From gbottu at vub.ac.be Wed Feb 3 05:50:38 2010 From: gbottu at vub.ac.be (Guy Bottu) Date: Wed, 03 Feb 2010 11:50:38 +0100 Subject: [EMBOSS] final version of wEMBOSS out ! Message-ID: <4B6954FE.9020505@vub.ac.be> Dear users of wEMBOSS, We just released version 2.2 of wEMBOSS. It has a completely cleaned and debugged code and is (at least for some while) the final version. If you have already wEMBOSS, you should definitively upgrade. You can download it from http://wemboss.sourceforge.net/ Note that if your previous installation of wEMBOSS is version 2.0 or higher, you can do the installation very easily by recovering the yourAnswers file from the previous installation and doing : perl install.pl < yourAnswers Regards, Marc Colet and Guy Bottu, the wEMBOSS development team From ajb at ebi.ac.uk Mon Feb 8 10:27:46 2010 From: ajb at ebi.ac.uk (ajb at ebi.ac.uk) Date: Mon, 8 Feb 2010 15:27:46 -0000 (UTC) Subject: [EMBOSS] Mailing list, ftp server and wiki downtime Message-ID: <49775.86.26.12.63.1265642866.squirrel@webmail.ebi.ac.uk> OBF, who host our mailing lists, ftp server and the new wiki, need to move some of their hardware at short notice this week. This will involve downtime to the above services. They will not be able to give much notice and it may be as soon as tomorrow afternoon (Tuesday the 9th). The only visible change will be new IP addresses on all their servers and sites. The physical downtime should be no more than a few hours, however the DNS changes will take significantly longer to propagate through the internet. Alan From tmargus at ebc.ee Wed Feb 10 11:07:19 2010 From: tmargus at ebc.ee (=?iso-8859-1?Q?T=F5nu_Margus?=) Date: Wed, 10 Feb 2010 18:07:19 +0200 Subject: [EMBOSS] Installing emboss ends with an error (OSX 10.6 macport 1.8.2 ) Message-ID: <34380485-BE2D-4B75-852A-FFF6833C927B@ebc.ee> Hi! I tried to install emboss into my mac (OSX 10.6 snow leopard ) by using macport (1.8.2) but finished with an error. It seems to me that I tangled into missing library (probably libjpeg), but I am still not sure about it. I used command "locate" to see which libjpeg libraries are installed and it seems that they are there. locate libjpeg /Applications/VLC.app/Contents/MacOS/lib/libjpeg.7.dylib /System/Library/Frameworks/JavaVM.framework/Versions/1.6.0/Libraries/libjpeg.jnilib /System/Library/Tcl/8.4/Img1.4/libjpegtcl1.0.dylib /System/Library/Tcl/8.5/Img1.4/libjpegtcl1.0.dylib What I am missing, and how to overcome this probelme? The part of macport debug output is below. % sudo port -d install emboss Password: ................ deleted .............. make[3]: Nothing to be done for `all-am'. /bin/sh ../libtool --tag=CC --mode=link /usr/bin/gcc-4.2 -O2 -arch x86_64 -L/opt/local/lib -o aaindexextract aaindexextract.o ../nucleus/libnucleus.la ../ajax/libajaxg.la ../ajax/libajax.la ../plplot/libeplplot.la -lX11 -lm /bin/sh ../libtool --tag=CC --mode=link /usr/bin/gcc-4.2 -O2 -arch x86_64 -L/opt/local/lib -o abiview abiview.o ../nucleus/libnucleus.la ../ajax/libajaxg.la ../ajax/libajax.la ../plplot/libeplplot.la -lX11 -lm /usr/bin/gcc-4.2 -O2 -arch x86_64 -o .libs/aaindexextract aaindexextract.o -L/opt/local/lib ../nucleus/.libs/libnucleus.dylib ../ajax/.libs/libajaxg.dylib ../ajax/.libs/libajax.dylib ../plplot/.libs/libeplplot.dylib -lX11 -lm ld: library not found for -lX11 collect2: ld returned 1 exit status /usr/bin/gcc-4.2 -O2 -arch x86_64 -o .libs/abiview abiview.o -L/opt/local/lib ../nucleus/.libs/libnucleus.dylib ../ajax/.libs/libajaxg.dylib ../ajax/.libs/libajax.dylib ../plplot/.libs/libeplplot.dylib -lX11 -lm make[2]: *** [aaindexextract] Error 1 make[2]: *** Waiting for unfinished jobs.... ld: library not found for -lX11 collect2: ld returned 1 exit status make[2]: *** [abiview] Error 1 make[1]: *** [all-recursive] Error 1 make: *** [all-recursive] Error 1 Error: Target org.macports.build returned: shell command " cd "/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_ports_science_EMBOSS/work/EMBOSS-6.0.1" && /usr/bin/make -j2 all " returned error 2 DEBUG: Backtrace: shell command " cd "/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_ports_science_EMBOSS/work/EMBOSS-6.0.1" && /usr/bin/make -j2 all " returned error 2 while executing "command_exec build" (procedure "portbuild::build_main" line 9) invoked from within "$procedure $targetname" Warning: the following items did not execute (for EMBOSS): org.macports.activate org.macports.build org.macports.destroot org.macports.install Error: Status 1 encountered during processing. To report a bug, see Best Regards, T?nu Margus Department of bioinformatics Tartu University Riia 23, 51010 Estonia tel: +372 737637 www: http://bioinfo.ut.ee/ From haslam at embl.de Wed Feb 10 11:47:32 2010 From: haslam at embl.de (haslam) Date: Wed, 10 Feb 2010 16:47:32 +0000 Subject: [EMBOSS] Installing emboss ends with an error (OSX 10.6 macport 1.8.2 ) In-Reply-To: <34380485-BE2D-4B75-852A-FFF6833C927B@ebc.ee> References: <34380485-BE2D-4B75-852A-FFF6833C927B@ebc.ee> Message-ID: <39647B6D-3F49-4D2C-9D60-293543F1A962@embl.de> Hi, It looks like X11 is the culprit. Are you sure you have it installed? Also - if you upgraded or copied macports over from a previous install on Leopard its worth removing and reinstalling macports. It needs to be recompiled - this tripped me up when I upgraded a machine. On 10 Feb 2010, at 16:07, T?nu Margus wrote: > ld: library not found for -lX11 From ajb at ebi.ac.uk Wed Feb 10 11:58:40 2010 From: ajb at ebi.ac.uk (ajb at ebi.ac.uk) Date: Wed, 10 Feb 2010 16:58:40 -0000 (UTC) Subject: [EMBOSS] Installing emboss ends with an error (OSX 10.6 macport 1.8.2 ) In-Reply-To: <34380485-BE2D-4B75-852A-FFF6833C927B@ebc.ee> References: <34380485-BE2D-4B75-852A-FFF6833C927B@ebc.ee> Message-ID: <53687.86.26.12.63.1265821120.squirrel@webmail.ebi.ac.uk> Hello T?nu, That specific error shows that EMBOSS is unable to find the X11 (X windows) libraries. Usually X11 is an optional, rather than default, installation option on your Apple MacOSX installation DVD. See, for example, http://www.macworld.com/article/142454/2009/08/install_snow_leopard.html After installing x11 then, on the EMBOSS side, either do a fresh extraction of the code or type "make clean" and do the ./configure command again. If you have installed X11 and are getting that error then let us know. HTH Alan > Hi! > > I tried to install emboss into my mac (OSX 10.6 snow leopard ) by using > macport (1.8.2) but finished with an error. It seems to me that I tangled > into missing library (probably libjpeg), but I am still not sure about it. > I used command "locate" to see which libjpeg libraries are installed and > it seems that they are there. > > locate libjpeg > /Applications/VLC.app/Contents/MacOS/lib/libjpeg.7.dylib > /System/Library/Frameworks/JavaVM.framework/Versions/1.6.0/Libraries/libjpeg.jnilib > /System/Library/Tcl/8.4/Img1.4/libjpegtcl1.0.dylib > /System/Library/Tcl/8.5/Img1.4/libjpegtcl1.0.dylib > > What I am missing, and how to overcome this probelme? > The part of macport debug output is below. > > > % sudo port -d install emboss > Password: > > ................ deleted .............. > > make[3]: Nothing to be done for `all-am'. > /bin/sh ../libtool --tag=CC --mode=link /usr/bin/gcc-4.2 -O2 -arch > x86_64 -L/opt/local/lib -o aaindexextract aaindexextract.o > ../nucleus/libnucleus.la ../ajax/libajaxg.la ../ajax/libajax.la > ../plplot/libeplplot.la -lX11 -lm > /bin/sh ../libtool --tag=CC --mode=link /usr/bin/gcc-4.2 -O2 -arch > x86_64 -L/opt/local/lib -o abiview abiview.o ../nucleus/libnucleus.la > ../ajax/libajaxg.la ../ajax/libajax.la ../plplot/libeplplot.la -lX11 -lm > /usr/bin/gcc-4.2 -O2 -arch x86_64 -o .libs/aaindexextract aaindexextract.o > -L/opt/local/lib ../nucleus/.libs/libnucleus.dylib > ../ajax/.libs/libajaxg.dylib ../ajax/.libs/libajax.dylib > ../plplot/.libs/libeplplot.dylib -lX11 -lm > ld: library not found for -lX11 > collect2: ld returned 1 exit status > /usr/bin/gcc-4.2 -O2 -arch x86_64 -o .libs/abiview abiview.o > -L/opt/local/lib ../nucleus/.libs/libnucleus.dylib > ../ajax/.libs/libajaxg.dylib ../ajax/.libs/libajax.dylib > ../plplot/.libs/libeplplot.dylib -lX11 -lm > make[2]: *** [aaindexextract] Error 1 > make[2]: *** Waiting for unfinished jobs.... > ld: library not found for -lX11 > collect2: ld returned 1 exit status > make[2]: *** [abiview] Error 1 > make[1]: *** [all-recursive] Error 1 > make: *** [all-recursive] Error 1 > Error: Target org.macports.build returned: shell command " cd > "/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_ports_science_EMBOSS/work/EMBOSS-6.0.1" > && /usr/bin/make -j2 all " returned error 2 > DEBUG: Backtrace: shell command " cd > "/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_ports_science_EMBOSS/work/EMBOSS-6.0.1" > && /usr/bin/make -j2 all " returned error 2 > while executing > "command_exec build" > (procedure "portbuild::build_main" line 9) > invoked from within > "$procedure $targetname" > Warning: the following items did not execute (for EMBOSS): > org.macports.activate org.macports.build org.macports.destroot > org.macports.install > Error: Status 1 encountered during processing. > To report a bug, see > > > Best Regards, > T?nu Margus > > > Department of bioinformatics > Tartu University > Riia 23, 51010 > Estonia > > tel: +372 737637 > www: http://bioinfo.ut.ee/ > > > > > _______________________________________________ > EMBOSS mailing list > EMBOSS at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/emboss > From jeedward at yahoo.com Fri Feb 12 10:35:05 2010 From: jeedward at yahoo.com (John Edward) Date: Fri, 12 Feb 2010 07:35:05 -0800 (PST) Subject: [EMBOSS] Draft paper submission deadline is extended: BCBGC-10, Orlando, USA Message-ID: <388240.3903.qm@web45913.mail.sp1.yahoo.com> It would be highly appreciated if you could share this announcement with your colleagues, students and individuals whose research is in bioinformatics, computational biology, genomics, data-mining, and related areas. Draft paper submission deadline is extended: BCBGC-10, Orlando, USA The 2010 International Conference on Bioinformatics, Computational Biology, Genomics and Chemoinformatics (BCBGC-10) (website: http://www.PromoteResearch.org) will be held during 12-14 of July 2010 in Orlando, FL, USA. BCBGC is an important event in the areas of bioinformatics, computational biology, genomics and chemoinformatics and focuses on all areas related to the conference. The conference will be held at the same time and location where several other major international conferences will be taking place. The conference will be held as part of 2010 multi-conference (MULTICONF-10). MULTICONF-10 will be held during July 12-14, 2010 in Orlando, Florida, USA. The primary goal of MULTICONF is to promote research and developmental activities in computer science, information technology, control engineering, and related fields. Another goal is to promote the dissemination of research to a multidisciplinary audience and to facilitate communication among researchers, developers, practitioners in different fields.The following conferences are planned to be organized as part of MULTICONF-10. * International Conference on Artificial Intelligence and Pattern Recognition (AIPR-10) * International Conference on Automation, Robotics and Control Systems (ARCS-10) * International Conference on Bioinformatics, Computational Biology, Genomics and Chemoinformatics (BCBGC-10) * International Conference on Computer Communications and Networks (CCN-10) * International Conference on Enterprise Information Systems and Web Technologies (EISWT-10) * International Conference on High Performance Computing Systems (HPCS-10) * International Conference on Information Security and Privacy (ISP-10) * International Conference on Image and Video Processing and Computer Vision (IVPCV-10) * International Conference on Software Engineering Theory and Practice (SETP-10) * International Conference on Theoretical and Mathematical Foundations of Computer Science (TMFCS-10) MULTICONF-10 will be held at Imperial Swan Hotel and Suites. It is a full-service resort that puts you in the middle of the fun! Located 1/2 block south of the famed International Drive, the hotel is just minutes from great entertainment like Walt Disney World? Resort, Universal Studios and Sea World Orlando. Guests can enjoy free scheduled transportation to these theme parks, as well as spacious accommodations, outdoor pools and on-site dining ? all situated on 10 tropically landscaped acres. Here, guests can experience a full-service resort with discount hotel pricing in Orlando. We invite draft paper submissions. Please see the website http://www.PromoteResearch.org for more details. Sincerely John Edward From yasser at iastate.edu Fri Feb 12 10:56:07 2010 From: yasser at iastate.edu (Yasser El-Manzalawy) Date: Fri, 12 Feb 2010 09:56:07 -0600 (CST) Subject: [EMBOSS] CfP: Immunoinformatics and Computational Immunology Workshop (ICIW 2010) Message-ID: <75691211105420@webmail.iastate.edu> We apologize for multiple posting. It would be greatly appreciated if this announcement could be shared with individuals whose research interests include Immunoinformatics and Computational Immunology. Call for Papers Immunoinformatics and Computational Immunology Workshop (ICIW 2010) ******************************************************************* To be held in conjunction with the ACM International Conference on Bioinformatics and Computational Biology (ACM-BCB) (http://www.cse.buffalo.edu/ACM-BCB2010/), Niagara Falls, NY, U.S.A. August 2-4, 2010 http://ailab.cs.iastate.edu/iciw2010 Naturally emerging or reemerging diseases pose some of the most serious threats to human health. Computational methods are urgently needed for developing new vaccines, therapies, and models to improve our understanding of the immune system, and reliable tools for focusing experimental investigations. The workshop aims to bring together researchers in computer scientists, computational biologists, structural biologists, virologists, bacteriologists, immunologists, vaccinologists, and