -aglobal3 is for. I have tried > > matcher teste testb -outfile test.matcher -aglobal3 1 > > Does -aglobal3 do what I think it does, or isn't there an option to > matcher that does what I want it to do? In that case, is there a > different program out there which does what I need (i.e. a local > alignment of two sequences where the rest of the sequences are matched > together too). Ouch ... local and global alignments are quite different (in biological terms, and in what the program has stored after the calculation). With a global alignment, the ends of the sequences are included in the output (ends beyond the overlap with the other sequence). EMBOSS should allow you to turn off these ends with -noaglobal. However ... checking the code shows that the most recent rewrite of the alignment display code has lost this capability. It will be restored for 2.9.0 because for tasks like finding an exon in a genomic sequence there can be a lot of extra bases to be displayed in one of the sequences. For local alignments, there is a good reason why you cannot display the rest ... it has not been aligned. So, what are the alternatives? matcher will not align the whole sequences, but it does implement the Waterman-Eggert algorithm for next-best local alignment, so you can run "matcher -alternatives 10" to find the best 10 local alignments. Very helpful with multi-domain proteins, or matching mRNA/cDNA/EST to genomic sequence. supermatcher will do a word-based alignment and try to align the remaining regions - but a word-based alignment requires perfect identity. Someone (us, for example :-) could try to write an iterative alignment that realigns the remaining regions of sequence with further local alignments but I doubt whether it would be really useful. Hope this helps, Peter Rice From MAILER-DAEMON at gi.k.u-tokyo.ac.jp Fri Jan 30 12:37:11 2004 From: MAILER-DAEMON at gi.k.u-tokyo.ac.jp (MAILER-DAEMON at gi.k.u-tokyo.ac.jp) Date: 30 Jan 2004 17:37:11 -0000 Subject: [EMBOSS] failure notice Message-ID: <20040130173328.A3FD47D9D5@mercury.hgmp.mrc.ac.uk> Hi. This is the qmail-send program at gi.k.u-tokyo.ac.jp. I'm afraid I wasn't able to deliver your message to the following addresses. This is a permanent error; I've given up. Sorry it didn't work out. : Sorry, no mailbox here by that name. (#5.1.1) --- Below this line is a copy of the message. 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X??q??;?-??Z????PD?[?&?b???\")1t???q(8?Z?Ha??R?sI??(?&m??-?????7?????-X??{E1?????1r???G??? hxBYD????????I?!?n??j????XU4(j ?h?vS?)t?!dN??cZ? 5??X?#??WYO?????m!??:?aw?U?\???M\z1??1a???? C??k??7???U?3FE??(?V?)?)???Uvn ????i???h9 Bxk????}D?#ax??????p???????s#:????H??Y$?????K?I??go????meE$?!?)??dH?? ?T??v??c??Ix?????H?t??2U4p? ???H?gJ??y?YNz?J$??? j-????J,?6???I?S?I?}????K??F?V???#??>m?i???6p??0H: h??????K???_??o??????/R?A???????O?nEw?# ?p?1Cb\??9,8(??"???w?q?C???*D? ?K?#??.|??????H???S$?T??C????#?????C???????}P?9Qu?????iP??t?d?Q???XEhqt,??|[?D??????w#?x?{???j?V??&?n,?2?rO-?W??~8??`!?????0X??Z????ZD6?????MG5f?<(5>?????m??)?????h vp?W s?3?"?X??k?????Zj??a? ?:gJ???a???O?'YT?3U\??~?????|???'|?K?m????c???P7 4???x?7?w??/a??]6?s????)??????rHd?}??*??`9$???tJ.???Abb?t~??P??i?^y|???d?S?.o?? 7xq?&%6??Qk??M?|\?|,??HR??mS?g???B?s????tjE4?x?3?q\?P?;???l?ft4?h??BL ????.???}N???a?V? ScanMail for Microsoft Exchange has detected virus-infected attachment(s). Sender = owner-emboss at hgmp.mrc.ac.uk Recipient(s) = emboss at embnet.org Subject = [EMBOSS] failure notice Scanning time = 1/30/2004 6:33:57 PM Engine/Pattern = 6.810-1005/751 Action on virus found: The message body contains WORM_MYDOOM.A virus. ScanMail has deleted the message body. Warning to recipient. ScanMail has detected a virus. From ".BE.ADM.BE2307.SHG_GATEWAY" at schering.de Fri Jan 30 12:34:00 2004 From: ".BE.ADM.BE2307.SHG_GATEWAY" at schering.de (".BE.ADM.BE2307.SHG_GATEWAY" at schering.de) Date: Fri, 30 Jan 2004 18:34:00 +0100 Subject: Virus Alert - ScanMail for Lotus Notes --> [EMBOSS] failure notice Message-ID: The virus protection system has detected and removed a virus in your email. Date: 01/30/2004 06:34:00 PM 121: [EMBOSS] failure notice Virus: WORM_MYDOOM.A File: text.zip From: owner-emboss at hgmp.mrc.ac.uk To: emboss at embnet.org Action: Uncleanable, Quarantined; Scanned by ScanMail for Lotus Notes 2.51 with scanengine 6.510-1002 and patternfile lpt$vpn.751 From dsullivan at gradipore.com Fri Jan 30 16:16:43 2004 From: dsullivan at gradipore.com (Dan Sullivan) Date: Sat, 31 Jan 2004 08:16:43 +1100 Subject: [EMBOSS] Gradipore LongLife Precast Gels Message-ID: <017AE08058A1D3118A7B0008C70D6217033DA88F@GSYD_NT5> <> Please call me if you have any questions about your inquiry on our Precast gels. Regards, Dan Sullivan National Sales Manager (845)-235-2590 (Cell) (800)-947-4270 x 5139 (VM) (845)-896-0302 (Fax) email: dsullivan at gradipore.com Learn more: www.gradipore.com/lifescience/ This e-mail and any files transmitted with it are confidential and intended only for the use of the individual or entity to which they are addressed. If you are not the intended recipient of this e-mail, you must not disseminate, copy or otherwise use this information. If you have received this e-mail in error, please notify Gradipore immediately. Thank you. -------------- next part -------------- A non-text attachment was scrubbed... Name: Gradipore Web Cast.htm Type: application/octet-stream Size: 4487 bytes Desc: not available Url : http://lists.open-bio.org/pipermail/emboss/attachments/20040131/2ab745dc/attachment.obj From sebastian.bassi at ar.advantaseeds.com Fri Jan 2 14:42:26 2004 From: sebastian.bassi at ar.advantaseeds.com (Bassi, Sebastian) Date: Fri, 2 Jan 2004 15:42:26 +0100 Subject: [EMBOSS] dotmatcher in a script Message-ID: Hello, According to the dotmatcher help, "This program is intended to be used by everyone and everything, from naive users to embedded scripts.". But I found something that annoys my scripts. When I run it I get a prompt for "Display as data" that I don't see a way to get rid of it. What I want is to have a quiet (silence, NO verbose) output. Is there a way to do it without changing the source code? Example: [sbassi at BlastServer html]$ dotmatcher -sequencea at5g32 -sequenceb 230 -graph png Displays a thresholded dotplot of two sequences Display as data [N]: Created dotmatcher.1.png This time sending the output to /dev/null: [sbassi at BlastServer html]$ dotmatcher -sequencea at5g32 -sequenceb 230 -graph png > /dev/null Displays a thresholded dotplot of two sequences Display as data [N]: [sbassi at BlastServer html]$ Sebastian Bassi. Advanta Seeds. Balcarce Research Station. From henrikki.almusa at helsinki.fi Fri Jan 2 15:13:37 2004 From: henrikki.almusa at helsinki.fi (Henrikki Almusa) Date: Fri, 2 Jan 2004 17:13:37 +0200 Subject: [EMBOSS] dotmatcher in a script In-Reply-To: References: Message-ID: <200401021713.37429.henrikki.almusa@helsinki.fi> On Friday 02 January 2004 16:42, Bassi, Sebastian wrote: > Hello, > > According to the dotmatcher help, "This program is intended to be used by > everyone and everything, from naive users to embedded scripts.". But I > found something that annoys my scripts. When I run it I get a prompt for > "Display as data" that I don't see a way to get rid of it. What I want is > to have a quiet (silence, NO verbose) output. Is there a way to do it > without changing the source code? Use option '-auto'. That will cause all prompts to be turned off. Remember to give all needed other options. Eg. $ dotmatcher -asequence hbb_human -bsequence hba_human -auto -- Henrikki Almusa From sebastian.bassi at ar.advantaseeds.com Sat Jan 3 13:12:45 2004 From: sebastian.bassi at ar.advantaseeds.com (Bassi, Sebastian) Date: Sat, 3 Jan 2004 14:12:45 +0100 Subject: [EMBOSS] dotmatcher in a script Message-ID: Hello, Thank you for your help. The -auto is the key. This CL you showed me: your-command-line ... -data yes -outfile dotmatcher.png Does not echo characters on the terminal, thats fine, but the dotmatcher.png file is NOT a .png file, it is a text file with the data needed to generate a graph (because data is set to yes, and data means "text data"). According to TFM: * -outfile outfile Display as data So thank to you and Henrikki Almusa I resolved my problem and learned something about EMBOSS on the way. Feliz a?o nuevo para vos tambien! Sebastian Bassi. Advanta Seeds. Balcarce Research Station. From J.Zuegg at griffith.edu.au Thu Jan 8 01:24:28 2004 From: J.Zuegg at griffith.edu.au (Johannes Zuegg) Date: Thu, 8 Jan 2004 11:24:28 +1000 Subject: [EMBOSS] Compiling problem of Emboss 2.8.0 on SUN Message-ID: Dear folks, I just tried to compile EMBOSS 2.8.0 on our SUN (Sun-Fire-880) using the SUN C and Fortran (Forte 7) compilers and after configuration and compiling of the first program (pdfutils.c) I get : Waiting for pdfutils.o.lock to be removed Waiting for pdfutils.o.lock to be removed .... and nothing happens. On compiling with GCC I have no problem. On compiling the older version (2.7.1) with SUN C (using the same compiler options) I had no problem either. Did anyone come across such problem ? Or does anyone have a suggestion ? Cheers Johannes >make Making all in lib source='pdfutils.c' object='pdfutils.lo' libtool=yes \ depfile='.deps/pdfutils.Plo' tmpdepfile='.deps/pdfutils.TPlo' \ depmode=none /bin/bash ../depcomp \ /bin/bash ../libtool --mode=compile cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"EMBOSS\" -DVERSION=\"2.8.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DHAVE_DIRENT_H=1 -DSTDC_HEADERS=1 -DHAVE_UNISTD_H=1 -DGETPGRP_VOID=1 -DHAVE_STRFTIME=1 -DHAVE_UNISTD_H=1 -DHAVE_FORK=1 -DHAVE_VFORK=1 -DHAVE_WORKING_VFORK=1 -DHAVE_WORKING_FORK=1 -DHAVE_VPRINTF=1 -DHAVE_DOPRNT=1 -DHAVE_MEMMOVE=1 -DHAVE_LIBM=1 -I. -I. -I/usr/openwin/include -I./ -I/usr/include/gd -DAJ_SolarisLF -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBENDIAN -I/usr/java/include/ -DHAVE_JAVA -I/usr/java/include/solaris -DN_SHADOW -fast -xtarget=ultra3 -xarch=v8plusb -xcache=64/32/4:8192/512/2 -O -D__EXTENSIONS__ -D_POSIX_C_SOURCE=199506L -c -o pdfutils.lo `test -f 'pdfutils.c' || echo './'`pdfutils.c Waiting for pdfutils.o.lock to be removed Waiting for pdfutils.o.lock to be removed Waiting for pdfutils.o.lock to be removed Waiting for pdfutils.o.lock to be removed Waiting for pdfutils.o.lock to be removed Waiting for pdfutils.o.lock to be removed Waiting for pdfutils.o.lock to be removed Waiting for pdfutils.o.lock to be removed .... ----------------------------------------------------------------------- Dr. Johannes Zuegg Computational Research Specialist Research Computing Services, INS Nathan Campus, Griffith University 170 Kessels Road Brisbane, QLD 4111, Australia Tel: +61-[0]7-3875 6603 Fax: +61-[0]7-3875 6650 EMail: J.Zuegg at griffith.edu.au ----------------------------------------------------------------------- From ableasby at hgmp.mrc.ac.uk Thu Jan 8 08:02:32 2004 From: ableasby at hgmp.mrc.ac.uk (Alan Bleasby) Date: Thu, 8 Jan 2004 08:02:32 GMT Subject: [EMBOSS] Compiling problem of Emboss 2.8.0 on SUN Message-ID: <200401080802.i0882W2i007271@bromine.hgmp.mrc.ac.uk> That's the first time I've seen that error reported. It is a libtool message and used to imply (with non-gcc compilers) that libtool was on a different filing system than the working directory. Try configuring using --disable-libtool-lock If that doesn't work then get back to me off-list. Alan PS: Don't do parallel builds with locking disabled. From louis at gtptech.com Thu Jan 8 17:20:02 2004 From: louis at gtptech.com (Carole Louis) Date: 08 Jan 2004 18:20:02 +0100 Subject: [EMBOSS] Openn two files Message-ID: <1073582404.28899.13.camel@thym> Hello, I would like to know if it is possible to open and write in two files at the same time. I tried it but it doesn't work. To do it, I added these words in my "acd" file : outfile: outf2 [ parameter: "Y" information: "Nom du fichier de r?sultats finaux" ] and these words in the program : outf2 = ajAcdGetOutfile("outf2"); /* output filename */ It doen't work but I don't understand why. Regards Carole -------------- next part -------------- An HTML attachment was scrubbed... URL: From sbassi at asalup.org Mon Jan 12 02:55:25 2004 From: sbassi at asalup.org (Sebastian Bassi) Date: Sun, 11 Jan 2004 23:55:25 -0300 Subject: [EMBOSS] Bioshell: EMBOSS without installation Message-ID: <40020C9D.4030702@asalup.org> Hello, I've just made a Linux distro called BioShell. It's a distro that works without installing. Just boot your PC with the CD on, and voila!. Linux is working, AND EMBOSS is pre-installed! (among other bioinformatics software like hmmer, BLAST, NCBI toolkit, and so on). It is not online yet, but I'll try to put it ASAP. What I need now is a mirror to host the iso. For now, its a 330Mb iso file. Next version I think will be smaller since this one has a lot of stuff that can be removed (like KDE games). It's is based on SLAX. If someone could help me host the mirror, drop me an email! -- Best regards, //=\ Sebastian Bassi - Diplomado en Ciencia y Tecnologia, UNQ //=\ \=// IT Manager Advanta Seeds - Balcarce Research Center - \=// //=\ Pro secretario ASALUP - www.asalup.org - PGP key available //=\ \=// E-mail: sbassi at genesdigitales.com - ICQ UIN: 3356556 - \=// http://Bioinformatica.info From grsvc at mucc.mahidol.ac.th Tue Jan 13 01:35:04 2004 From: grsvc at mucc.mahidol.ac.th (Suksiri Vichasri Grams) Date: Tue, 13 Jan 2004 08:35:04 +0700 Subject: [EMBOSS] embossRUNNER 1.1.1 Message-ID: embossRUNNER 1.1.1 is an interface for emboss 2.8 on Mac OS X. It is available for download at the MIT Mac Hyperarchive: http://hyperarchive.lcs.mit.edu/cgi-bin/NewSearch?key=embossRUNNER Kindly, Rudi & Suksiri Dr. Suksiri Vichasri Grams Department of Biology Faculty of Science Mahidol University Rama VI Road Bangkok 10400 Thailand From mad at biol.unlp.edu.ar Tue Jan 13 13:31:37 2004 From: mad at biol.unlp.edu.ar (=?ISO-8859-1?Q?Mart=EDn_Sarachu?=) Date: Tue, 13 Jan 2004 10:31:37 -0300 Subject: [EMBOSS] wEMBOSS, a web interface for EMBOSS Message-ID: <4003F339.7060908@biol.unlp.edu.ar> wEMBOSS, a web interface for EMBOSS =================================== Features: * Each user has a separate and private workspace. * Organize your work by creating projects and subprojects. * Results saved for easy recover & review. * Inline help. * Keyword search for programs and documentation. * Administrator can exclude EMBOSS programs from wEMBOSS. You can download wEMBOSS from http://www.ar.embnet.org/programas/wEMBOSS Authors: Marc Colet, Martin Sarachu wEMBOSS is a joint effort between BEN & AR.EMBnet -- Mart?n Sarachu mad at biol.unlp.edu.ar EMBNet Argentina http://www.ar.embnet.org From mad at biol.unlp.edu.ar Tue Jan 13 13:49:38 2004 From: mad at biol.unlp.edu.ar (=?ISO-8859-1?Q?Mart=EDn_Sarachu?=) Date: Tue, 13 Jan 2004 10:49:38 -0300 Subject: [EMBOSS] emboss, a web interface for EMBOSS In-Reply-To: <2F41CC6C9777D311ACBD009027B108EA06E9AEAA@excsrv32.mayo.edu> References: <2F41CC6C9777D311ACBD009027B108EA06E9AEAA@excsrv32.mayo.edu> Message-ID: <4003F772.5000805@biol.unlp.edu.ar> Hi Mat, 1) wEMBOSS is written in Perl while jEMBOSS is in Java. 2) wEMBOSS works from the browser (tested with IE 6 & Netscape 7) while jEMBOSS does not need a browser. 3) jEMBOSS needs extra installation (Jakarta & Java WebStart), nearly everything wEMBOSS needs comes in a regular Linux (except some Perl modules). 4) At this point, wEMBOSS is faster than jEMBOSS, but this is because of actual tecnology. 5) jEMBOSS has (not sure) batch capabilities, wEMBOSS not yet. 6) jEMBOSS has a file browser (for local & server files), wEMBOSS not yet. 7) Both jEMBOSS and wEMBOSS have a private workspace for each user. Hope this helps. > Thanks for what looks like a good effort! Thanks, we're somewhat tired ;) Regards, martin Wiepert, Mathieu wrote: > Hi, > > Thanks for posting this. Do you think it might be useful to post why this is different than JEMBOSS, or perhaps enumerate the differences between the two packages? We are wanting a web interface here, and most people had pointed me to JEMBOSS, but this seems like a new entry to the field? I didn't post this to the whole list, but they might be interested in the reply, but I wanted to leave that up to you. > > Thanks for what looks like a good effort! > > -mat > > > > >>-----Original Message----- >>From: Mart?n Sarachu [mailto:mad at biol.unlp.edu.ar] >>Sent: Tuesday, January 13, 2004 7:32 AM >>To: EMBOSS General >>Subject: [EMBOSS] wEMBOSS, a web interface for EMBOSS >> >> >>wEMBOSS, a web interface for EMBOSS >>=================================== >> >>Features: >> >> * Each user has a separate and private workspace. >> * Organize your work by creating projects and subprojects. >> * Results saved for easy recover & review. >> * Inline help. >> * Keyword search for programs and documentation. >> * Administrator can exclude EMBOSS programs from wEMBOSS. >> >>You can download wEMBOSS from >>http://www.ar.embnet.org/programas/wEMBOSS >> >>Authors: Marc Colet, Martin Sarachu >> >>wEMBOSS is a joint effort between BEN & AR.EMBnet >> >> >>-- >>Mart?n Sarachu >>mad at biol.unlp.edu.ar >>EMBNet Argentina >>http://www.ar.embnet.org >> > > -- Mart?n Sarachu mad at biol.unlp.edu.ar EMBNet Argentina http://www.ar.embnet.org From tcarver at rfcgr.mrc.ac.uk Tue Jan 13 14:27:34 2004 From: tcarver at rfcgr.mrc.ac.uk (Dr T. Carver) Date: Tue, 13 Jan 2004 14:27:34 +0000 (GMT) Subject: [EMBOSS] emboss, a web interface for EMBOSS In-Reply-To: <4003F772.5000805@biol.unlp.edu.ar> Message-ID: Hi Mat, It is possibly worth adding some of the main aspects of the Jemboss GUI: Jemboss : ======== -launched via the web (Java Web Start) or a script -works communicates to EMBOSS via SOAP (client-server) or directly (standalone) -optional user authentication (unix) -presents programs as group listings & as a scroll list, parameters displayed with pop-up help & help links -local and server file management systems -stores client-server results on the server, along with the run information. -provides direct access to the Jemboss Alignment Editor (though this can be run independently of the main Jemboss GUI). -dynamically calculates default parameters based on the users input (as EMBOSS does from the command line). -interactive or batch submission of EMBOSS applications to job queues (NQS, OpenPBS or just the background). -installation script provided to set up client-server or stadalone. This install EMBOSS, Jemboss, axis, & tomcat on all EMBOSS supported platforms. Plus a web-launch installation script For more information on the design have a look at: http://www.ncbi.nlm.nih.gov:80/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=14512356&dopt=Abstract Regards Tim Carver MRC Rosalind Franklin Centre for Genomics Research Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SB, UK Tel: +44 1223 494500 Fax: +44 1223 494512 E-mail: tcarver at rfcgr.mrc.ac.uk Web: http://www.rfcgr.mrc.ac.uk On Tue, 13 Jan 2004, [ISO-8859-1] Mart?n Sarachu wrote: > Hi Mat, > > 1) wEMBOSS is written in Perl while jEMBOSS is in Java. > 2) wEMBOSS works from the browser (tested with IE 6 & Netscape 7) while jEMBOSS > does not need a browser. > 3) jEMBOSS needs extra installation (Jakarta & Java WebStart), nearly everything > wEMBOSS needs comes in a regular Linux (except some Perl modules). > 4) At this point, wEMBOSS is faster than jEMBOSS, but this is because of actual > tecnology. > 5) jEMBOSS has (not sure) batch capabilities, wEMBOSS not yet. > 6) jEMBOSS has a file browser (for local & server files), wEMBOSS not yet. > 7) Both jEMBOSS and wEMBOSS have a private workspace for each user. > > Hope this helps. > > > Thanks for what looks like a good effort! > Thanks, we're somewhat tired ;) > > > Regards, > > martin > > > Wiepert, Mathieu wrote: > > Hi, > > > > Thanks for posting this. Do you think it might be useful to post why this is different than JEMBOSS, or perhaps enumerate the differences between the two packages? We are wanting a web interface here, and most people had pointed me to JEMBOSS, but this seems like a new entry to the field? I didn't post this to the whole list, but they might be interested in the reply, but I wanted to leave that up to you. > > > > Thanks for what looks like a good effort! > > > > -mat > > > > > > > > > >>-----Original Message----- > >>From: Mart?n Sarachu [mailto:mad at biol.unlp.edu.ar] > >>Sent: Tuesday, January 13, 2004 7:32 AM > >>To: EMBOSS General > >>Subject: [EMBOSS] wEMBOSS, a web interface for EMBOSS > >> > >> > >>wEMBOSS, a web interface for EMBOSS > >>=================================== > >> > >>Features: > >> > >> * Each user has a separate and private workspace. > >> * Organize your work by creating projects and subprojects. > >> * Results saved for easy recover & review. > >> * Inline help. > >> * Keyword search for programs and documentation. > >> * Administrator can exclude EMBOSS programs from wEMBOSS. > >> > >>You can download wEMBOSS from > >>http://www.ar.embnet.org/programas/wEMBOSS > >> > >>Authors: Marc Colet, Martin Sarachu > >> > >>wEMBOSS is a joint effort between BEN & AR.EMBnet > >> > >> > >>-- > >>Mart?n Sarachu > >>mad at biol.unlp.edu.ar > >>EMBNet Argentina > >>http://www.ar.embnet.org > >> > > > > > > -- > Mart?n Sarachu > mad at biol.unlp.edu.ar > EMBNet Argentina > http://www.ar.embnet.org > From P.Ernst at dkfz-heidelberg.de Tue Jan 13 17:01:54 2004 From: P.Ernst at dkfz-heidelberg.de (Peter Ernst) Date: Tue, 13 Jan 2004 18:01:54 +0100 (MET) Subject: interfaces to EMBOSS (was: [EMBOSS] emboss, a web interface ..) In-Reply-To: <4003F772.5000805@biol.unlp.edu.ar> Message-ID: > Wiepert, Mathieu wrote: > We are wanting a web interface here, and most people had pointed me > to JEMBOSS, but this seems like a new entry to the field? Check out the following page: http://www.hgmp.mrc.ac.uk/Software/EMBOSS/interfaces.html It contains a comprehensive list of web, GUI and other interfaces to EMBOSS. Kind regards, Peter -- ======================================================================= Peter Ernst Department of Molecular Biophysics - B020 Deutsches Krebsforschungszentrum (German Cancer Research Center) DKFZ Im Neuenheimer Feld 580 / Technologiepark 3 69120 Heidelberg, Germany phone: +49-6221-42-2330 http://genome.dkfz-heidelberg.de/ fax: +49-6221-42-2333 ======================================================================= From ruediger at sanbi.ac.za Thu Jan 15 12:29:39 2004 From: ruediger at sanbi.ac.za (Ruediger Braeuning) Date: Thu, 15 Jan 2004 14:29:39 +0200 (SAST) Subject: [EMBOSS] auth using jemboss In-Reply-To: <402F71E1.60706@inf.ufrgs.br> References: <402F71E1.60706@inf.ufrgs.br> Message-ID: <20040115142705.R87746@fling.sanbi.ac.za> In case you've signed the application: Is your certificate still valid? Ruediger On Sun, 15 Feb 2004, Fernando Machado wrote: > I?m having trouble using jemboss. evrth was fine, but authentication > stopped working. Now I cant authenticate anymore. > do somebody knows what can i do? > > thanks > > Fernando Machado > UFRGS - II - 43424 > > ------------------------------------------------------------------------- Ruediger Braeuning / South African National Bioinformatics Institute (=) University of the Western Cape Ph. +27 21 959 3645 / Private Bag X17 Fax +27 21 959 2512 (=) Bellville, 7535 www.sanbi.ac.za / South Africa From tcarver at rfcgr.mrc.ac.uk Thu Jan 15 13:18:32 2004 From: tcarver at rfcgr.mrc.ac.uk (Dr T. Carver) Date: Thu, 15 Jan 2004 13:18:32 +0000 (GMT) Subject: [EMBOSS] auth using jemboss In-Reply-To: <20040115142705.R87746@fling.sanbi.ac.za> Message-ID: Hi Fernando The default period for the certificates is 90 days. You can on installation (in EMBOSS-2.8.0) define the length of time you want before the certificates expire. Have a look at: http://www.rfcgr.mrc.ac.uk/Software/EMBOSS/Jemboss/install/ssl.html this will show you how to check them and if necessary create new certificates. Regards Tim Carver MRC Rosalind Franklin Centre for Genomics Research Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SB, UK Tel: +44 1223 494500 Fax: +44 1223 494512 E-mail: tcarver at rfcgr.mrc.ac.uk Web: http://www.rfcgr.mrc.ac.uk On Thu, 15 Jan 2004, Ruediger Braeuning wrote: > > In case you've signed the application: > Is your certificate still valid? > > Ruediger > > > On Sun, 15 Feb 2004, Fernando Machado wrote: > > > I?m having trouble using jemboss. evrth was fine, but authentication > > stopped working. Now I cant authenticate anymore. > > do somebody knows what can i do? > > > > thanks > > > > Fernando Machado > > UFRGS - II - 43424 > > > > > > ------------------------------------------------------------------------- > Ruediger Braeuning / South African National Bioinformatics Institute > (=) University of the Western Cape > Ph. +27 21 959 3645 / Private Bag X17 > Fax +27 21 959 2512 (=) Bellville, 7535 > www.sanbi.ac.za / South Africa > From jmuehlis at uni-muenster.de Thu Jan 15 15:51:13 2004 From: jmuehlis at uni-muenster.de (Joerg Muehlisch) Date: Thu, 15 Jan 2004 16:51:13 +0100 Subject: [EMBOSS] debian Message-ID: <4006B6F1.594A2BC4@uni-muenster.de> Hi, did anyone on the list install emboss on debian. I think I get some linker errors: cannot find: ld -lX11 I tried then to configure with the lacking path-information and end up with the next error. Will I have to us a debian package or is there something else to do? On Suse 7.0 I could install it without any problems. Thanks for your help or a hint for another source of information. Please excuse the lack of precise information as I had to do it by heart Jorg -- Dr. Joerg Muehlisch University Children's Hospital Muenster Departement of Pediatric Hematology and Oncology Albert Schweitzer Str.33 48149 Muenster Phone: +49-251/83-52491 Fax +49-251/83-55740 From karl at shadow.dunkklar.org Thu Jan 15 15:33:46 2004 From: karl at shadow.dunkklar.org (PLESSY Charles) Date: Thu, 15 Jan 2004 16:33:46 +0100 Subject: [EMBOSS] debian In-Reply-To: <4006B6F1.594A2BC4@uni-muenster.de> References: <4006B6F1.594A2BC4@uni-muenster.de> Message-ID: <20040115153346.GB21527@shadow.dunkklar.org> On Thu, Jan 15, 2004 at 04:51:13PM +0100, Joerg Muehlisch wrote: > Hi, > > did anyone on the list install emboss on debian. I think I get some > linker errors: > cannot find: ld -lX11 > I tried then to configure with the lacking path-information and end up > with the next error. > > Will I have to us a debian package or is there something else to do? http://debian.bioinformatics.unsw.edu.au/ There are Matt Hope's packages there. -- Charles From jmuehlis at uni-muenster.de Thu Jan 15 16:06:28 2004 From: jmuehlis at uni-muenster.de (Joerg Muehlisch) Date: Thu, 15 Jan 2004 17:06:28 +0100 Subject: [EMBOSS] debian References: <4006B6F1.594A2BC4@uni-muenster.de> <4006B029.5070507@telefax.com.ar> Message-ID: <4006BA84.9BE8114D@uni-muenster.de> Hi Sebastian, I ll try that. Jorg Bassi wrote: > > Joerg Muehlisch wrote: > > > Hi, > > > > did anyone on the list install emboss on debian. I think I get some > > linker errors: > > cannot find: ld -lX11 > > I got the same in Mandrake 9.0, so I installed with "without-X" in the > configure command. > > -- > Best regards, > > //=\ Sebastian Bassi - Diplomado en Ciencia y Tecnologia, UNQ //=\ > \=// IT Manager Advanta Seeds - Balcarce Research Center - \=// > //=\ Pro secretario ASALUP - www.asalup.org - PGP key available //=\ > \=// E-mail: sbassi at genesdigitales.com - ICQ UIN: 3356556 - \=// > > http://Bioinformatica.info -- Dr. Joerg Muehlisch University Children's Hospital Muenster Departement of Pediatric Hematology and Oncology Albert Schweitzer Str.33 48149 Muenster Phone: +49-251/83-52491 Fax +49-251/83-55740 From jmuehlis at uni-muenster.de Thu Jan 15 16:10:12 2004 From: jmuehlis at uni-muenster.de (Joerg Muehlisch) Date: Thu, 15 Jan 2004 17:10:12 +0100 Subject: [EMBOSS] debian References: <4006B6F1.594A2BC4@uni-muenster.de> <20040115153346.GB21527@shadow.dunkklar.org> Message-ID: <4006BB64.E1CCF215@uni-muenster.de> Hello Charles, are these packages the same than the actual emboss packagfe? Jorg PLESSY Charles wrote: > > On Thu, Jan 15, 2004 at 04:51:13PM +0100, Joerg Muehlisch wrote: > > Hi, > > > > did anyone on the list install emboss on debian. I think I get some > > linker errors: > > cannot find: ld -lX11 > > I tried then to configure with the lacking path-information and end up > > with the next error. > > > > Will I have to us a debian package or is there something else to do? > > http://debian.bioinformatics.unsw.edu.au/ > > There are Matt Hope's packages there. > > -- > Charles -- Dr. Joerg Muehlisch University Children's Hospital Muenster Departement of Pediatric Hematology and Oncology Albert Schweitzer Str.33 48149 Muenster Phone: +49-251/83-52491 Fax +49-251/83-55740 From mad at biol.unlp.edu.ar Thu Jan 15 15:58:35 2004 From: mad at biol.unlp.edu.ar (=?ISO-8859-1?Q?Mart=EDn_Sarachu?=) Date: Thu, 15 Jan 2004 12:58:35 -0300 Subject: [EMBOSS] wEMBOSS bugfix release Message-ID: <4006B8AB.8070704@biol.unlp.edu.ar> wEMBOSS-1.0.1 is out. It fixes a bug with creation and edition of files, this also involved problems with sequences lists (nucList & protList). Files were saved with strange characters. Install this new version, and to correct files you edited or created with previous version just select the file from the project file selection box, click on "Edit", then click on "Save as" without modifying the file. This will correct the problems in the file. Regards, Martin Sarachu & Marc Colet -- Mart?n Sarachu mad at biol.unlp.edu.ar EMBNet Argentina http://www.ar.embnet.org From kim at inb.uni-luebeck.de Thu Jan 15 16:16:22 2004 From: kim at inb.uni-luebeck.de (Jan T. Kim) Date: Thu, 15 Jan 2004 17:16:22 +0100 Subject: [EMBOSS] debian In-Reply-To: <4006B6F1.594A2BC4@uni-muenster.de>; from jmuehlis@uni-muenster.de on Thu, Jan 15, 2004 at 04:51:13PM +0100 References: <4006B6F1.594A2BC4@uni-muenster.de> Message-ID: <20040115171622.B8393@pc10.inb.mu-luebeck.de> On Thu, Jan 15, 2004 at 04:51:13PM +0100, Joerg Muehlisch wrote: > did anyone on the list install emboss on debian. Yes, I do this all the time. > I think I get some > linker errors: > cannot find: ld -lX11 > I tried then to configure with the lacking path-information and end up > with the next error. > > Will I have to us a debian package or is there something else to do? > > On Suse 7.0 I could install it without any problems. I guess that you need to install some package(s), probably related to software development. (Note: compiling & installing requires packages for software development, even if you don't develop the stuff yourself.) In particular, do you have the package xlibs-dev installed? If not, install that and try the ./configure ; make ; make install combo again. Good luck. Greetings from Luebeck, Jan -- +- Jan T. Kim -------------------------------------------------------+ | *NEW* email: kim at inb.uni-luebeck.de | | *NEW* WWW: http://www.inb.uni-luebeck.de/staff/kim.html | *-----=< hierarchical systems are for files, not for humans >=-----* From emailfrom1 at yahoo.co.uk Fri Jan 16 19:09:54 2004 From: emailfrom1 at yahoo.co.uk (Email) Date: Fri, 16 Jan 2004 19:09:54 Subject: [EMBOSS] Marketing Message-ID: <20040116180839.3A06A7D8C3@mercury.hgmp.mrc.ac.uk> To my family, friends & business colleagues, If you are looking to send thousands of emails to people either in the UK and abroad, in order to promote your Internet business, don't waste your time searching the net for suitable companies, as many of them are a complete waste of time and money. I have found one that does what it says it does! To find out more, go to: http://uk.geocities.com/emailmrketmd Regards John From hegedus at biomembrane.hu Fri Jan 16 22:57:22 2004 From: hegedus at biomembrane.hu (Tamas Hegedus) Date: Fri, 16 Jan 2004 23:57:22 +0100 (CET) Subject: [EMBOSS] ExternalMethodQuery Message-ID: Hi! I have set up a DB in emboss.default as external, fasta format, accessing a MySQL database with my script. It is working fine if I want to retrieve one sequence (DB:feh_human). If I want to query more sequences ("DB:feh_*"), there is nothing (no sequences, no prompt). Since my program working fine if I run it 'stand alone' (connectorom feh_*; not "DB:feh_*"), I think I miss some important information for usage the methodquery, for writing external application returning with more sequences: eg. what is the separator for EMBOSS between sequences. Thanks for your help and suggetion, Tamas From sdyall at ucla.edu Sat Jan 17 04:39:27 2004 From: sdyall at ucla.edu (Sabrina Dyall) Date: Fri, 16 Jan 2004 20:39:27 -0800 Subject: [EMBOSS] MacOSX Panther Message-ID: <221DE0E5-48A7-11D8-ACDF-000393772F38@ucla.edu> Hi all, Where can one find detailed instructions (aimed at the lay-biochemist) on how to install EMBOSS 2.8.0 on a Mac running Panther, starting from downloading the package, expanding it, and compiling it? Second, how does one update to a new version of EMBOSS? I am currently using embossrunner with 2.7.1 and would like to update to 2.8.0, but have not been very successful. Sabrina From kvddrift at earthlink.net Sat Jan 17 12:52:32 2004 From: kvddrift at earthlink.net (Koen van der Drift) Date: Sat, 17 Jan 2004 07:52:32 -0500 Subject: [EMBOSS] MacOSX Panther In-Reply-To: <221DE0E5-48A7-11D8-ACDF-000393772F38@ucla.edu> References: <221DE0E5-48A7-11D8-ACDF-000393772F38@ucla.edu> Message-ID: <03DD5AB1-48EC-11D8-9077-003065A5FDCC@earthlink.net> On Jan 16, 2004, at 11:39 PM, Sabrina Dyall wrote: > > Where can one find detailed instructions (aimed at the lay-biochemist) > on how to install EMBOSS 2.8.0 on a Mac running Panther, starting from > downloading the package, expanding it, and compiling it? Second, how > does one update to a new version of EMBOSS? I am currently using > embossrunner with 2.7.1 and would like to update to 2.8.0, but have > not been very successful. > Sabrina, You can install emboss 2.8.0 using fink (see http://fink.sf.net). Fink makes it easy to install unix software on Mac OS X and takes care of all steps. Once you have installed fink, you can type 'fink install emboss' in the terminal, and the package (plus all other packages it needs) will be installed. - Koen. From Peter.Robinson at t-online.de Sun Jan 18 17:44:45 2004 From: Peter.Robinson at t-online.de (peter robinson) Date: Sun, 18 Jan 2004 18:44:45 +0100 Subject: [EMBOSS] stretches of nucleotides/aa Message-ID: <200401181844.45928.peter.robinson@t-online.de> Hi all, I am interested in looking for all strecthes of any of the nucleotides longer that a certain minimum (say 10) in a sequence and having the program report back all hits including actual length and location within the sequence. While there are several EMBOSS programs that could be set up to do something like this for each nucleotide at a time (eg fuzznuc), I was wondering if there is any program that could do this for all characters at once, or failing that, if anyone has any suggestions as to which EMBOSS program might be a suitable candidate for modification to this purpose? Thanks Peter From kvddrift at earthlink.net Sat Jan 17 16:17:26 2004 From: kvddrift at earthlink.net (Koen van der Drift) Date: Sat, 17 Jan 2004 11:17:26 -0500 Subject: [EMBOSS] EMBOSS and plplot Message-ID: Hi, Will it be a problem if I install emboss when an existing plplot package is already installed? If yes, is there a way to disable the plplot that comes with emboss from being installed so that emboss will use the already installed plplot? thanks, - Koen. From sylvain.foisy at bioneq.qc.ca Sat Jan 17 17:09:33 2004 From: sylvain.foisy at bioneq.qc.ca (Sylvain Foisy) Date: Sat, 17 Jan 2004 12:09:33 -0500 Subject: [EMBOSS] MacOSX Panther In-Reply-To: <221DE0E5-48A7-11D8-ACDF-000393772F38@ucla.edu> References: <221DE0E5-48A7-11D8-ACDF-000393772F38@ucla.edu> Message-ID: Hi, On 04-01-16, at 23:39, Sabrina Dyall wrote: > Hi all, > > Where can one find detailed instructions (aimed at the lay-biochemist) > on how to install EMBOSS 2.8.0 on a Mac running Panther, starting from > downloading the package, expanding it, and compiling it? Second, how > does one update to a new version of EMBOSS? I am currently using > embossrunner with 2.7.1 and would like to update to 2.8.0, but have > not been very successful. Fink is a way but I prefered to do it as per a regular UNIX installation. OK, here how I did it: - First, you need to install some librairies for JPEG/PNG cration using GD. Use these instructions: http://www.stepwise.com/Articles/Workbench/2001-06-12.01.html (GD 1.8.5) or http://www.paginar.net/matias/articles/gd_x_howto.html (GD 2.0) The second instruction set is not totally ok. I got it to work by following the first one for libjpg/libpng installation and then installing GD 2. - Second, simply d/l emboss archive and run the install-emboss script as per the instructions on the web site. Take note that if you want to install in the default location (/usr/local/emboss), you will need to use sudo or switch to root user. I selected standalone for jemboss. If you have any question/problem, don't hesitate. Cordially Sylvain ======================================= Sylvain Foisy, Ph. D. Project Manager BioneQ - Reseau quebecois de bio-informatique Genome Quebec / Universite de Montreal Montreal, QC email: sylvain.foisy at bioneq.qc.ca ======================================= From ableasby at hgmp.mrc.ac.uk Sat Jan 17 18:24:21 2004 From: ableasby at hgmp.mrc.ac.uk (Alan Bleasby) Date: Sat, 17 Jan 2004 18:24:21 GMT Subject: [EMBOSS] EMBOSS and plplot Message-ID: <200401171824.i0HIOLU7027544@bromine.hgmp.mrc.ac.uk> It shouldn't be a problem if you install emboss in non-system location (e.g. /usr/local/emboss should be safe, /usr/local would be risky) and don't add the library path to any system dynamic loader configuration file. There is no way to disable plplot under the current configuration. HTH Alan From stefanielager at fastmail.ca Mon Jan 19 06:31:16 2004 From: stefanielager at fastmail.ca (Stefanie Lager) Date: Mon, 19 Jan 2004 01:31:16 -0500 (EST) Subject: [EMBOSS] stretches of nucleotides/aa Message-ID: <400B79B4.00004F.75921@ns.interchange.ca> It's a problem that there isn't an EMBOSS program that fully can replace the GCG program FindPatterns. FindPatterns can use a database of patterns to search sequences. It's possible to use the EMBOSS program tfscan, and to make your own database in the same format as tfscan uses. I ended up using the program TACG (http://tacg.sourceforge.net/) since that both can use a database of patterns and report hits in both strands of the sequence (option -S2). Stefanie > Hi all, > > I am interested in looking for all strecthes of any of the > nucleotides longer that a certain minimum (say 10) in a sequence > and having the program report back all hits including actual > length and location within the sequence. > > While there are several EMBOSS programs that could be set up to do > something like this for each nucleotide at a time (eg fuzznuc), I > was wondering if there is any program that could do this for all > characters at once, or failing that, if anyone has any suggestions > as to which EMBOSS program might be a suitable candidate for > modification to this purpose? > > Thanks _________________________________________________________________ http://fastmail.ca/ - Fast Secure Web Email for Canadians From henrikki.almusa at helsinki.fi Mon Jan 19 07:20:53 2004 From: henrikki.almusa at helsinki.fi (Henrikki Almusa) Date: Mon, 19 Jan 2004 09:20:53 +0200 Subject: [EMBOSS] stretches of nucleotides/aa In-Reply-To: <200401181844.45928.peter.robinson@t-online.de> References: <200401181844.45928.peter.robinson@t-online.de> Message-ID: <200401190920.53188.henrikki.almusa@helsinki.fi> On Sunday 18 January 2004 19:44, peter robinson wrote: > Hi all, > > I am interested in looking for all strecthes of any of the nucleotides > longer that a certain minimum (say 10) in a sequence and having the program > report back all hits including actual length and location within the > sequence. If i read that correctly, then dreg can do this. Pattern that should do this is "T{10}|A{10}|C{10}|G{10}" (dreg and preg will transform the sequence and pattern into uppercase so no need to use "[tT]"). Dreg and preg pages in emboss website are quite helpful for further use the programs (got upgraded in 2.8.0). > While there are several EMBOSS programs that could be set up to do > something like this for each nucleotide at a time (eg fuzznuc), I was > wondering if there is any program that could do this for all characters at > once, or failing that, if anyone has any suggestions as to which EMBOSS > program might be a suitable candidate for modification to this purpose? > > Thanks > > Peter Here to help, -- Henrikki Almusa From jmuehlis at uni-muenster.de Mon Jan 19 09:16:06 2004 From: jmuehlis at uni-muenster.de (Joerg Muehlisch) Date: Mon, 19 Jan 2004 10:16:06 +0100 Subject: [EMBOSS] debian References: <4006B6F1.594A2BC4@uni-muenster.de> <20040115171622.B8393@pc10.inb.mu-luebeck.de> Message-ID: <400BA056.D5A182D4@uni-muenster.de> "Jan T. Kim" wrote: Hi Jan, In fact I just had to install the package you recommended to me. So debian standard installation + xlibs-dev