systems biologists to share research challenges, research results, methods, and advances in immunoinformatics and computational immunology. Topics of interest include, but are not limited to: - Structural Immunoinformatics - Epitope analysis and prediction - MHC-peptide binding site analysis and prediction - Immunoinformatics Databases, Knowledge Bases, Ontologies - Computational modeling of immune system - Analysis and prediction of minor histocompatibility antigens - Predictive models for organ transplantation - Immunogenomics - Vaccine design - Artificial immune systems and other biologically-inspired paradigms - Multi-agent based modeling of immune response - Allergenicity prediction - Gene expression changes in adaptive immune response - Comparative approaches to immunology Important Dates: **************** Deadline for submissions: March 1, 2010 Notification of acceptance: April 20, 2010 Camera-ready of accepted papers: May 5, 2010 Workshop date: August 2, 2010 Author Instructions: ******************** Authors should prepare a Portable Document Format (PDF) version of their full paper. Regular papers must be no longer than 10 pages, papers on evolving research and work in progress should be no longer than 5 pages, following the ACM two-column format for conference proceedings (http://www.acm.org/sigs/publications/proceedings-templates) All accepted papers will be included in a Workshop Proceedings to be published on line and included with the conference proceedings on the CD. Authors of selected papers will have an opportunity to extend their workshop papers for publication (subject to peer review) in Journal of Immunological Methods and Immunome Research Journal. Papers should be submitted electronically (in PDF form) through ?EasyChair? at: https://www.easychair.org/login.cgi?conf=iciw2010 Organizing committee: ********************* Vasant Honavar (Iowa State University, USA)) Morten Nielsen (Technical University of Denmark, Denmark) Yasser EL-Manzalawy (Iowa State University, USA) Program Committee (Tentative): ****************************** Katherine Buckley (University of Toronto, Canada) Anne De Groot (URI Institute for Immunology and Informatics, USA) Uri Hershberg (Yale University, USA) Can Kesmir (Utrecht University, Netherlands) Steven Kleinstein (Yale University, USA) Andrzej Kloczkowski (Iowa State University, USA) German Nudelman (Mount Sinai School of Medicine, USA) Bjoern Peters (La Jolla institute of allergy and immunology, USA) Nikolai Petrovsky (Flinders University, Australia) Natasa Przulj (University of California Irvine, USA) Julia Ponomarenko (University of California, San Diego, USA) Johannes Sollner (Emergentec biodevelopment GmbH, Austria) Changhui Yan (North Dakota State University, USA) Guanglan Zhang (Dana-Farber Cancer Institute, USA) -- Yasser EL-Manzalawy Artificial Intelligence Research Laboratory Center for Computational Intelligence, Learning, & Discovery Department of Computer Science 215 Atanasoff Hall Iowa State University Ames, Iowa 50011-1040 voice: (515) 294-7331 fax: (515) 294-0258 email: yasser at cs.iastate.edu Web: www.cs.iastate.edu/~yasser From jeedward at yahoo.com Mon Feb 22 12:20:32 2010 From: jeedward at yahoo.com (John Edward) Date: Mon, 22 Feb 2010 09:20:32 -0800 (PST) Subject: [EMBOSS] Call for papers: BCBGC-10, Orlando, USA, July 2010 Message-ID: <651300.81613.qm@web45912.mail.sp1.yahoo.com> It would be highly appreciated if you could share this announcement with your colleagues, students and individuals whose research is in bioinformatics, computational biology, genomics, data-mining, and related areas. Call for papers: BCBGC-10, Orlando, USA, July 2010 The 2010 International Conference on Bioinformatics, Computational Biology, Genomics and Chemoinformatics (BCBGC-10) (website: http://www.PromoteResearch.org ) will be held during 12-14 of July 2010 in Orlando, FL, USA. BCBGC is an important event in the areas of bioinformatics, computational biology, genomics and chemoinformatics and focuses on all areas related to the conference. The conference will be held at the same time and location where several other major international conferences will be taking place. The conference will be held as part of 2010 multi-conference (MULTICONF-10). MULTICONF-10 will be held during July 12-14, 2010 in Orlando, Florida, USA. The primary goal of MULTICONF is to promote research and developmental activities in computer science, information technology, control engineering, and related fields. Another goal is to promote the dissemination of research to a multidisciplinary audience and to facilitate communication among researchers, developers, practitioners in different fields. The following conferences are planned to be organized as part of MULTICONF-10. ? International Conference on Artificial Intelligence and Pattern Recognition (AIPR-10) ? International Conference on Automation, Robotics and Control Systems (ARCS-10) ? International Conference on Bioinformatics, Computational Biology, Genomics and Chemoinformatics (BCBGC-10) ? International Conference on Computer Communications and Networks (CCN-10) ? International Conference on Enterprise Information Systems and Web Technologies (EISWT-10) ? International Conference on High Performance Computing Systems (HPCS-10) ? International Conference on Information Security and Privacy (ISP-10) ? International Conference on Image and Video Processing and Computer Vision (IVPCV-10) ? International Conference on Software Engineering Theory and Practice (SETP-10) ? International Conference on Theoretical and Mathematical Foundations of Computer Science (TMFCS-10) MULTICONF-10 will be held at Imperial Swan Hotel and Suites. It is a full-service resort that puts you in the middle of the fun! Located 1/2 block south of the famed International Drive, the hotel is just minutes from great entertainment like Walt Disney World? Resort, Universal Studios and Sea World Orlando. Guests can enjoy free scheduled transportation to these theme parks, as well as spacious accommodations, outdoor pools and on-site dining ? all situated on 10 tropically landscaped acres. Here, guests can experience a full-service resort with discount hotel pricing in Orlando. We invite draft paper submissions. Please see the website http://www.PromoteResearch.org for more details. Sincerely John Edward From Perdeep.Mehta at STJUDE.ORG Mon Feb 22 18:21:38 2010 From: Perdeep.Mehta at STJUDE.ORG (Mehta, Perdeep) Date: Mon, 22 Feb 2010 17:21:38 -0600 Subject: [EMBOSS] restrict In-Reply-To: <4A8AD193.8050102@ebi.ac.uk> References: <4A8AD193.8050102@ebi.ac.uk> Message-ID: <6EAE916704479E4BB6AB5A133BA224F728A54626D5@SJMEMXMBS11.stjude.sjcrh.local> Hi, I want to use the "restrict" program in EMBOSS package to do a restriction digest of a nucleotide sequence. When I ran restrict, it threw the following error; EMBOSS An error in restrict.c at line 147: Cannot locate enzyme file. Run REBASEEXTRACT I believe this program should use a data file for restriction enzymes, Rebase. I noticed this is missing from our installation under ~/data/REBASE subdir. I just see a "dummyfile" there. I have a few questions on EMBOSS restriction analysis and will appreciate any ideas or thoughts on these. 