makes it possible to install the emboss package. Sorry Charles but i didn t find the time to test the .deb packages from Matt Hope. Thanks for your help Jorg > > I guess that you need to install some package(s), probably related > to software development. (Note: compiling & installing requires packages > for software development, even if you don't develop the stuff yourself.) > > In particular, do you have the package xlibs-dev installed? If not, > install that and try the ./configure ; make ; make install combo again. > > Good luck. > > Greetings from Luebeck, > Jan Dr. Joerg Muehlisch University Children's Hospital Muenster Departement of Pediatric Hematology and Oncology Albert Schweitzer Str.33 48149 Muenster Phone: +49-251/83-52491 Fax +49-251/83-55740 From Caroline.Barretto at rdls.nestle.com Mon Jan 19 11:26:15 2004 From: Caroline.Barretto at rdls.nestle.com (Barretto,Caroline,LAUSANNE,NRC/BAS) Date: Mon, 19 Jan 2004 12:26:15 +0100 Subject: [EMBOSS] problem to retrieve sequences with seqret after indexing the data base Message-ID: Dear all, I have indexed a database with "dbifasta" and modified the ".embossrc" file: When I use the seqret command to retrieve the sequence, here is the error I got: $ seqret Database:NC_005126 Reads and writes (returns) sequences Error: Database Entry 'NC_005126' not found Error: Unable to read sequence 'Database:NC_005126' Died: seqret terminated: Bad value for option [sequence] and no prompt But this sequence is present in the database file... Do you know why I cannot find it ? Thank you very much for your help... Best regards Caroline. -------------- next part -------------- An HTML attachment was scrubbed... URL: From stefanielager at fastmail.ca Tue Jan 20 12:45:40 2004 From: stefanielager at fastmail.ca (Stefanie Lager) Date: Tue, 20 Jan 2004 07:45:40 -0500 (EST) Subject: [EMBOSS] Nexus format Message-ID: <400D22F4.00022B.54281@ns.interchange.ca> When i use seqret and output protein alignments in Nexus format it says "datatype=DNA missing=N" . Is it possible to make it recognice that the sequence is a protein sequence and not a DNA sequence? Stefanie _________________________________________________________________ http://fastmail.ca/ - Fast Secure Web Email for Canadians From J.Zuegg at griffith.edu.au Wed Jan 21 02:27:03 2004 From: J.Zuegg at griffith.edu.au (Johannes Zuegg) Date: Wed, 21 Jan 2004 12:27:03 +1000 Subject: [EMBOSS] JEmboss on AFS Message-ID: Dear folks, Does someone have a patch or solution to make JEmboss able to access a AFS directories ? Or at least know the best place to look at (besides openAFS), to include a corresponding AFS-token code into jembossctl.c Cheers Johannes ----------------------------------------------------------------------- Dr. Johannes Zuegg Computational Research Specialist Research Computing Services, INS Nathan Campus, Griffith University 170 Kessels Road Brisbane, QLD 4111, Australia Tel: +61-[0]7-3875 6603 Fax: +61-[0]7-3875 6650 EMail: J.Zuegg at griffith.edu.au ----------------------------------------------------------------------- From simon.andrews at bbsrc.ac.uk Wed Jan 21 09:13:51 2004 From: simon.andrews at bbsrc.ac.uk (simon andrews (BI)) Date: Wed, 21 Jan 2004 09:13:51 -0000 Subject: [EMBOSS] Making Jemboss available to all Message-ID: <2DC41140A89ED411989D00508BDCD9ED01E28C7E@bi-exsrv1.iapc.bbsrc.ac.uk> I'm trying to install the Jemboss client in such a way that it's accessible to everyone on our site. For other applications I've done this by installing them on a network share which is visible to everyone and then getting them to run them from there. I can't get this to work with Jemboss though. The problem seems to be that I need to refer to the program location using a windows UNC path (\\server\share\Jemboss\run_jemboss.bat), rather than by using a mapped drive (X:\Jemboss\run_jemboss.bat). The latter method works fine, but this isn't an option when I've got to make this accessible to everyone. Using a UNC path seems to mess up the classpath so that Jemboss can't find the modules it needs. Having asked about this in a Java newsgroup it appears there may be an internal java function to locate the initial directory of the java application, rather than the current method of defining a classpath. Is there any way this could be implemented in Jemboss to allow for this kind of installation? The relevant thread can be found here: http://groups.google.com/groups?threadm=bujmqf%24k8t%241%40south.jnrs.ja.net Cheers Simon. -- Simon Andrews PhD Bioinformatics Dept The Babraham Institute simon.andrews at bbsrc.ac.uk +44 (0)1223 496463 From tcarver at rfcgr.mrc.ac.uk Wed Jan 21 14:31:36 2004 From: tcarver at rfcgr.mrc.ac.uk (Dr T. Carver) Date: Wed, 21 Jan 2004 14:31:36 +0000 (GMT) Subject: [EMBOSS] Making Jemboss available to all In-Reply-To: <2DC41140A89ED411989D00508BDCD9ED01E28C7E@bi-exsrv1.iapc.bbsrc.ac.uk> Message-ID: Hi Simon This isn't a problem I have encountered before. It may be useful if you provided the script. An alternative of course is just to set up a web launch page: http://www.rfcgr.mrc.ac.uk/Software/EMBOSS/Jemboss/install/deploy.html Regards Tim Carver MRC Rosalind Franklin Centre for Genomics Research Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SB, UK Tel: +44 1223 494500 Fax: +44 1223 494512 E-mail: tcarver at rfcgr.mrc.ac.uk Web: http://www.rfcgr.mrc.ac.uk On Wed, 21 Jan 2004, simon andrews (BI) wrote: > I'm trying to install the Jemboss client in such a way that it's accessible to everyone on our site. For other applications I've done this by installing them on a network share which is visible to everyone and then getting them to run them from there. I can't get this to work with Jemboss though. > > The problem seems to be that I need to refer to the program location using a windows UNC path (\\server\share\Jemboss\run_jemboss.bat), rather than by using a mapped drive (X:\Jemboss\run_jemboss.bat). The latter method works fine, but this isn't an option when I've got to make this accessible to everyone. Using a UNC path seems to mess up the classpath so that Jemboss can't find the modules it needs. > > Having asked about this in a Java newsgroup it appears there may be an internal java function to locate the initial directory of the java application, rather than the current method of defining a classpath. Is there any way this could be implemented in Jemboss to allow for this kind of installation? The relevant thread can be found here: > > http://groups.google.com/groups?threadm=bujmqf%24k8t%241%40south.jnrs.ja.net > > Cheers > > Simon. > > -- > Simon Andrews PhD > Bioinformatics Dept > The Babraham Institute > > simon.andrews at bbsrc.ac.uk > +44 (0)1223 496463 > From simon.andrews at bbsrc.ac.uk Wed Jan 21 15:01:34 2004 From: simon.andrews at bbsrc.ac.uk (simon andrews (BI)) Date: Wed, 21 Jan 2004 15:01:34 -0000 Subject: [EMBOSS] Making Jemboss available to all Message-ID: <2DC41140A89ED411989D00508BDCD9ED01E28C81@bi-exsrv1.iapc.bbsrc.ac.uk> > -----Original Message----- > From: Dr T. Carver [mailto:tcarver at rfcgr.mrc.ac.uk] > Subject: Re: [EMBOSS] Making Jemboss available to all > Tim - thanks for the reply. > This isn't a problem I have encountered before. > It may be useful if you provided the script. The launch script I'm using is just the standard jemboss.bat launch script which is included in the Jemboss download package. I'm linking to this script using a windows shortcut. The reason this doesn't just work is that when you create the shortcut it asks for a target and a "start in" directory. The target is no problem, but I can't use a UNC path as the directory to start in. This appears to be a limitation of the MS cmd shell: C:\>cd \\server\share '\\server\share' CMD does not support UNC paths as current directories. This then causes the jemboss.bat to fail as it includes the line: start javaw -classpath .;Jemboss.jar;JembossAlignment.jar;etc... Because the Jemboss directory isn't the same as ".", the classpath statement fails and Jemboss with the error "Program could not find the main class. Program will exit" I've tried substituting the . in the classpath for the full UNC path, and whilst this doesn't itself throw an error I still get the same error message as before when I try to run it. From the little information I've found it appears that the JRE itself doesn't allow UNC paths in a classpath statement (I'm not 100% sure about this though). As I said before, if I map \\server\share to X: then I can successfully run Jemboss either from a shortcut directly, or indirectly using X:\Jemboss\ in the classpath. This isn't an option sitewide though as there isn't a drive letter I can guarantee will be free. > An alternative of course is just to set up a web launch page: I've looked at that and that seems to be one way around this. The problem with this is that our site standard image currently doesn't include Java Web Start so I'd have to get that installed first. It would also mean that Jemboss wouldn't appear with all the other applications we've got set up. From emailfrom1 at yahoo.co.uk Wed Jan 21 19:16:07 2004 From: emailfrom1 at yahoo.co.uk (Email) Date: Wed, 21 Jan 2004 19:16:07 Subject: [EMBOSS] Addresses Message-ID: <20040121181527.42ABE7D898@mercury.hgmp.mrc.ac.uk> To my family, friends & business colleagues, If you are looking to send thousands of emails to people either in the UK and abroad, in order to promote your Internet business, don't waste your time searching the net for suitable companies, as many of them are a complete waste of time and money. I have found one that does what it says it does! To find out more, go to: http://uk.geocities.com/emailbusiness1 Regards John From maoj at mail.nih.gov Wed Jan 21 19:50:21 2004 From: maoj at mail.nih.gov (Jean Mao) Date: Wed, 21 Jan 2004 14:50:21 -0500 Subject: [EMBOSS] about trasfac database Message-ID: <11b701c3e057$cdb20b40$494de780@CIT.NIH.GOV> Does anyone know where I can download an older version of transfac db for free? Thanks. Jean From R-6-721447-21420248-2-9873-US2-8552FB77 at xmr3.com Thu Jan 22 05:07:53 2004 From: R-6-721447-21420248-2-9873-US2-8552FB77 at xmr3.com (International Scientific Communications, Inc.) Date: Thu, 22 Jan 2004 00:07:53 -0500 Subject: [EMBOSS] Laboratory Instrumentation News - January 2004 Message-ID: An HTML attachment was scrubbed... URL: From simon.andrews at bbsrc.ac.uk Thu Jan 22 10:01:45 2004 From: simon.andrews at bbsrc.ac.uk (simon andrews (BI)) Date: Thu, 22 Jan 2004 10:01:45 -0000 Subject: [EMBOSS] Solved: Making Jemboss available to all Message-ID: <2DC41140A89ED411989D00508BDCD9ED01E28C86@bi-exsrv1.iapc.bbsrc.ac.uk> Following a series of helpful emails from Tim Carver at RFCGR I've now managed to set up the Jemboss client so that it's accessible to a whole site from a Windows network share. If anyone is interested in doing this in the future I thought I'd summarise how I did it. These instructions detail how you would install Jemboss onto \\server\share First, download the Jemboss client from: ftp://ftp.rfcgr.mrc.ac.uk/pub/EMBOSS/Jemboss/Jemboss-current.zip Create the directory \\server\share\Jemboss and unzip the downloaded file into there. Open \\server\share\Jemboss\jemboss.bat in a text editor You need to edit the line which starts: start javaw -classpath .;Jemboss.jar;JembossAlignment.jar;axis.jar... You need to change the initial . to \\server\share\Jemboss and then prefix each of the xxxx.jar entries with \\server\share\Jemboss\ . The only entry you don't need to prefix is the very last one which defines the first class to launch. You will end up with a very long command which looks something like this: start javaw -classpath \\server\share\Jemboss;\\server\share\Jemboss\Jemboss.jar; ..snip.. \\server\share\Jemboss\grout.jar org.emboss.jemboss.Jemboss You now need to make the directory \\server\share\Jemboss\resources and copy into it an appropriate jemboss.properties file to connect to your Jemboss server. Details of how to construct the jemboss.properties file can be found here: http://www.rfcgr.mrc.ac.uk/Software/EMBOSS/Jemboss/install/properties.html Finally, to run the program easily you can create a shortcut to the jemboss.bat file. It's also a good idea when creating the shortcut to go into its properties and under the Shortcut tab change the Run variable to "Minimised". If you don't do this you get a brief flash of a DOS window when you launch Jemboss, and then a wait until the first jemboss window appears. We found that our users got impatient in this time and clicked the link again. From matovue at hotmail.com Thu Jan 22 11:00:58 2004 From: matovue at hotmail.com (Enock Matovu) Date: Thu, 22 Jan 2004 11:00:58 +0000 Subject: [EMBOSS] Problem with emboss Message-ID: An HTML attachment was scrubbed... URL: From idrummon at receptor.mgh.harvard.edu Thu Jan 22 13:11:56 2004 From: idrummon at receptor.mgh.harvard.edu (Iain Drummond) Date: Thu, 22 Jan 2004 08:11:56 -0500 Subject: [EMBOSS] Problem with emboss In-Reply-To: Message-ID: you might need to install the libraries themselves if they are not in /usr/local/lib or something like that. look at the library requirements for emboss: http://www.hgmp.mrc.ac.uk/Software/EMBOSS/Doc/Admin_guide/adminguide/node3.h tml#SECTION00330000000000000000 Also try looking at your login profile and be sure that you have defined the environmental variables that tells emboss where to find the library: i'm using tcsh on mac os x setenv PLPLOT_LIB "/usr/local/lib" its different for other unix shells it is also suggested to set the LD_LIBRARY_PATH environmental variable in your login file. one of these steps might help. good luck -- Iain Drummond, Ph.D. Assistant Professor Department of Medicine, Harvard Medical School and Renal Unit, Massachusetts General Hospital idrummond at partners.org idrummon at receptor.mgh.harvard.edu Lab Home Page: http://danio.mgh.harvard.edu > From: "Enock Matovu" > Date: Thu, 22 Jan 2004 11:00:58 +0000 > To: emboss at embnet.org > Subject: [EMBOSS] Problem with emboss > > we have installed emboss. But when we type in any command such as wossname, he > replies wossname: error while loading shared libraries: libnuclesu.so.0: > cannot > > open shared object file: no such file or directory > > What shall we do to overcome this? We are real amateurs with linux and all > stuff > > Regards > > > Enock Matovu, > Livestock Health Research Institute > P. O. Box 96 Tororo > Uganda > +256 77 550 226 > > > The new MSN 8: smart spam protection and > 2 months FREE* From Sean.Maceachern at dpi.vic.gov.au Fri Jan 23 05:42:12 2004 From: Sean.Maceachern at dpi.vic.gov.au (Sean.Maceachern at dpi.vic.gov.au) Date: Fri, 23 Jan 2004 16:42:12 +1100 Subject: [EMBOSS] Coderet Message-ID: Hello, I am trying to use coderet to extract cds from some genbank flat files. I am running into a problem regarding the desriptor line in the output fasta files. eg) >nm_000367_cds_1 ATGGATGGTACAAGAACTTCACTTGACATTGAAGAGTACTCGGATACTGAGGTACAGAAA AACCAAGTACTAACTCTGGAAGAATGGCAAGACAAGTGGGTGAACGGCAAGACTGCTTTT I was hoping someone would be able to tell me how I can change the descriptor line from the generic output above (nm_000367_cds_1) to include the GI : ID form the flat file? I also think it would be a good idea if the id could be followed by a definition line to make the output more closely resemble the output from NCBI. eg) >gi|4507652 Homo sapiens thiopurine S-methyltransferase (TPMT), mRNA ATGGATGGTACAAGAACTTCACTTGACATTGAAGAGTACTCGGATACTGAGGTACAGAAA AACCAAGTACTAACTCTGGAAGAATGGCAAGACAAGTGGGTGAACGGCAAGACTGCTTTT Is there anyway to currently do this using the existing options? I am mostly interested in changing the output from the (nm _ ID) to the (gi | ID) but I think the deffinition line would also be useful. I'm assuming that it shouldn't be too hard as all of this information exists in the flat file, which looks fairly easy to parse. If there is no way to currently do this I would appreciate it if someone could suggest where and if I could modify the existing script to complete the above. Thanks, Sean MacEachern From henrikki.almusa at helsinki.fi Fri Jan 23 06:36:54 2004 From: henrikki.almusa at helsinki.fi (Henrikki Almusa) Date: Fri, 23 Jan 2004 08:36:54 +0200 Subject: [EMBOSS] Coderet In-Reply-To: References: Message-ID: <200401230836.54223.henrikki.almusa@helsinki.fi> On Friday 23 January 2004 07:42, Sean.Maceachern at dpi.vic.gov.au wrote: > Hello, > > I am trying to use coderet to extract cds from some genbank flat files. I > am running into a problem regarding the desriptor line in the output fasta > files. > > eg) > > >nm_000367_cds_1 > ATGGATGGTACAAGAACTTCACTTGACATTGAAGAGTACTCGGATACTGAGGTACAGAAA > AACCAAGTACTAACTCTGGAAGAATGGCAAGACAAGTGGGTGAACGGCAAGACTGCTTTT > > I was hoping someone would be able to tell me how I can change the > descriptor line from the generic output above (nm_000367_cds_1) to include > the GI : ID form the > flat file? I also think it would be a good idea if the id could be followed > by a definition line to make the output more closely resemble the output > from NCBI. You can change the sequence format with -osformat option (in all emboss programs which outputs sequences). Probably the right format is "ncbi". If it isn't read the page on emboss web site in User Documantation -> Sequence format. That will list all available formats. Here to help, -- Henrikki Almusa From David.Bauer at SCHERING.DE Fri Jan 23 07:16:00 2004 From: David.Bauer at SCHERING.DE (David.Bauer at SCHERING.DE) Date: Fri, 23 Jan 2004 08:16:00 +0100 Subject: [EMBOSS] Coderet Message-ID: Hi, the problem is that -osformat ncbi with coderet creates the NCBI pipe notation but it does not parse the GI number from the CDS feature. I think it's a good idea to transfer more tags from the CDS feature into the ID line of coderet. I'm not sure if /gene, /protein_id and /product are mandatory for CDS. But if they are there it would be nice to transfer them into the description of the extracted cds and/or mRNA sequence. David. Henrikki Almusa An: Sean.Maceachern at dpi.vic.gov.au Gesendet von: Kopie: emboss at embnet.org owner-emboss at hgmp. Thema: Re: [EMBOSS] Coderet mrc.ac.uk 23.01.04 07:36 On Friday 23 January 2004 07:42, Sean.Maceachern at dpi.vic.gov.au wrote: > Hello, > > I am trying to use coderet to extract cds from some genbank flat files. I > am running into a problem regarding the desriptor line in the output fasta > files. > > eg) > > >nm_000367_cds_1 > ATGGATGGTACAAGAACTTCACTTGACATTGAAGAGTACTCGGATACTGAGGTACAGAAA > AACCAAGTACTAACTCTGGAAGAATGGCAAGACAAGTGGGTGAACGGCAAGACTGCTTTT > > I was hoping someone would be able to tell me how I can change the > descriptor line from the generic output above (nm_000367_cds_1) to include > the GI : ID form the > flat file? I also think it would be a good idea if the id could be followed > by a definition line to make the output more closely resemble the output > from NCBI. You can change the sequence format with -osformat option (in all emboss programs which outputs sequences). Probably the right format is "ncbi". If it isn't read the page on emboss web site in User Documantation -> Sequence format. That will list all available formats. Here to help, -- Henrikki Almusa From sinnottj at cs.man.ac.uk Mon Jan 26 15:24:33 2004 From: sinnottj at cs.man.ac.uk (James Sinnott) Date: Mon, 26 Jan 2004 15:24:33 +0000 Subject: [EMBOSS] Problems converting sequences with seqret Message-ID: <200401261524.33620.sinnottj@cs.man.ac.uk> Hi, I'm building an application that should allow the user to work with a set of sequences in an arbitrary format (e.g. FastA) regardless of the formats the sequences may actually be stored in (clustal, nexus, msf, etc.) I need to be able to convert sequences to and back-from the users' desired format behind the scenes, and seqret seems to be the most suitable tool for this. However, I've found a problem in that seqret seems to output some sequence formats that it cannot subsequently re-read! As an example, I converted a set of FastaA files into clustal, phylip, msf, & nexus formats and then tried to re-convert the files back into FastA format. The clustal & phylip files all worked OK, but several of the msf and all of the nexus files were found to be unreadable by seqret when trying to re-convert them. Am I doing anything wrong? Is this a common issue with seqret? Any help would be gratefully accepted! Best regards, James Sinnott. From simon.andrews at bbsrc.ac.uk Mon Jan 26 16:03:44 2004 From: simon.andrews at bbsrc.ac.uk (simon andrews (BI)) Date: Mon, 26 Jan 2004 16:03:44 -0000 Subject: [EMBOSS] Problems converting sequences with seqret