1. What Rebase file we need to download to get "restrict" working? I tried but there are files with different formats. 2. Is there a maximum size limit of a nucleotide sequence that I can use? Can I use the whole Human genome or at least a full chromosome to digest with a particular restriction enzyme? 3. What program can give me the list of all possible fragments generated as well? Since I have not seen the output of "restrict", perhaps that is already doing that. Thanks for any suggestions. Perdeep Mehta Email Disclaimer: www.stjude.org/emaildisclaimer From david.bauer at bayerhealthcare.com Tue Feb 23 01:55:49 2010 From: david.bauer at bayerhealthcare.com (david.bauer at bayerhealthcare.com) Date: Tue, 23 Feb 2010 07:55:49 +0100 Subject: [EMBOSS] Antwort: restrict In-Reply-To: <6EAE916704479E4BB6AB5A133BA224F728A54626D5@SJMEMXMBS11.stjude.sjcrh.local> Message-ID: Hi, emboss-bounces at lists.open-bio.org schrieb am 23/02/2010 00:21:38: > I have a few questions on EMBOSS restriction analysis and will > appreciate any ideas or thoughts on these. > > 1. What Rebase file we need to download to get "restrict" working? I > tried but there are files with different formats. Go to the /pub/rebase dir on ftp.neb.com. Download the withrefm.xxx and proto.xxx files (xxx stands for the version number, just take the latest that's there) Run rebaseextract -infile withrefm.xxx -protofile proto.xxx This reformats the neb files for use with emboss. You should now see 4 files embossre.... in the REBASE directory > 2. Is there a maximum size limit of a nucleotide sequence that I can > use? Can I use the whole Human genome or at least a full chromosome > to digest with a particular restriction enzyme? I'm not sure about the whole genome but I have used it for individual chromosomes without problems. > 3. What program can give me the list of all possible fragments > generated as well? Since I have not seen the output of "restrict", > perhaps that is already doing that. You can run restrict with the option -fragments to get them. Hope this helps, David. From Perdeep.Mehta at STJUDE.ORG Tue Feb 23 10:04:33 2010 From: Perdeep.Mehta at STJUDE.ORG (Mehta, Perdeep) Date: Tue, 23 Feb 2010 09:04:33 -0600 Subject: [EMBOSS] Antwort: restrict In-Reply-To: References: <6EAE916704479E4BB6AB5A133BA224F728A54626D5@SJMEMXMBS11.stjude.sjcrh.local> Message-ID: <6EAE916704479E4BB6AB5A133BA224F728A54626D7@SJMEMXMBS11.stjude.sjcrh.local> Thank you, including Duleep and David Lapointe for the prompt responses and for describing it in complete detail. I got what I couldn't find going through REBASE website and looking into EMBOSS' web pages. Excuse me for my ignorance, where can I find a manual or a good documentation on the EMBOSS package. regards, perdeep From: david.bauer at bayerhealthcare.com [mailto:david.bauer at bayerhealthcare.com] Sent: Tuesday, February 23, 2010 12:56 AM To: Mehta, Perdeep Cc: emboss; emboss-bounces at lists.open-bio.org Subject: Antwort: [EMBOSS] restrict Hi, emboss-bounces at lists.open-bio.org schrieb am 23/02/2010 00:21:38: > I have a few questions on EMBOSS restriction analysis and will > appreciate any ideas or thoughts on these. > > 1. What Rebase file we need to download to get "restrict" working? I > tried but there are files with different formats. Go to the /pub/rebase dir on ftp.neb.com. Download the withrefm.xxx and proto.xxx files (xxx stands for the version number, just take the latest that's there) Run rebaseextract -infile withrefm.xxx -protofile proto.xxx This reformats the neb files for use with emboss. You should now see 4 files embossre.... in the REBASE directory > 2. Is there a maximum size limit of a nucleotide sequence that I can > use? Can I use the whole Human genome or at least a full chromosome > to digest with a particular restriction enzyme? I'm not sure about the whole genome but I have used it for individual chromosomes without problems. > 3. What program can give me the list of all possible fragments > generated as well? Since I have not seen the output of "restrict", > perhaps that is already doing that. You can run restrict with the option -fragments to get them. Hope this helps, David. ________________________________ Email Disclaimer: www.stjude.org/emaildisclaimer From hrh at fmi.ch Tue Feb 23 10:45:17 2010 From: hrh at fmi.ch (Hotz, Hans-Rudolf) Date: Tue, 23 Feb 2010 16:45:17 +0100 Subject: [EMBOSS] Antwort: restrict In-Reply-To: <6EAE916704479E4BB6AB5A133BA224F728A54626D7@SJMEMXMBS11.stjude.sjcrh.local> Message-ID: On 2/23/10 4:04 PM, "Mehta, Perdeep" wrote: > Thank you, including Duleep and David Lapointe for the prompt responses and > for describing it in complete detail. I got what I couldn't find going > through REBASE website and looking into EMBOSS' web pages. Excuse me for my > ignorance, where can I find a manual or a good documentation on the EMBOSS > package. Have you looked at the EMBOSS homepage? http://emboss.sourceforge.net/ where all the applications are nicely explained http://emboss.sourceforge.net/apps/release/6.2/emboss/apps/groups.html Hans > regards, > perdeep > > > From: david.bauer at bayerhealthcare.com [mailto:david.bauer at bayerhealthcare.com] > Sent: Tuesday, February 23, 2010 12:56 AM > To: Mehta, Perdeep > Cc: emboss; emboss-bounces at lists.open-bio.org > Subject: Antwort: [EMBOSS] restrict > > > Hi, > > emboss-bounces at lists.open-bio.org schrieb am 23/02/2010 00:21:38: > >> I have a few questions on EMBOSS restriction analysis and will >> appreciate any ideas or thoughts on these. >> >> 1. What Rebase file we need to download to get "restrict" working? I >> tried but there are files with different formats. > > Go to the /pub/rebase dir on ftp.neb.com. > Download the withrefm.xxx and proto.xxx files > (xxx stands for the version number, just take the latest that's there) > Run rebaseextract -infile withrefm.xxx -protofile proto.xxx > This reformats the neb files for use with emboss. You should now see > 4 files embossre.... in the REBASE directory > >> 2. Is there a maximum size limit of a nucleotide sequence that I can >> use? Can I use the whole Human genome or at least a full chromosome >> to digest with a particular restriction enzyme? > > I'm not sure about the whole genome but I have used it for individual > chromosomes without problems. > >> 3. What program can give me the list of all possible fragments >> generated as well? Since I have not seen the output of "restrict", >> perhaps that is already doing that. > > You can run restrict with the option -fragments to get them. > > Hope this helps, > David. > > ________________________________ > Email Disclaimer: www.stjude.org/emaildisclaimer > > _______________________________________________ > EMBOSS mailing list > EMBOSS at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/emboss From gbottu at vub.ac.be Wed Feb 3 10:50:38 2010 From: gbottu at vub.ac.be (Guy Bottu) Date: Wed, 03 Feb 2010 11:50:38 +0100 Subject: [EMBOSS] final version of wEMBOSS out ! Message-ID: <4B6954FE.9020505@vub.ac.be> Dear users of wEMBOSS, We just released version 2.2 of wEMBOSS. It has a completely cleaned and debugged code and is (at least for some while) the final version. If you have already wEMBOSS, you should definitively upgrade. You can download it from http://wemboss.sourceforge.net/ Note that if your previous installation of wEMBOSS is version 2.0 or higher, you can do the installation very easily by recovering the yourAnswers file from the previous installation and doing : perl install.pl < yourAnswers Regards, Marc Colet and Guy Bottu, the wEMBOSS development team From ajb at ebi.ac.uk Mon Feb 8 15:27:46 2010 From: ajb at ebi.ac.uk (ajb at ebi.ac.uk) Date: Mon, 8 Feb 2010 15:27:46 -0000 (UTC) Subject: [EMBOSS] Mailing list, ftp server and wiki downtime Message-ID: <49775.86.26.12.63.1265642866.squirrel@webmail.ebi.ac.uk> OBF, who host our mailing lists, ftp server and the new wiki, need to move some of their hardware at short notice this week. This will involve downtime to the above services. They will not be able to give much notice and it may be as soon as tomorrow afternoon (Tuesday the 9th). The only visible change will be new IP addresses on all their servers and sites. The physical downtime should be no more than a few hours, however the DNS changes will take significantly longer to propagate through the internet. Alan From tmargus at ebc.ee Wed Feb 10 16:07:19 2010 From: tmargus at ebc.ee (=?iso-8859-1?Q?T=F5nu_Margus?=) Date: Wed, 10 Feb 2010 18:07:19 +0200 Subject: [EMBOSS] Installing emboss ends with an error (OSX 10.6 macport 1.8.2 ) Message-ID: <34380485-BE2D-4B75-852A-FFF6833C927B@ebc.ee> Hi! I tried to install emboss into my mac (OSX 10.6 snow leopard ) by using macport (1.8.2) but finished with an error. It seems to me that I tangled into missing library (probably libjpeg), but I am still not sure about it. I used command "locate" to see which libjpeg libraries are installed and it seems that they are there. locate libjpeg /Applications/VLC.app/Contents/MacOS/lib/libjpeg.7.dylib /System/Library/Frameworks/JavaVM.framework/Versions/1.6.0/Libraries/libjpeg.jnilib /System/Library/Tcl/8.4/Img1.4/libjpegtcl1.0.dylib /System/Library/Tcl/8.5/Img1.4/libjpegtcl1.0.dylib What I am missing, and how to overcome this probelme? The part of macport debug output is below. % sudo port -d install emboss Password: ................ deleted .............. make[3]: Nothing to be done for `all-am'. /bin/sh ../libtool --tag=CC --mode=link /usr/bin/gcc-4.2 -O2 -arch x86_64 -L/opt/local/lib -o aaindexextract aaindexextract.o ../nucleus/libnucleus.la ../ajax/libajaxg.la ../ajax/libajax.la ../plplot/libeplplot.la -lX11 -lm /bin/sh ../libtool --tag=CC --mode=link /usr/bin/gcc-4.2 -O2 -arch x86_64 -L/opt/local/lib -o abiview abiview.o ../nucleus/libnucleus.la ../ajax/libajaxg.la ../ajax/libajax.la ../plplot/libeplplot.la -lX11 -lm /usr/bin/gcc-4.2 -O2 -arch x86_64 -o .libs/aaindexextract aaindexextract.o -L/opt/local/lib ../nucleus/.libs/libnucleus.dylib ../ajax/.libs/libajaxg.dylib ../ajax/.libs/libajax.dylib ../plplot/.libs/libeplplot.dylib -lX11 -lm ld: library not found for -lX11 collect2: ld returned 1 exit status /usr/bin/gcc-4.2 -O2 -arch x86_64 -o .libs/abiview abiview.o -L/opt/local/lib ../nucleus/.libs/libnucleus.dylib ../ajax/.libs/libajaxg.dylib ../ajax/.libs/libajax.dylib ../plplot/.libs/libeplplot.dylib -lX11 -lm make[2]: *** [aaindexextract] Error 1 make[2]: *** Waiting for unfinished jobs.... ld: library not found for -lX11 collect2: ld returned 1 exit status make[2]: *** [abiview] Error 1 make[1]: *** [all-recursive] Error 1 make: *** [all-recursive] Error 1 Error: Target org.macports.build returned: shell command " cd "/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_ports_science_EMBOSS/work/EMBOSS-6.0.1" && /usr/bin/make -j2 all " returned error 2 DEBUG: Backtrace: shell command " cd "/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_ports_science_EMBOSS/work/EMBOSS-6.0.1" && /usr/bin/make -j2 all " returned error 2 while executing "command_exec build" (procedure "portbuild::build_main" line 9) invoked from within "$procedure $targetname" Warning: the following items did not execute (for EMBOSS): org.macports.activate org.macports.build org.macports.destroot org.macports.install Error: Status 1 encountered during processing. To report a bug, see Best Regards, T?nu Margus Department of bioinformatics Tartu University Riia 23, 51010 Estonia tel: +372 737637 www: http://bioinfo.ut.ee/ From haslam at embl.de Wed Feb 10 16:47:32 2010 From: haslam at embl.de (haslam) Date: Wed, 10 Feb 2010 16:47:32 +0000 Subject: [EMBOSS] Installing emboss ends with an error (OSX 10.6 macport 1.8.2 ) In-Reply-To: <34380485-BE2D-4B75-852A-FFF6833C927B@ebc.ee> References: <34380485-BE2D-4B75-852A-FFF6833C927B@ebc.ee> Message-ID: <39647B6D-3F49-4D2C-9D60-293543F1A962@embl.de> Hi, It looks like X11 is the culprit. Are you sure you have it installed? Also - if you upgraded or copied macports over from a previous install on Leopard its worth removing and reinstalling macports. It needs to be recompiled - this tripped me up when I upgraded a machine. On 10 Feb 2010, at 16:07, T?nu Margus wrote: > ld: library not found for -lX11 From ajb at ebi.ac.uk Wed Feb 10 16:58:40 2010 From: ajb at ebi.ac.uk (ajb at ebi.ac.uk) Date: Wed, 10 Feb 2010 16:58:40 -0000 (UTC) Subject: [EMBOSS] Installing emboss ends with an error (OSX 10.6 macport 1.8.2 ) In-Reply-To: <34380485-BE2D-4B75-852A-FFF6833C927B@ebc.ee> References: <34380485-BE2D-4B75-852A-FFF6833C927B@ebc.ee> Message-ID: <53687.86.26.12.63.1265821120.squirrel@webmail.ebi.ac.uk> Hello T?nu, That specific error shows that EMBOSS is unable to find the X11 (X windows) libraries. Usually X11 is an optional, rather than default, installation option on your Apple MacOSX installation DVD. See, for example, http://www.macworld.com/article/142454/2009/08/install_snow_leopard.html After installing x11 then, on the EMBOSS side, either do a fresh extraction of the code or type "make clean" and do the ./configure command again. If you have installed X11 and are getting that error then let us know. HTH Alan > Hi! > > I tried to install emboss into my mac (OSX 10.6 snow leopard ) by using > macport (1.8.2) but finished with an error. It seems to me that I tangled > into missing library (probably libjpeg), but I am still not sure about it. > I used command "locate" to see which libjpeg libraries are installed and > it seems that they are there. > > locate libjpeg > /Applications/VLC.app/Contents/MacOS/lib/libjpeg.7.dylib > /System/Library/Frameworks/JavaVM.framework/Versions/1.6.0/Libraries/libjpeg.jnilib > /System/Library/Tcl/8.4/Img1.4/libjpegtcl1.0.dylib > /System/Library/Tcl/8.5/Img1.4/libjpegtcl1.0.dylib > > What I am missing, and how to overcome this probelme? > The part of macport debug output is below. > > > % sudo port -d install emboss > Password: > > ................ deleted .............. > > make[3]: Nothing to be done for `all-am'. > /bin/sh ../libtool --tag=CC --mode=link /usr/bin/gcc-4.2 -O2 -arch > x86_64 -L/opt/local/lib -o aaindexextract aaindexextract.o > ../nucleus/libnucleus.la ../ajax/libajaxg.la ../ajax/libajax.la > ../plplot/libeplplot.la -lX11 -lm > /bin/sh ../libtool --tag=CC --mode=link /usr/bin/gcc-4.2 -O2 -arch > x86_64 -L/opt/local/lib -o abiview abiview.o ../nucleus/libnucleus.la > ../ajax/libajaxg.la ../ajax/libajax.la ../plplot/libeplplot.la -lX11 -lm > /usr/bin/gcc-4.2 -O2 -arch x86_64 -o .libs/aaindexextract aaindexextract.o > -L/opt/local/lib ../nucleus/.libs/libnucleus.dylib > ../ajax/.libs/libajaxg.dylib ../ajax/.libs/libajax.dylib > ../plplot/.libs/libeplplot.dylib -lX11 -lm > ld: library not found for -lX11 > collect2: ld returned 1 exit status > /usr/bin/gcc-4.2 -O2 -arch x86_64 -o .libs/abiview abiview.o > -L/opt/local/lib ../nucleus/.libs/libnucleus.dylib > ../ajax/.libs/libajaxg.dylib ../ajax/.libs/libajax.dylib > ../plplot/.libs/libeplplot.dylib -lX11 -lm > make[2]: *** [aaindexextract] Error 1 > make[2]: *** Waiting for unfinished jobs.... > ld: library not found for -lX11 > collect2: ld returned 1 exit status > make[2]: *** [abiview] Error 1 > make[1]: *** [all-recursive] Error 1 > make: *** [all-recursive] Error 1 > Error: Target org.macports.build returned: shell command " cd > "/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_ports_science_EMBOSS/work/EMBOSS-6.0.1" > && /usr/bin/make -j2 all " returned error 2 > DEBUG: Backtrace: shell command " cd > "/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_ports_science_EMBOSS/work/EMBOSS-6.0.1" > && /usr/bin/make -j2 all " returned error 2 > while executing > "command_exec build" > (procedure "portbuild::build_main" line 9) > invoked from within > "$procedure $targetname" > Warning: the following items did not execute (for EMBOSS): > org.macports.activate org.macports.build org.macports.destroot > org.macports.install > Error: Status 1 encountered during processing. > To report a bug, see > > > Best Regards, > T?nu Margus > > > Department of bioinformatics > Tartu University > Riia 23, 51010 > Estonia > > tel: +372 737637 > www: http://bioinfo.ut.ee/ > > > > > _______________________________________________ > EMBOSS mailing list > EMBOSS at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/emboss > From jeedward at yahoo.com Fri Feb 12 15:35:05 2010 From: jeedward at yahoo.com (John Edward) Date: Fri, 12 Feb 2010 07:35:05 -0800 (PST) Subject: [EMBOSS] Draft paper submission deadline is extended: BCBGC-10, Orlando, USA Message-ID: <388240.3903.qm@web45913.mail.sp1.yahoo.com> It would be highly appreciated if you could share this announcement with your colleagues, students and individuals whose research is in bioinformatics, computational biology, genomics, data-mining, and related areas. Draft paper submission deadline is extended: BCBGC-10, Orlando, USA The 2010 International Conference on Bioinformatics, Computational Biology, Genomics and Chemoinformatics (BCBGC-10) (website: http://www.PromoteResearch.org) will be held during 12-14 of July 2010 in Orlando, FL, USA. BCBGC is an important event in the areas of bioinformatics, computational biology, genomics and chemoinformatics and focuses on all areas related to the conference. The conference will be held at the same time and location where several other major international conferences will be taking place. The conference will be held as part of 2010 multi-conference (MULTICONF-10). MULTICONF-10 will be held during July 12-14, 2010 in Orlando, Florida, USA. The primary goal of MULTICONF is to promote research and developmental activities in computer science, information technology, control engineering, and related fields. Another goal is to promote the dissemination of research to a multidisciplinary audience and to facilitate communication among researchers, developers, practitioners in different fields.The following conferences are planned to be organized as part of MULTICONF-10. * International Conference on Artificial Intelligence and Pattern Recognition (AIPR-10) * International Conference on Automation, Robotics and Control Systems (ARCS-10) * International Conference on Bioinformatics, Computational Biology, Genomics and Chemoinformatics (BCBGC-10) * International Conference on Computer Communications and Networks (CCN-10) * International Conference on Enterprise Information Systems and Web Technologies (EISWT-10) * International Conference on High Performance Computing Systems (HPCS-10) * International Conference on Information Security and Privacy (ISP-10) * International Conference on Image and Video Processing and Computer Vision (IVPCV-10) * International Conference on Software Engineering Theory and Practice (SETP-10) * International Conference on Theoretical and Mathematical Foundations of Computer Science (TMFCS-10) MULTICONF-10 will be held at Imperial Swan Hotel and Suites. It is a full-service resort that puts you in the middle of the fun! Located 1/2 block south of the famed International Drive, the hotel is just minutes from great entertainment like Walt Disney World? Resort, Universal Studios and Sea World Orlando. Guests can enjoy free scheduled transportation to these theme parks, as well as spacious accommodations, outdoor pools and on-site dining ? all situated on 10 tropically landscaped acres. Here, guests can experience a full-service resort with discount hotel pricing in Orlando. We invite draft paper submissions. Please see the website http://www.PromoteResearch.org for more details. Sincerely John Edward From yasser at iastate.edu Fri Feb 12 15:56:07 2010 From: yasser at iastate.edu (Yasser El-Manzalawy) Date: Fri, 12 Feb 2010 09:56:07 -0600 (CST) Subject: [EMBOSS] CfP: Immunoinformatics and Computational Immunology Workshop (ICIW 2010) Message-ID: <75691211105420@webmail.iastate.edu> We apologize for multiple posting. It would be greatly appreciated if this announcement could be shared with individuals whose research interests include Immunoinformatics and Computational Immunology. Call for Papers Immunoinformatics and Computational Immunology Workshop (ICIW 2010) ******************************************************************* To be held in conjunction with the ACM International Conference on Bioinformatics and Computational Biology (ACM-BCB) (http://www.cse.buffalo.edu/ACM-BCB2010/), Niagara Falls, NY, U.S.A. August 2-4, 2010 http://ailab.cs.iastate.edu/iciw2010 Naturally emerging or reemerging diseases pose some of the most serious threats to human health. Computational methods are urgently needed for developing new vaccines, therapies, and models to improve our understanding of the immune system, and reliable tools for focusing experimental investigations. The workshop aims to bring together researchers in computer scientists, computational biologists, structural biologists, virologists, bacteriologists, immunologists, vaccinologists, and systems biologists to share research challenges, research results, methods, and advances in immunoinformatics and computational immunology. Topics of interest include, but are not limited to: - Structural Immunoinformatics - Epitope analysis and prediction - MHC-peptide binding site analysis and prediction - Immunoinformatics Databases, Knowledge Bases, Ontologies - Computational modeling of immune system - Analysis and prediction of minor histocompatibility antigens - Predictive models for organ transplantation - Immunogenomics - Vaccine design - Artificial immune systems and other biologically-inspired paradigms - Multi-agent based modeling of immune response - Allergenicity prediction - Gene expression changes in adaptive immune response - Comparative approaches to immunology Important Dates: **************** Deadline for submissions: March 1, 2010 Notification of acceptance: April 20, 2010 Camera-ready of accepted papers: May 5, 2010 Workshop date: August 2, 2010 Author Instructions: ******************** Authors should prepare a Portable Document Format (PDF) version of their full paper. Regular papers must be no longer than 10 pages, papers on evolving research and work in progress should be no longer than 5 pages, following the ACM two-column format for conference proceedings (http://www.acm.org/sigs/publications/proceedings-templates) All accepted papers will be included in a Workshop Proceedings to be published on line and included with the conference proceedings on the CD. Authors of selected papers will have an opportunity to extend their workshop papers for publication (subject to peer review) in Journal of Immunological Methods and Immunome Research Journal. Papers should be submitted electronically (in PDF form) through ?EasyChair? at: https://www.easychair.org/login.cgi?conf=iciw2010 Organizing committee: ********************* Vasant Honavar (Iowa State University, USA)) Morten Nielsen (Technical University of Denmark, Denmark) Yasser EL-Manzalawy (Iowa State University, USA) Program Committee (Tentative): ****************************** Katherine Buckley (University of Toronto, Canada) Anne De Groot (URI Institute for Immunology and Informatics, USA) Uri Hershberg (Yale University, USA) Can Kesmir (Utrecht University, Netherlands) Steven Kleinstein (Yale University, USA) Andrzej Kloczkowski (Iowa State University, USA) German Nudelman (Mount Sinai School of Medicine, USA) Bjoern Peters (La Jolla institute of allergy and immunology, USA) Nikolai Petrovsky (Flinders University, Australia) Natasa Przulj (University of California Irvine, USA) Julia Ponomarenko (University of California, San Diego, USA) Johannes Sollner (Emergentec biodevelopment GmbH, Austria) Changhui Yan (North Dakota State University, USA) Guanglan Zhang (Dana-Farber Cancer Institute, USA) -- Yasser EL-Manzalawy Artificial Intelligence Research Laboratory Center for Computational Intelligence, Learning, & Discovery Department of Computer Science 215 Atanasoff Hall Iowa State University Ames, Iowa 50011-1040 voice: (515) 294-7331 fax: (515) 294-0258 email: yasser at cs.iastate.edu Web: www.cs.iastate.edu/~yasser From jeedward at yahoo.com Mon Feb 22 17:20:32 2010 From: jeedward at yahoo.com (John Edward) Date: Mon, 22 Feb 2010 09:20:32 -0800 (PST) Subject: [EMBOSS] Call for papers: BCBGC-10, Orlando, USA, July 2010 Message-ID: <651300.81613.qm@web45912.mail.sp1.yahoo.com> It would be highly appreciated if you could share this announcement with your colleagues, students and individuals whose research is in bioinformatics, computational biology, genomics, data-mining, and related areas. Call for papers: BCBGC-10, Orlando, USA, July 2010 The 2010 International Conference on Bioinformatics, Computational Biology, Genomics and Chemoinformatics (BCBGC-10) (website: http://www.PromoteResearch.org ) will be held during 12-14 of July 2010 in Orlando, FL, USA. BCBGC is an important event in the areas of bioinformatics, computational biology, genomics and chemoinformatics and focuses on all areas related to the conference. The conference will be held at the same time and location where several other major international conferences will be taking place. The conference will be held as part of 2010 multi-conference (MULTICONF-10). MULTICONF-10 will be held during July 12-14, 2010 in Orlando, Florida, USA. The primary goal of MULTICONF is to promote research and developmental activities in computer science, information technology, control engineering, and related fields. Another goal is to promote the dissemination of research to a multidisciplinary audience and to facilitate communication among researchers, developers, practitioners in different fields. The following conferences are planned to be organized as part of MULTICONF-10. ? International Conference on Artificial Intelligence and Pattern Recognition (AIPR-10) ? International Conference on Automation, Robotics and Control Systems (ARCS-10) ? International Conference on Bioinformatics, Computational Biology, Genomics and Chemoinformatics (BCBGC-10) ? International Conference on Computer Communications and Networks (CCN-10) ? International Conference on Enterprise Information Systems and Web Technologies (EISWT-10) ? International Conference on High Performance Computing Systems (HPCS-10) ? International Conference on Information Security and Privacy (ISP-10) ? International Conference on Image and Video Processing and Computer Vision (IVPCV-10) ? International Conference on Software Engineering Theory and Practice (SETP-10) ? International Conference on Theoretical and Mathematical Foundations of Computer Science (TMFCS-10) MULTICONF-10 will be held at Imperial Swan Hotel and Suites. It is a full-service resort that puts you in the middle of the fun! Located 1/2 block south of the famed International Drive, the hotel is just minutes from great entertainment like Walt Disney World? Resort, Universal Studios and Sea World Orlando. Guests can enjoy free scheduled transportation to these theme parks, as well as spacious accommodations, outdoor pools and on-site dining ? all situated on 10 tropically landscaped acres. Here, guests can experience a full-service resort with discount hotel pricing in Orlando. We invite draft paper submissions. Please see the website http://www.PromoteResearch.org for more details. Sincerely John Edward From Perdeep.Mehta at STJUDE.ORG Mon Feb 22 23:21:38 2010 From: Perdeep.Mehta at STJUDE.ORG (Mehta, Perdeep) Date: Mon, 22 Feb 2010 17:21:38 -0600 Subject: [EMBOSS] restrict In-Reply-To: <4A8AD193.8050102@ebi.ac.uk> References: <4A8AD193.8050102@ebi.ac.uk> Message-ID: <6EAE916704479E4BB6AB5A133BA224F728A54626D5@SJMEMXMBS11.stjude.sjcrh.local> Hi, I want to use the "restrict" program in EMBOSS package to do a restriction digest of a nucleotide sequence. When I ran restrict, it threw the following error; EMBOSS An error in restrict.c at line 147: Cannot locate enzyme file. Run REBASEEXTRACT I believe this program should use a data file for restriction enzymes, Rebase. I noticed this is missing from our installation under ~/data/REBASE subdir. I just see a "dummyfile" there. I have a few questions on EMBOSS restriction analysis and will appreciate any ideas or thoughts on these. 1. What Rebase file we need to download to get "restrict" working? I tried but there are files with different formats. 2. Is there a maximum size limit of a nucleotide sequence that I can use? Can I use the whole Human genome or at least a full chromosome to digest with a particular restriction enzyme? 3. What program can give me the list of all possible fragments generated as well? Since I have not seen the output of "restrict", perhaps that is already doing that. Thanks for any suggestions. Perdeep Mehta Email Disclaimer: www.stjude.org/emaildisclaimer From david.bauer at bayerhealthcare.com Tue Feb 23 06:55:49 2010 From: david.bauer at bayerhealthcare.com (david.bauer at bayerhealthcare.com) Date: Tue, 23 Feb 2010 07:55:49 +0100 Subject: [EMBOSS] Antwort: restrict In-Reply-To: <6EAE916704479E4BB6AB5A133BA224F728A54626D5@SJMEMXMBS11.stjude.sjcrh.local> Message-ID: Hi, emboss-bounces at lists.open-bio.org schrieb am 23/02/2010 00:21:38: > I have a few questions on EMBOSS restriction analysis and will > appreciate any ideas or thoughts on these. > > 1. What Rebase file we need to download to get "restrict" working? I > tried but there are files with different formats. Go to the /pub/rebase dir on ftp.neb.com. Download the withrefm.xxx and proto.xxx files (xxx stands for the version number, just take the latest that's there) Run rebaseextract -infile withrefm.xxx -protofile proto.xxx This reformats the neb files for use with emboss. You should now see 4 files embossre.... in the REBASE directory > 2. Is there a maximum size limit of a nucleotide sequence that I can > use? Can I use the whole Human genome or at least a full chromosome > to digest with a particular restriction enzyme? I'm not sure about the whole genome but I have used it for individual chromosomes without problems. > 3. What program can give me the list of all possible fragments > generated as well? Since I have not seen the output of "restrict", > perhaps that is already doing that. You can run restrict with the option -fragments to get them. Hope this helps, David. From Perdeep.Mehta at STJUDE.ORG Tue Feb 23 15:04:33 2010 From: Perdeep.Mehta at STJUDE.ORG (Mehta, Perdeep) Date: Tue, 23 Feb 2010 09:04:33 -0600 Subject: [EMBOSS] Antwort: restrict In-Reply-To: References: <6EAE916704479E4BB6AB5A133BA224F728A54626D5@SJMEMXMBS11.stjude.sjcrh.local> Message-ID: <6EAE916704479E4BB6AB5A133BA224F728A54626D7@SJMEMXMBS11.stjude.sjcrh.local> Thank you, including Duleep and David Lapointe for the prompt responses and for describing it in complete detail. I got what I couldn't find going through REBASE website and looking into EMBOSS' web pages. Excuse me for my ignorance, where can I find a manual or a good documentation on the EMBOSS package. regards, perdeep From: david.bauer at bayerhealthcare.com [mailto:david.bauer at bayerhealthcare.com] Sent: Tuesday, February 23, 2010 12:56 AM To: Mehta, Perdeep Cc: emboss; emboss-bounces at lists.open-bio.org Subject: Antwort: [EMBOSS] restrict Hi, emboss-bounces at lists.open-bio.org schrieb am 23/02/2010 00:21:38: > I have a few questions on EMBOSS restriction analysis and will > appreciate any ideas or thoughts on these. > > 1. What Rebase file we need to download to get "restrict" working? I > tried but there are files with different formats. Go to the /pub/rebase dir on ftp.neb.com. Download the withrefm.xxx and proto.xxx files (xxx stands for the version number, just take the latest that's there) Run rebaseextract -infile withrefm.xxx -protofile proto.xxx This reformats the neb files for use with emboss. You should now see 4 files embossre.... in the REBASE directory > 2. Is there a maximum size limit of a nucleotide sequence that I can > use? Can I use the whole Human genome or at least a full chromosome > to digest with a particular restriction enzyme? I'm not sure about the whole genome but I have used it for individual chromosomes without problems. > 3. What program can give me the list of all possible fragments > generated as well? Since I have not seen the output of "restrict", > perhaps that is already doing that. You can run restrict with the option -fragments to get them. Hope this helps, David. ________________________________ Email Disclaimer: www.stjude.org/emaildisclaimer From hrh at fmi.ch Tue Feb 23 15:45:17 2010 From: hrh at fmi.ch (Hotz, Hans-Rudolf) Date: Tue, 23 Feb 2010 16:45:17 +0100 Subject: [EMBOSS] Antwort: restrict In-Reply-To: <6EAE916704479E4BB6AB5A133BA224F728A54626D7@SJMEMXMBS11.stjude.sjcrh.local> Message-ID: On 2/23/10 4:04 PM, "Mehta, Perdeep" wrote: > Thank you, including Duleep and David Lapointe for the prompt responses and > for describing it in complete detail. I got what I couldn't find going > through REBASE website and looking into EMBOSS' web pages. Excuse me for my > ignorance, where can I find a manual or a good documentation on the EMBOSS > package. Have you looked at the EMBOSS homepage? http://emboss.sourceforge.net/ where all the applications are nicely explained http://emboss.sourceforge.net/apps/release/6.2/emboss/apps/groups.html Hans > regards, > perdeep > > > From: david.bauer at bayerhealthcare.com [mailto:david.bauer at bayerhealthcare.com] > Sent: Tuesday, February 23, 2010 12:56 AM > To: Mehta, Perdeep > Cc: emboss; emboss-bounces at lists.open-bio.org > Subject: Antwort: [EMBOSS] restrict > > > Hi, > > emboss-bounces at lists.open-bio.org schrieb am 23/02/2010 00:21:38: > >> I have a few questions on EMBOSS restriction analysis and will >> appreciate any ideas or thoughts on these. >> >> 1. What Rebase file we need to download to get "restrict" working? I >> tried but there are files with different formats. > > Go to the /pub/rebase dir on ftp.neb.com. > Download the withrefm.xxx and proto.xxx files > (xxx stands for the version number, just take the latest that's there) > Run rebaseextract -infile withrefm.xxx -protofile proto.xxx > This reformats the neb files for use with emboss. You should now see > 4 files embossre.... in the REBASE directory > >> 2. Is there a maximum size limit of a nucleotide sequence that I can >> use? Can I use the whole Human genome or at least a full chromosome >> to digest with a particular restriction enzyme? > > I'm not sure about the whole genome but I have used it for individual > chromosomes without problems. > >> 3. What program can give me the list of all possible fragments >> generated as well? Since I have not seen the output of "restrict", >> perhaps that is already doing that. > > You can run restrict with the option -fragments to get them. > > Hope this helps, > David. > > ________________________________ > Email Disclaimer: www.stjude.org/emaildisclaimer > > _______________________________________________ > EMBOSS mailing list > EMBOSS at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/emboss