Message-ID: <2DC41140A89ED411989D00508BDCD9ED01E28C8D@bi-exsrv1.iapc.bbsrc.ac.uk> > -----Original Message----- > From: James Sinnott [mailto:sinnottj at cs.man.ac.uk] > Sent: 26 January 2004 15:25 > To: emboss at embnet.org > Subject: [EMBOSS] Problems converting sequences with seqret > > > However, I've found a problem in that seqret seems to output > some sequence formats that it cannot subsequently re-read! > > several of the msf and all of the nexus files were found > to be unreadable by seqret when trying to re-convert them. There looks to be a bug in seqret. I can't reproduce this with msf files (may just be the data I was using), but certainly there's something wrong with the nexus parser. If you use the dna.msf file included with EMBOSS as a test case $ uname -sr Linux 2.4.22-1.2149.nptlsmp $ embossversion Writes the current EMBOSS version number 2.8.0 $ seqret /usr/local/share/EMBOSS/test/data/dna.msf nexus::nexus.txt Reads and writes (returns) sequences $ seqret nexus::nexus.txt fasta::stdout Reads and writes (returns) sequences Segmentation fault Running a debug on the second process doesn't show much. The matrix seems to be read OK, but then it segfaults. An strace on the process doesn't show any system calls going awry so I'm not sure what's going wrong. Certainly something to look at... Simon. -- Simon Andrews PhD Bioinformatics Dept The Babraham Institute simon.andrews at bbsrc.ac.uk +44 (0)1223 496463 From Sean.Maceachern at dpi.vic.gov.au Tue Jan 27 01:17:37 2004 From: Sean.Maceachern at dpi.vic.gov.au (Sean.Maceachern at dpi.vic.gov.au) Date: Tue, 27 Jan 2004 12:17:37 +1100 Subject: [EMBOSS] Coderet Message-ID: Thanks for the replies, I have tried a number of the -osformat options before I posted my original request. What I was hoping to find out was how to replicate the NCBI output. The current -osformat ncbi option seems to replicate NCBI's cds output in fasta format only and does not replicate the descriptor line very well. I was thinking that as the file usually comes from an NCBI flat file that it would be good if the output resembled the NCBI output that is provided on the web (cds links and eutils) to allow sequences from both the net and coderet to be combined in the same fasta file. I have not done any programming in c++ so I was hoping that someone might be able how to suggest how I can get the output from coderet to resemble that of NCBI's I think it could be done by parsing the sections in BOLD from the first few lines of the feature table. LOCUS NM_000367 2742 bp mRNA linear PRI 31-OCT-2000 DEFINITION Homo sapiens thiopurine S-methyltransferase (TPMT), mRNA. ACCESSION NM_000367 VERSION NM_000367.1 GI:4507652 KEYWORDS . SOURCE Homo sapiens (human) ie) >gi|4507652 Homo sapiens thiopurine S-methyltransferase (TPMT), mRNA ATGGATGGTACAAGAACTTCACTTGACATTGAAGAGTACTCGGATACTGAGGTACAGAAA AACCAAGTACTAACTCTGGAAGAATGGCAAGACAAGTGGGTGAACGGCAAGACTGCTTTT Does anyone know if this already exists in a coderet option or how I would be able to modfiy this in the original script? Thanks Sean MacEachern David.Bauer at SCHERING.DE on 23/01/2004 06:16:00 PM To: henrikki.almusa at helsinki.fi cc: emboss at embnet.org, Sean.Maceachern at dpi.vic.gov.au Subject: Re: [EMBOSS] Coderet Hi, the problem is that -osformat ncbi with coderet creates the NCBI pipe notation but it does not parse the GI number from the CDS feature. I think it's a good idea to transfer more tags from the CDS feature into the ID line of coderet. I'm not sure if /gene, /protein_id and /product are mandatory for CDS. But if they are there it would be nice to transfer them into the description of the extracted cds and/or mRNA sequence. David. Henrikki Almusa An: Sean.Maceachern at dpi.vic.gov.au Gesendet von: Kopie: emboss at embnet.org owner-emboss at hgmp. Thema: Re: [EMBOSS] Coderet mrc.ac.uk 23.01.04 07:36 On Friday 23 January 2004 07:42, Sean.Maceachern at dpi.vic.gov.au wrote: > Hello, > > I am trying to use coderet to extract cds from some genbank flat files. I > am running into a problem regarding the desriptor line in the output fasta > files. > > eg) > > >nm_000367_cds_1 > ATGGATGGTACAAGAACTTCACTTGACATTGAAGAGTACTCGGATACTGAGGTACAGAAA > AACCAAGTACTAACTCTGGAAGAATGGCAAGACAAGTGGGTGAACGGCAAGACTGCTTTT > > I was hoping someone would be able to tell me how I can change the > descriptor line from the generic output above (nm_000367_cds_1) to include > the GI : ID form the > flat file? I also think it would be a good idea if the id could be followed > by a definition line to make the output more closely resemble the output > from NCBI. You can change the sequence format with -osformat option (in all emboss programs which outputs sequences). Probably the right format is "ncbi". If it isn't read the page on emboss web site in User Documantation -> Sequence format. That will list all available formats. Here to help, -- Henrikki Almusa From MAILER-DAEMON at mx2.radiant.net Tue Jan 27 14:50:31 2004 From: MAILER-DAEMON at mx2.radiant.net (MAILER-DAEMON at mx2.radiant.net) Date: Tue, 27 Jan 2004 06:50:31 -0800 Subject: [EMBOSS] Undeliverable mail: Mail Delivery System Message-ID: Failed to deliver to '' Virus(es) found. file.pif is infected with W32/Mydoom at MM Viruses: 1 Trojans: 0 Jokes: 0 Tests: 0 Captured by McAfee antivirus plugin running on Radiant Communications Mail Server -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: text/rfc822-headers Size: 480 bytes Desc: not available URL: From postmaster at fwncism1.leidenuniv.nl Tue Jan 27 16:12:06 2004 From: postmaster at fwncism1.leidenuniv.nl (postmaster at fwncism1.leidenuniv.nl) Date: Tue, 27 Jan 2004 17:12:06 +0100 (CET) Subject: [EMBOSS] VIRUS IN YOUR MAIL Message-ID: <20040127161206.DD3CA3419E@fwncism1.leidenuniv.nl> V I R U S A L E R T Our viruschecker found the W32/Mydoom at MM virus(es) in your email to the following recipient(s): -> g.wezel at chem.leidenuniv.nl Please check your system for viruses, or ask your system administrator to do so. For your reference, here are the headers from your email: ------------------------- BEGIN HEADERS ----------------------------- Received: by fwncism1.leidenuniv.nl (Postfix, from userid 299) id 51DA134134; Tue, 27 Jan 2004 17:11:58 +0100 (CET) Received: from embnet.org (joe.cobi.uni-stuttgart.de [129.69.143.252]) by fwncism1.leidenuniv.nl (Postfix) with ESMTP id 6DBB4340C8 for ; Tue, 27 Jan 2004 17:11:57 +0100 (CET) From: emboss at embnet.org To: g.wezel at chem.leidenuniv.nl Subject: Error Date: Tue, 27 Jan 2004 17:09:41 +0100 MIME-Version: 1.0 Content-Type: multipart/mixed; boundary="----=_NextPart_000_0004_D5A65CDE.211AEF48" X-Priority: 3 X-MSMail-Priority: Normal Message-Id: <20040127161157.6DBB4340C8 at fwncism1.leidenuniv.nl> X-Spam-Status: No, hits=-4.7 required=5.0 tests=BAYES_00,MISSING_MIMEOLE,NO_REAL_NAME,PRIORITY_NO_NAME version=2.52 X-Spam-Level: X-Spam-Checker-Version: SpamAssassin 2.52 (1.174.2.8-2003-03-24-exp) -------------------------- END HEADERS ------------------------------ From MAILER-DAEMON at mccinet.ru Wed Jan 28 14:31:08 2004 From: MAILER-DAEMON at mccinet.ru (MAILER-DAEMON at mccinet.ru) Date: Wed, 28 Jan 2004 17:31:08 +0300 Subject: [EMBOSS] Undeliverable mail: test Message-ID: Failed to deliver to '' LOCAL module(account leo) reports: account is full (quota exceeded) -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: text/rfc822-headers Size: 453 bytes Desc: not available URL: From igor at elbrus.caltech.edu Wed Jan 28 17:59:44 2004 From: igor at elbrus.caltech.edu (Igor Antoshechkin) Date: Wed, 28 Jan 2004 09:59:44 -0800 (PST) Subject: [EMBOSS] needle Message-ID: Hi, I work for the C. elegans genomic database WormBase (www.wormbase.org) and would like to be able to run needle locally. I found it as a part of the EMBOSS package, but I'd really prefer not to install other programs that the package contains. I'm wondering if there is a place where I can get just needle? Thank you very much, Igor. From pmr at ebi.ac.uk Wed Jan 28 18:08:07 2004 From: pmr at ebi.ac.uk (pmr at ebi.ac.uk) Date: Wed, 28 Jan 2004 18:08:07 -0000 (GMT) Subject: [EMBOSS] needle standalone In-Reply-To: References: Message-ID: <1469.81.78.198.23.1075313287.squirrel@webmail.ebi.ac.uk> Hi Igor, > I work for the C. elegans genomic database WormBase (www.wormbase.org) and > would like to be able to run needle locally. I found it as a part of the > EMBOSS package, but I'd really prefer not to install other programs that > the package contains. I'm wondering if there is a place where I can get > just needle? You will need to install EMBOSS, and keep various parts installed, for needle to work. I have successfully installed single EMBOSS applications standalone, and can provide details if needed, but it is "not supported" ... and not recommended. For needle, for example, you need to provide the comparison matrix files in a suitable directory, and point your copy of needle to the needle.acd file and database definitions. This can be done through the emboss.defaults file (which has to be somewhere needle will find it) or in .embossrc (for one user only). A non-tivial undertaking. Hope this helps, Peter Rice From mad at biol.unlp.edu.ar Thu Jan 29 15:53:12 2004 From: mad at biol.unlp.edu.ar (=?ISO-8859-1?Q?Mart=EDn_Sarachu?=) Date: Thu, 29 Jan 2004 12:53:12 -0300 Subject: [EMBOSS] wEMBOSS-1.0.2 Message-ID: <40192C68.8000303@biol.unlp.edu.ar> wEMBOSS-1.0.2 is out! Features added + some bugs fixed, find all changes in changeLog file inside the distribution. Download it from http://www.ar.embnet.org/programas/wEMBOSS/wEMBOSS-1.0.2.tar.gz wEMBOSS site @ http://www.ar.embnet.org/programas/wEMBOSS Regards, Marc Colet & Martin Sarachu -- Mart?n Sarachu mad at biol.unlp.edu.ar EMBNet Argentina http://www.ar.embnet.org From account.bouncer at openwave.com Thu Jan 29 16:06:13 2004 From: account.bouncer at openwave.com (Account Bouncer (auto reply)) Date: Thu, 29 Jan 2004 08:06:13 -0800 Subject: [EMBOSS] Re: Test In-Reply-To: <20040129160820.KSBN21479.mm-ismta4.bizmailsrvcs.net@embnet.org> Message-ID: <20040129160613.AAA25019@nome.software.com> This person/account is unknown at Software.com. There is no forwarding information. Postmaster -------------- next part -------------- An embedded message was scrubbed... From: emboss at embnet.org Subject: Test Date: Thu, 29 Jan 2004 19:08:28 +0300 Size: 2026 URL: From postmaster at msg2s.netvision.net.il Thu Jan 29 18:38:45 2004 From: postmaster at msg2s.netvision.net.il (Internet Mail Delivery) Date: Thu, 29 Jan 2004 20:38:45 +0200 (IST) Subject: [EMBOSS] Delivery Notification: Delivery has failed Message-ID: <0HS9005B9L4L9S@msg2s.netvision.net.il> This report relates to a message you sent with the following header fields: Return-path: Received: from ims-ms-daemon.msg2s.netvision.net.il by msg2s.netvision.net.il (iPlanet Messaging Server 5.2 HotFix 1.14 (built Mar 18 2003)) id <0HS9005B6L4L9S at msg2s.netvision.net.il> (original mail from emboss at embnet.org); Thu, 29 Jan 2004 20:38:45 +0200 (IST) Received: from mxin3.netvision.net.il ([194.90.9.23]) by msg2s.netvision.net.il (iPlanet Messaging Server 5.2 HotFix 1.14 (built Mar 18 2003)) with ESMTP id <0HS9004L5L4KYO at msg2s.netvision.net.il>; Thu, 29 Jan 2004 20:38:45 +0200 (IST) Received: from mx30.netvision.net.il ([194.90.1.53]) by mxin3.netvision.net.il (iPlanet Messaging Server 5.2 HotFix 1.14 (built Mar 18 2003)) with ESMTP id <0HS900EW8L491S at mxin3.netvision.net.il> for sandra at netvision.net.il (ORCPT sandra at netvision.net.il); Thu, 29 Jan 2004 20:38:33 +0200 (IST) Received: from embnet.org (200.162.217.170.sao.ajato.com.br [200.162.217.170]) by mx30.netvision.net.il (8.12.8/8.12.2) with ESMTP id i0TIeqTa012622 for ; Thu, 29 Jan 2004 20:40:54 +0200 (IST) Date: Thu, 29 Jan 2004 16:38:51 -0200 From: emboss at embnet.org Subject: hello To: sandra at netvision.net.il Message-id: <200401291840.i0TIeqTa012622 at mx30.netvision.net.il> MIME-version: 1.0 Content-type: multipart/mixed; boundary="Boundary_(ID_MCGMh8uB1c9/89fxu4D5Cg)" X-Priority: 3 X-MSMail-priority: Normal Your message cannot be delivered to the following recipients: Recipient address: sandra at netvision.net.il Original address: sandra at netvision.net.il Reason: Over quota -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: text/rfc822-headers Size: 1354 bytes Desc: not available URL: From karin.lagesen at labmed.uio.no Fri Jan 30 14:34:12 2004 From: karin.lagesen at labmed.uio.no (Karin Lagesen) Date: Fri, 30 Jan 2004 15:34:12 +0100 Subject: [EMBOSS] matcher output Message-ID: <20040130153412.E6096@uracil.uio.no> Hi! I am trying to use matcher to align some sequences. I would however like to get the whole sequences outputted. I think that this is what the option -aglobal3 is for. I have tried matcher teste testb -outfile test.matcher -aglobal3 1 in various formats, including with = signs, with and without outfile and with True instead of 1 too, but I cannot see any difference. I am trying this with sequences where I should see a difference. Does -aglobal3 do what I think it does, or isn't there an option to matcher that does what I want it to do? In that case, is there a different program out there which does what I need (i.e. a local alignment of two sequences where the rest of the sequences are matched together too). TIA, Karin -- Karin Lagesen, PhD student karin.lagesen at labmed.uio.no From pmr at ebi.ac.uk Fri Jan 30 14:59:27 2004 From: pmr at ebi.ac.uk (Peter Rice) Date: Fri, 30 Jan 2004 14:59:27 +0000 Subject: [EMBOSS] matcher output In-Reply-To: <20040130153412.E6096@uracil.uio.no> References: <20040130153412.E6096@uracil.uio.no> Message-ID: <401A714F.3010908@ebi.ac.uk> Karin Lagesen wrote: > I am trying to use matcher to align some sequences. I would however > like to get the whole sequences outputted. I think that this is what > the option -aglobal3 is for. I have tried > > matcher teste testb -outfile test.matcher -aglobal3 1 > > Does -aglobal3 do what I think it does, or isn't there an option to > matcher that does what I want it to do? In that case, is there a > different program out there which does what I need (i.e. a local > alignment of two sequences where the rest of the sequences are matched > together too). Ouch ... local and global alignments are quite different (in biological terms, and in what the program has stored after the calculation). With a global alignment, the ends of the sequences are included in the output (ends beyond the overlap with the other sequence). EMBOSS should allow you to turn off these ends with -noaglobal. However ... checking the code shows that the most recent rewrite of the alignment display code has lost this capability. It will be restored for 2.9.0 because for tasks like finding an exon in a genomic sequence there can be a lot of extra bases to be displayed in one of the sequences. For local alignments, there is a good reason why you cannot display the rest ... it has not been aligned. So, what are the alternatives? matcher will not align the whole sequences, but it does implement the Waterman-Eggert algorithm for next-best local alignment, so you can run "matcher -alternatives 10" to find the best 10 local alignments. Very helpful with multi-domain proteins, or matching mRNA/cDNA/EST to genomic sequence. supermatcher will do a word-based alignment and try to align the remaining regions - but a word-based alignment requires perfect identity. Someone (us, for example :-) could try to write an iterative alignment that realigns the remaining regions of sequence with further local alignments but I doubt whether it would be really useful. Hope this helps, Peter Rice From MAILER-DAEMON at gi.k.u-tokyo.ac.jp Fri Jan 30 17:37:11 2004 From: MAILER-DAEMON at gi.k.u-tokyo.ac.jp (MAILER-DAEMON at gi.k.u-tokyo.ac.jp) Date: 30 Jan 2004 17:37:11 -0000 Subject: [EMBOSS] failure notice Message-ID: <20040130173328.A3FD47D9D5@mercury.hgmp.mrc.ac.uk> Hi. This is the qmail-send program at gi.k.u-tokyo.ac.jp. I'm afraid I wasn't able to deliver your message to the following addresses. This is a permanent error; I've given up. Sorry it didn't work out. : Sorry, no mailbox here by that name. (#5.1.1) --- Below this line is a copy of the message. Return-Path: Received: (qmail 5456 invoked from network); 30 Jan 2004 17:37:10 -0000 Received: from unknown (HELO embnet.org) (137.122.147.102) by ursa.gi.k.u-tokyo.ac.jp with SMTP; 30 Jan 2004 17:37:10 -0000 From: emboss at embnet.org To: dan at gi.k.u-tokyo.ac.jp Subject: Date: Fri, 30 Jan 2004 12:46:09 -0500 MIME-Version: 1.0 Content-Type: multipart/mixed; boundary="----=_NextPart_000_0000_7A7FB7D9.E0B92503" X-Priority: 3 X-MSMail-Priority: Normal This is a multi-part message in MIME format. ------=_NextPart_000_0000_7A7FB7D9.E0B92503 Content-Type: text/plain; charset="Windows-1252" Content-Transfer-Encoding: 7bit ? ?v1?%t?s???s!Y??U/Wn?r!]???tqR????HR??c??;???vA?X.???i???"?#??n?m???,??????ig*:rG?p??S?2????a&?#??V ?beb?9??w????[?"??????J????????D}sj??? ?WH?e??s,??~H?I?.?_{?K?6>???D?`?f? ??f??h?????#??K {???????p?t???kw?????dD`A]p>)?6Q ?????1???!????eJn? ?FCID?????&K??e}??????9? ??I#????)?Jp?g)?????tJ???E???????`.?N??M?>.?$I?~f???<^???K??4??jZ)}X????q?#&?????????}0?????No??#~???a?u??1??;C6?6k)j????u?X??yHJE8?Y??J^R?J>>?)~???}??$bn????XUKs.?(GC)??`{"????Ol??_??S8&^^??r)?s???*v?7&????#???P??*n?A??7_'9??y&?n????9N&?7??mM?J???y?}????!\? #????d?`(?\O?????G???[??^ 1$?9?t?????EH???$<)?/??;i]?x?{?'?):r??7n~??d???s???????????\???l[?e[??i??????e??mN%X???????BLR???lT??k?xf?3? 4?>??d??????p???*??5?????#3?????9?E?BRL?$&?/?RG?/j,?O???VM????????YL)6??C????'L???I??k?N%kR6???A??4??V???sZO?Z?$?#?._9?S??k???m$?????????? X??q??;?-??Z????PD?[?&?b???\")1t???q(8?Z?Ha??R?sI??(?&m??-?????7?????-X??{E1?????1r???G??? hxBYD????????I?!?n??j????XU4(j ?h?vS?)t?!dN??cZ? 5??X?#??WYO?????m!??:?aw?U?\???M\z1??1a???? C??k??7???U?3FE??(?V?)?)???Uvn ????i???h9 Bxk????}D?#ax??????p???????s#:????H??Y$?????K?I??go????meE$?!?)??dH?? ?T??v??c??Ix?????H?t??2U4p? ???H?gJ??y?YNz?J$??? j-????J,?6???I?S?I?}????K??F?V???#??>m?i???6p??0H: h??????K???_??o??????/R?A???????O?nEw?# ?p?1Cb\??9,8(??"???w?q?C???*D? ?K?#??.|??????H???S$?T??C????#?????C???????}P?9Qu?????iP??t?d?Q???XEhqt,??|[?D??????w#?x?{???j?V??&?n,?2?rO-?W??~8??`!?????0X??Z????ZD6?????MG5f?<(5>?????m??)?????h vp?W s?3?"?X??k?????Zj??a? ?:gJ???a???O?'YT?3U\??~?????|???'|?K?m????c???P7 4???x?7?w??/a??]6?s????)??????rHd?}??*??`9$???tJ.???Abb?t~??P??i?^y|???d?S?.o?? 7xq?&%6??Qk??M?|\?|,??HR??mS?g???B?s????tjE4?x?3?q\?P?;???l?ft4?h??BL ????.???}N???a?V? ScanMail for Microsoft Exchange has detected virus-infected attachment(s). Sender = owner-emboss at hgmp.mrc.ac.uk Recipient(s) = emboss at embnet.org Subject = [EMBOSS] failure notice Scanning time = 1/30/2004 6:33:57 PM Engine/Pattern = 6.810-1005/751 Action on virus found: The message body contains WORM_MYDOOM.A virus. ScanMail has deleted the message body. Warning to recipient. ScanMail has detected a virus. From ".BE.ADM.BE2307.SHG_GATEWAY" at schering.de Fri Jan 30 17:34:00 2004 From: ".BE.ADM.BE2307.SHG_GATEWAY" at schering.de (".BE.ADM.BE2307.SHG_GATEWAY" at schering.de) Date: Fri, 30 Jan 2004 18:34:00 +0100 Subject: Virus Alert - ScanMail for Lotus Notes --> [EMBOSS] failure notice Message-ID: The virus protection system has detected and removed a virus in your email. Date: 01/30/2004 06:34:00 PM 121: [EMBOSS] failure notice Virus: WORM_MYDOOM.A File: text.zip From: owner-emboss at hgmp.mrc.ac.uk To: emboss at embnet.org Action: Uncleanable, Quarantined; Scanned by ScanMail for Lotus Notes 2.51 with scanengine 6.510-1002 and patternfile lpt$vpn.751 From dsullivan at gradipore.com Fri Jan 30 21:16:43 2004 From: dsullivan at gradipore.com (Dan Sullivan) Date: Sat, 31 Jan 2004 08:16:43 +1100 Subject: [EMBOSS] Gradipore LongLife Precast Gels Message-ID: <017AE08058A1D3118A7B0008C70D6217033DA88F@GSYD_NT5> <> Please call me if you have any questions about your inquiry on our Precast gels. Regards, Dan Sullivan National Sales Manager (845)-235-2590 (Cell) (800)-947-4270 x 5139 (VM) (845)-896-0302 (Fax) email: dsullivan at gradipore.com Learn more: www.gradipore.com/lifescience/ This e-mail and any files transmitted with it are confidential and intended only for the use of the individual or entity to which they are addressed. If you are not the intended recipient of this e-mail, you must not disseminate, copy or otherwise use this information. If you have received this e-mail in error, please notify Gradipore immediately. Thank you. -------------- next part -------------- A non-text attachment was scrubbed... Name: Gradipore Web Cast.htm Type: application/octet-stream Size: 4487 bytes Desc: not available URL: