From john.walshaw at bbsrc.ac.uk Mon Nov 5 11:36:44 2007 From: john.walshaw at bbsrc.ac.uk (john walshaw (JIC)) Date: Mon, 5 Nov 2007 16:36:44 -0000 Subject: [EMBOSS] dbigcg/dbxgcg and GCG 11 Message-ID: Hello, am I right in thinking that dbigcg and dbxgcg don't support GCG 11 database formats? best wishes, Dr John Walshaw Department of Computational & Systems Biology John Innes Centre Norwich Research Park, Colney, Norwich NR4 7UH, UK From john.walshaw at bbsrc.ac.uk Mon Nov 5 12:00:21 2007 From: john.walshaw at bbsrc.ac.uk (john walshaw (JIC)) Date: Mon, 5 Nov 2007 17:00:21 -0000 Subject: [EMBOSS] dbigcg/dbxgcg and GCG 11 In-Reply-To: Message-ID: Thanks Tu, I'm having trouble with GCG databases made from EMBL-format data - have you also got it to work with them? Neither dbigcg nor dbxgcg produce errors when applied to GCG 11 db files, but dbxgcg produces .pxac and .pxid files with Count = 0. dbigcg seems to work but then seqret returns a 'seqGcgReadSeq bad ID line'. It works ok for GCG 10 format dbs. regards, John -----Original Message----- From: Zheng Jin Tu [mailto:ztu at msi.umn.edu] Sent: 05 November 2007 16:54 To: john walshaw (JIC) Cc: emboss at emboss.open-bio.org Subject: Re: [EMBOSS] dbigcg/dbxgcg and GCG 11 I am using dbigcg for indexing gcgdb for emboss use setenv GCGDB /usr/local/db/gcgdb/current dbigcg -idformat genbank -directory $GCGDB/gcggenbank -filename '*.seq' \ -dbname genbank -release 160 -date 09/01/07 -outfile gb_dbigcg.log & Thanks, TU ---------------------------------------------------- On Mon, 5 Nov 2007, john walshaw (JIC) wrote: > > Hello, > > am I right in thinking that dbigcg and dbxgcg don't support GCG 11 > database formats? > > best wishes, > > Dr John Walshaw > Department of Computational & Systems Biology > John Innes Centre > Norwich Research Park, Colney, Norwich NR4 7UH, UK > > > _______________________________________________ > EMBOSS mailing list > EMBOSS at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/emboss > -- From ztu at msi.umn.edu Mon Nov 5 11:53:40 2007 From: ztu at msi.umn.edu (Zheng Jin Tu) Date: Mon, 5 Nov 2007 10:53:40 -0600 (CST) Subject: [EMBOSS] dbigcg/dbxgcg and GCG 11 In-Reply-To: References: Message-ID: I am using dbigcg for indexing gcgdb for emboss use setenv GCGDB /usr/local/db/gcgdb/current dbigcg -idformat genbank -directory $GCGDB/gcggenbank -filename '*.seq' \ -dbname genbank -release 160 -date 09/01/07 -outfile gb_dbigcg.log & Thanks, TU ---------------------------------------------------- On Mon, 5 Nov 2007, john walshaw (JIC) wrote: > > Hello, > > am I right in thinking that dbigcg and dbxgcg don't support GCG 11 > database formats? > > best wishes, > > Dr John Walshaw > Department of Computational & Systems Biology > John Innes Centre > Norwich Research Park, Colney, Norwich NR4 7UH, UK > > > _______________________________________________ > EMBOSS mailing list > EMBOSS at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/emboss > -- From pmr at ebi.ac.uk Mon Nov 5 13:35:13 2007 From: pmr at ebi.ac.uk (Peter Rice) Date: Mon, 05 Nov 2007 18:35:13 +0000 Subject: [EMBOSS] dbigcg/dbxgcg and GCG 11 In-Reply-To: References: Message-ID: <472F6261.7040606@ebi.ac.uk> Dear John, > I'm having trouble with GCG databases made from EMBL-format data - have > you also got it to work with them? > > Neither dbigcg nor dbxgcg produce errors when applied to GCG 11 db > files, but dbxgcg produces .pxac and .pxid files with Count = 0. dbigcg > seems to work but then seqret returns a 'seqGcgReadSeq bad ID line'. > > It works ok for GCG 10 format dbs. No other reports of problems in EMBOSS 5.0.0 ... Can you send me a small example (maybe one of the smaller database files) that fails so I can test. regards, Peter Rice From kvddrift at earthlink.net Thu Nov 8 18:23:45 2007 From: kvddrift at earthlink.net (Koen van der Drift) Date: Thu, 8 Nov 2007 18:23:45 -0500 Subject: [EMBOSS] error building on Mac OS X 10.5 (Leopard) Message-ID: <497EE58F-31AE-40AC-9FBA-F53BEC25295C@earthlink.net> Hi, I get the following error when building emboss 5.0.0 on Mac OS X 10.5: ... gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION= \"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"EMBOSS \" -DVERSION=\"5.0.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 - DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 - DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_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_FORK=1 - DHAVE_VFORK=1 -DHAVE_WORKING_VFORK=1 -DHAVE_WORKING_FORK=1 - DHAVE_VPRINTF=1 -DHAVE_MEMMOVE=1 -DHAVE_LIBM=1 -DPLD_png=1 -I. -I/usr/ X11/include -I./ -I/usr/include/gd -DPREFIX=\"/sw\" -DBUILD_DIR=\".\" - DDRV_DIR=\".\" -DEMBOSS_TOP=\"/sw/src/fink.build/emboss-5.0.0-3/ EMBOSS-5.0.0\" -DAJ_MACOSXLF -Dstat64=stat -I/sw/include -DBENDIAN -I/ System/Library/Frameworks/JavaVM.framework/Versions/1.4.2/Home - DHAVE_JAVA -I/System/Library/Frameworks/JavaVM.framework/Versions/ 1.4.2/Home/include -DNO_AUTH -O2 -c plctrl.c -fno-common -DPIC - o .libs/plctrl.o In file included from plctrl.c:46: /usr/include/sys/stat.h:261: error: redefinition of 'struct stat' make[2]: *** [plctrl.lo] Error 1 make[1]: *** [all-recursive] Error 1 make: *** [all-recursive] Error 1 Any suggestions what I could do to patch the source so it will compile? thanks, - Koen. From sufei at mail.sdu.edu.cn Thu Nov 8 22:02:07 2007 From: sufei at mail.sdu.edu.cn (sufei) Date: Fri, 09 Nov 2007 11:02:07 +0800 Subject: [EMBOSS] help Message-ID: <394577439.25188@mail.sdu.edu.cn> i want to install Jemboss.But i have failed many times. I use FC7,who can tell me where have the RPM package for Jemboss. Thanks! From hayany79 at gmail.com Mon Nov 19 13:52:35 2007 From: hayany79 at gmail.com (JEEYOUNG LEE) Date: Tue, 20 Nov 2007 03:52:35 +0900 Subject: [EMBOSS] Match mass sequences for mass sequences Message-ID: <663dd39f0711191052p313f7a63w91323caa9df8d760@mail.gmail.com> Dear Sir I'm sorry for a perhaps naive question. I want to align sequences of 1000 pairs. For example, "A" file includes 1000 sequences and "B" file includes 1000 sequences and two file will be compared. I'd like to find certain sequence( X gene) of A file which have high sequence similarity with some sequence ( X' gene) in B file. Then, certain gene (Y) in "A" file will be matched with Y' gene which have high identity in B file. Finally, I want to get matched 1000 pairs and their identity score. At one time, can I match mass sequences using Jemboss? How can I handle this problem? Sincerely, Lee, Jee Young From pmr at ebi.ac.uk Tue Nov 20 03:58:21 2007 From: pmr at ebi.ac.uk (Peter Rice) Date: Tue, 20 Nov 2007 08:58:21 +0000 Subject: [EMBOSS] Match mass sequences for mass sequences In-Reply-To: <663dd39f0711191052p313f7a63w91323caa9df8d760@mail.gmail.com> References: <663dd39f0711191052p313f7a63w91323caa9df8d760@mail.gmail.com> Message-ID: <4742A1AD.1060807@ebi.ac.uk> JEEYOUNG LEE wrote: > Dear Sir > > I'm sorry for a perhaps naive question. > I want to align sequences of 1000 pairs. For example, "A" file > includes 1000 sequences and "B" file includes 1000 sequences and two > file will be compared. I'd like to find certain sequence( X gene) of A > file which have high sequence similarity with some sequence ( X' gene) > in B file. Then, certain gene (Y) in "A" file will be matched with Y' > gene which have high identity in B file. Finally, I want to get > matched 1000 pairs and their identity score. At one time, can I match > mass sequences using Jemboss? How can I handle this problem? In EMBOSS 5.0.0 the wordfinder program is designed to do this. It uses a word-based algorithm (n consecutive identical bases) and then aligns using a limited window size. One warning ... the alignment includes the original word match, which may (in low identity cases) not be the highest alignment score. Wordfinder has additional options to select the matches you want. Older EMBOSS releases had only supermatcher which is less sophisticated in selecting matches. Hope that helps Peter Rice From john.walshaw at bbsrc.ac.uk Fri Nov 23 07:19:24 2007 From: john.walshaw at bbsrc.ac.uk (john walshaw (JIC)) Date: Fri, 23 Nov 2007 12:19:24 -0000 Subject: [EMBOSS] water/needle interpreting swiss-format protein sequence files as DNA Message-ID: Hello, If I create two swiss-format protein sequence files by using seqret on an EMBOSS protein sequence DB, then use these two files as the input to water or needle, I have to use "-sprotein1 -sprotein2" - otherwise they are treated as DNA sequences. In older versions of EMBOSS the files would automatically be treated as protein - I tried this out with a few legacy installations and the need to force the sequences to be protein appears to have been introduced in 4.1.0. I first noticed this problem when using 5.0.0, but version 4.0.0 automatically recognizes them as protein. Is this intentional? (i.e. to ensure that DNA sequences with lots of ambiguity codes don't get misinterpreted as protein). If not, then I'll post full details. best wishes, John Walshaw Department of Computational & Systems Biology John Innes Centre, Norwich Research Park, Colney, Norwich NR4 7UH, UK From pmr at ebi.ac.uk Fri Nov 23 07:48:13 2007 From: pmr at ebi.ac.uk (Peter Rice) Date: Fri, 23 Nov 2007 12:48:13 +0000 Subject: [EMBOSS] water/needle interpreting swiss-format protein sequence files as DNA In-Reply-To: References: Message-ID: <4746CC0D.8080902@ebi.ac.uk> john walshaw (JIC) wrote: > Hello, > > If I create two swiss-format protein sequence files by using seqret on > an EMBOSS protein sequence DB, then use these two files as the input to > water or needle, I have to use "-sprotein1 -sprotein2" - otherwise they > are treated as DNA sequences. Hmm ... so the ID line is being read as EMBL rather than SWISSPROT/UNIPROT. Can you send me the files and I will take a look. regards, Peter From golharam at umdnj.edu Wed Nov 28 14:51:56 2007 From: golharam at umdnj.edu (Ryan Golhar) Date: Wed, 28 Nov 2007 14:51:56 -0500 Subject: [EMBOSS] Vienna 1.6.5 Message-ID: <474DC6DC.9010104@umdnj.edu> Vienna 1.6.5 has been released. Right now, EMBOSS 5 uses 1.6.4. There are any plans on upgrading EMBOSS to use 1.6.5? Is all the needs to be done is updating the ACD files? Ryan From pmr at ebi.ac.uk Thu Nov 29 03:15:58 2007 From: pmr at ebi.ac.uk (Peter Rice) Date: Thu, 29 Nov 2007 08:15:58 +0000 Subject: [EMBOSS] Vienna 1.6.5 In-Reply-To: <474DC6DC.9010104@umdnj.edu> References: <474DC6DC.9010104@umdnj.edu> Message-ID: <474E753E.7070504@ebi.ac.uk> Ryan Golhar wrote: > Vienna 1.6.5 has been released. Right now, EMBOSS 5 uses 1.6.4. There > are any plans on upgrading EMBOSS to use 1.6.5? > > Is all the needs to be done is updating the ACD files? There will be more ... we modified the code for Vienna to cope with the RNA sequence/structure files. We would like to update Vienna ... I'll leave it up to Alan to take a look. Meanwhile, I am working through updating phylip to the latest release. A lot of minor code changes to check through, but whould be there in the next EMBOSS release. We changed out strategy for EMBASSY integration to work more with ACD files and simple wrapper applications - specifically to make updaing easier. regards, Peter From gatesmi at ninds.nih.gov Thu Nov 29 16:59:14 2007 From: gatesmi at ninds.nih.gov (Gates, Michael (NIH/NINDS) [F]) Date: Thu, 29 Nov 2007 16:59:14 -0500 Subject: [EMBOSS] Is a backport of emboss 5.0 to debian etch avalable? Message-ID: Hello I noticed in October there was a discussion of adding Emboss to backports for debian etch. Searching for emboss there did not yield any results. Has this in fact happened? If not, to whom can I plead to for it to happen? Is there -somewhere- a binary of emboss packaged the "debian way" for etch? Sadly "upgrading" to lenny/testing (where EMBOSS does exist) instead caused problems with R/Cran (or at least R interacting with Tcl/Tk). And for those of us whose bioinformatics consists of mainly of R and Emboss, this is .... a painful state of affairs. Alas. Or do I hear the gentle calls of "./configure make make install" in my near future? Michael Gates From golharam at umdnj.edu Thu Nov 29 20:31:15 2007 From: golharam at umdnj.edu (Ryan Golhar) Date: Thu, 29 Nov 2007 20:31:15 -0500 Subject: [EMBOSS] Is a backport of emboss 5.0 to debian etch avalable? In-Reply-To: References: Message-ID: <474F67E3.4020703@umdnj.edu> We have RPMs available for EMBOSS. If you know how to construct deb package, perhaps you can convert them...I've never tried myself. Gates, Michael (NIH/NINDS) [F] wrote: > Hello > > I noticed in October there was a discussion of adding Emboss to backports for debian etch. Searching for emboss there did not yield any results. Has this in fact happened? If not, to whom can I plead to for it to happen? Is there -somewhere- a binary of emboss packaged the "debian way" for etch? > > Sadly "upgrading" to lenny/testing (where EMBOSS does exist) instead caused problems with R/Cran (or at least R interacting with Tcl/Tk). And for those of us whose bioinformatics consists of mainly of R and Emboss, this is .... a painful state of affairs. Alas. > > Or do I hear the gentle calls of "./configure make make install" in my near future? > > Michael Gates > > _______________________________________________ > EMBOSS mailing list > EMBOSS at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/emboss > > From charles-listes-emboss at plessy.org Thu Nov 29 23:23:11 2007 From: charles-listes-emboss at plessy.org (charles-listes-emboss at plessy.org) Date: Fri, 30 Nov 2007 13:23:11 +0900 Subject: [EMBOSS] Is a backport of emboss 5.0 to debian etch avalable? In-Reply-To: References: Message-ID: <20071130042311.GA15647@kunpuu.plessy.org> Le Thu, Nov 29, 2007 at 04:59:14PM -0500, Gates, Michael (NIH/NINDS) [F] a ?crit : > > Hello > > I noticed in October there was a discussion of adding Emboss to > backports for debian etch. Searching for emboss there did not yield > any results. Has this in fact happened? If not, to whom can I plead to > for it to happen? Is there -somewhere- a binary of emboss packaged > the "debian way" for etch? Dear Michael, we definitely consider preparing official emboss packages for the backports.org facility. But in the meantime, you can use the backport I just prepared on my personnal website: http://charles.plessy.org/debian/emboss/ I prepared them in a minimal Etch chroot (with security updates), so I could not test them, but I do not see a reason why they should not work. These unofficial packages are unfortunately not GPG signed. Please tell me if it is a problem. The Debian source package (same for Sid/Lenny, and unofficial Etch) contain the psiphi patch: http://svn.debian.org/wsvn/pkg-emboss/emboss/trunk/debian/patches/psiphi-fix-2007-07-27.patch?op=file&rev=0&sc=0 (same as ftp://emboss.open-bio.org/pub/EMBOSS/fixes/patches ) Please report any problem or suggestion to me, or to the Debian-Med mailing list (CC'ed): http://lists.debian.org/debian-med/ Have a nice day, -- Charles Plessy Debian-Med packaging team Wak?, Saitama, Japan From gbottu at vub.ac.be Fri Nov 30 06:44:27 2007 From: gbottu at vub.ac.be (Guy Bottu) Date: Fri, 30 Nov 2007 12:44:27 +0100 Subject: [EMBOSS] wrappers4EMBOSS 2.0.0 released Message-ID: <474FF79B.9000804@vub.ac.be> Dear colleagues, You might have noticed that the wEMBOSS SourceForge site had not been updated for quite a while. The reason is the tragic disease and decease of our site manager and fellow developer Martin Sarachu from the Argentinean EMBnet Node (see http://www.embnet.org/files/shared/EMBnetNews/embnet_news13_3-high.pdf). The maintenance of the wEMBOSS project has now resumed and we can announce the release of a new version 2.0.0 of wrappers4EMBOSS. A new version of wEMBOSS (with version 2 of wrappers4EMBOSS included) is to be expected for begin 2008. An important change in wrappers4EMBOSS is that it now uses the EMBASSY module MYEMBOSS rather then EMBOSS itself for compiling and installing. This has two advantages : it goes much faster (which can be convenient if you need to redo it several times) and it avoids overwriting customizations you might have performed directly in the installed version of EMBOSS rather than in the source (addressing an issue raised by some users). Problem is that the manual in HTML format is now installed in .../share/EMBOSS/doc/html/embassy/myseq. A future version of wEMBOSS will fully address the problem of manual location ; for the moment users of wEMBOSS and some other GUI's might have to copy the manual entries "manually" to another location. There are two new modules : an interface to a local installation of the InterProScan server and an interface to a local installation of Maarten Hekkelman's MRS software for indexing databanks. The MRS module contains a program mrsindexsearch, which is much like the SRS based indexsearch. It also provides a tool for using a local MRS as sequence databank access mechanism for EMBOSS and a command line scripting tool. For a complete list of changes, you can consult the Changelog http://sourceforge.net/project/shownotes.php?group_id=170030&release_id=557931 As far as we know, wrappers4EMBOSS 2.0.0 and wEMBOSS 1.7.1 work well with all versions of EMBOSS from 3.0.0 to 5.0.0. If you however notice a bug, let us know. Also, since we do not have an SRS server anymore, we do not have the expertise for continuing supporting SRS beyond version 8.1 ; if you have a version 8.2 and notice a need for change in our SRS module, suggestions are welcome. Regards, Belgian EMBnet Node - wEMBOSS development team, Guy Bottu From pmr at ebi.ac.uk Fri Nov 30 07:36:14 2007 From: pmr at ebi.ac.uk (Peter Rice) Date: Fri, 30 Nov 2007 12:36:14 +0000 Subject: [EMBOSS] wrappers4EMBOSS 2.0.0 released In-Reply-To: <474FF79B.9000804@vub.ac.be> References: <474FF79B.9000804@vub.ac.be> Message-ID: <475003BE.5090608@ebi.ac.uk> Guy Bottu wrote: > An important change in wrappers4EMBOSS is that it now uses the EMBASSY module > MYEMBOSS rather then EMBOSS itself for compiling and installing. We are interested in any feedback from other using MYEMBOSS. We are preparing a book for programmers and all experiences (and requests for more information) are very useful. Martin Sarachu is greatly missed. A sad loss. Peter From john.walshaw at bbsrc.ac.uk Mon Nov 5 16:36:44 2007 From: john.walshaw at bbsrc.ac.uk (john walshaw (JIC)) Date: Mon, 5 Nov 2007 16:36:44 -0000 Subject: [EMBOSS] dbigcg/dbxgcg and GCG 11 Message-ID: Hello, am I right in thinking that dbigcg and dbxgcg don't support GCG 11 database formats? best wishes, Dr John Walshaw Department of Computational & Systems Biology John Innes Centre Norwich Research Park, Colney, Norwich NR4 7UH, UK From john.walshaw at bbsrc.ac.uk Mon Nov 5 17:00:21 2007 From: john.walshaw at bbsrc.ac.uk (john walshaw (JIC)) Date: Mon, 5 Nov 2007 17:00:21 -0000 Subject: [EMBOSS] dbigcg/dbxgcg and GCG 11 In-Reply-To: Message-ID: Thanks Tu, I'm having trouble with GCG databases made from EMBL-format data - have you also got it to work with them? Neither dbigcg nor dbxgcg produce errors when applied to GCG 11 db files, but dbxgcg produces .pxac and .pxid files with Count = 0. dbigcg seems to work but then seqret returns a 'seqGcgReadSeq bad ID line'. It works ok for GCG 10 format dbs. regards, John -----Original Message----- From: Zheng Jin Tu [mailto:ztu at msi.umn.edu] Sent: 05 November 2007 16:54 To: john walshaw (JIC) Cc: emboss at emboss.open-bio.org Subject: Re: [EMBOSS] dbigcg/dbxgcg and GCG 11 I am using dbigcg for indexing gcgdb for emboss use setenv GCGDB /usr/local/db/gcgdb/current dbigcg -idformat genbank -directory $GCGDB/gcggenbank -filename '*.seq' \ -dbname genbank -release 160 -date 09/01/07 -outfile gb_dbigcg.log & Thanks, TU ---------------------------------------------------- On Mon, 5 Nov 2007, john walshaw (JIC) wrote: > > Hello, > > am I right in thinking that dbigcg and dbxgcg don't support GCG 11 > database formats? > > best wishes, > > Dr John Walshaw > Department of Computational & Systems Biology > John Innes Centre > Norwich Research Park, Colney, Norwich NR4 7UH, UK > > > _______________________________________________ > EMBOSS mailing list > EMBOSS at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/emboss > -- From ztu at msi.umn.edu Mon Nov 5 16:53:40 2007 From: ztu at msi.umn.edu (Zheng Jin Tu) Date: Mon, 5 Nov 2007 10:53:40 -0600 (CST) Subject: [EMBOSS] dbigcg/dbxgcg and GCG 11 In-Reply-To: References: Message-ID: I am using dbigcg for indexing gcgdb for emboss use setenv GCGDB /usr/local/db/gcgdb/current dbigcg -idformat genbank -directory $GCGDB/gcggenbank -filename '*.seq' \ -dbname genbank -release 160 -date 09/01/07 -outfile gb_dbigcg.log & Thanks, TU ---------------------------------------------------- On Mon, 5 Nov 2007, john walshaw (JIC) wrote: > > Hello, > > am I right in thinking that dbigcg and dbxgcg don't support GCG 11 > database formats? > > best wishes, > > Dr John Walshaw > Department of Computational & Systems Biology > John Innes Centre > Norwich Research Park, Colney, Norwich NR4 7UH, UK > > > _______________________________________________ > EMBOSS mailing list > EMBOSS at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/emboss > -- From pmr at ebi.ac.uk Mon Nov 5 18:35:13 2007 From: pmr at ebi.ac.uk (Peter Rice) Date: Mon, 05 Nov 2007 18:35:13 +0000 Subject: [EMBOSS] dbigcg/dbxgcg and GCG 11 In-Reply-To: References: Message-ID: <472F6261.7040606@ebi.ac.uk> Dear John, > I'm having trouble with GCG databases made from EMBL-format data - have > you also got it to work with them? > > Neither dbigcg nor dbxgcg produce errors when applied to GCG 11 db > files, but dbxgcg produces .pxac and .pxid files with Count = 0. dbigcg > seems to work but then seqret returns a 'seqGcgReadSeq bad ID line'. > > It works ok for GCG 10 format dbs. No other reports of problems in EMBOSS 5.0.0 ... Can you send me a small example (maybe one of the smaller database files) that fails so I can test. regards, Peter Rice From kvddrift at earthlink.net Thu Nov 8 23:23:45 2007 From: kvddrift at earthlink.net (Koen van der Drift) Date: Thu, 8 Nov 2007 18:23:45 -0500 Subject: [EMBOSS] error building on Mac OS X 10.5 (Leopard) Message-ID: <497EE58F-31AE-40AC-9FBA-F53BEC25295C@earthlink.net> Hi, I get the following error when building emboss 5.0.0 on Mac OS X 10.5: ... gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION= \"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"EMBOSS \" -DVERSION=\"5.0.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 - DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 - DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_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_FORK=1 - DHAVE_VFORK=1 -DHAVE_WORKING_VFORK=1 -DHAVE_WORKING_FORK=1 - DHAVE_VPRINTF=1 -DHAVE_MEMMOVE=1 -DHAVE_LIBM=1 -DPLD_png=1 -I. -I/usr/ X11/include -I./ -I/usr/include/gd -DPREFIX=\"/sw\" -DBUILD_DIR=\".\" - DDRV_DIR=\".\" -DEMBOSS_TOP=\"/sw/src/fink.build/emboss-5.0.0-3/ EMBOSS-5.0.0\" -DAJ_MACOSXLF -Dstat64=stat -I/sw/include -DBENDIAN -I/ System/Library/Frameworks/JavaVM.framework/Versions/1.4.2/Home - DHAVE_JAVA -I/System/Library/Frameworks/JavaVM.framework/Versions/ 1.4.2/Home/include -DNO_AUTH -O2 -c plctrl.c -fno-common -DPIC - o .libs/plctrl.o In file included from plctrl.c:46: /usr/include/sys/stat.h:261: error: redefinition of 'struct stat' make[2]: *** [plctrl.lo] Error 1 make[1]: *** [all-recursive] Error 1 make: *** [all-recursive] Error 1 Any suggestions what I could do to patch the source so it will compile? thanks, - Koen. From sufei at mail.sdu.edu.cn Fri Nov 9 03:02:07 2007 From: sufei at mail.sdu.edu.cn (sufei) Date: Fri, 09 Nov 2007 11:02:07 +0800 Subject: [EMBOSS] help Message-ID: <394577439.25188@mail.sdu.edu.cn> i want to install Jemboss.But i have failed many times. I use FC7,who can tell me where have the RPM package for Jemboss. Thanks! From hayany79 at gmail.com Mon Nov 19 18:52:35 2007 From: hayany79 at gmail.com (JEEYOUNG LEE) Date: Tue, 20 Nov 2007 03:52:35 +0900 Subject: [EMBOSS] Match mass sequences for mass sequences Message-ID: <663dd39f0711191052p313f7a63w91323caa9df8d760@mail.gmail.com> Dear Sir I'm sorry for a perhaps naive question. I want to align sequences of 1000 pairs. For example, "A" file includes 1000 sequences and "B" file includes 1000 sequences and two file will be compared. I'd like to find certain sequence( X gene) of A file which have high sequence similarity with some sequence ( X' gene) in B file. Then, certain gene (Y) in "A" file will be matched with Y' gene which have high identity in B file. Finally, I want to get matched 1000 pairs and their identity score. At one time, can I match mass sequences using Jemboss? How can I handle this problem? Sincerely, Lee, Jee Young From pmr at ebi.ac.uk Tue Nov 20 08:58:21 2007 From: pmr at ebi.ac.uk (Peter Rice) Date: Tue, 20 Nov 2007 08:58:21 +0000 Subject: [EMBOSS] Match mass sequences for mass sequences In-Reply-To: <663dd39f0711191052p313f7a63w91323caa9df8d760@mail.gmail.com> References: <663dd39f0711191052p313f7a63w91323caa9df8d760@mail.gmail.com> Message-ID: <4742A1AD.1060807@ebi.ac.uk> JEEYOUNG LEE wrote: > Dear Sir > > I'm sorry for a perhaps naive question. > I want to align sequences of 1000 pairs. For example, "A" file > includes 1000 sequences and "B" file includes 1000 sequences and two > file will be compared. I'd like to find certain sequence( X gene) of A > file which have high sequence similarity with some sequence ( X' gene) > in B file. Then, certain gene (Y) in "A" file will be matched with Y' > gene which have high identity in B file. Finally, I want to get > matched 1000 pairs and their identity score. At one time, can I match > mass sequences using Jemboss? How can I handle this problem? In EMBOSS 5.0.0 the wordfinder program is designed to do this. It uses a word-based algorithm (n consecutive identical bases) and then aligns using a limited window size. One warning ... the alignment includes the original word match, which may (in low identity cases) not be the highest alignment score. Wordfinder has additional options to select the matches you want. Older EMBOSS releases had only supermatcher which is less sophisticated in selecting matches. Hope that helps Peter Rice From john.walshaw at bbsrc.ac.uk Fri Nov 23 12:19:24 2007 From: john.walshaw at bbsrc.ac.uk (john walshaw (JIC)) Date: Fri, 23 Nov 2007 12:19:24 -0000 Subject: [EMBOSS] water/needle interpreting swiss-format protein sequence files as DNA Message-ID: Hello, If I create two swiss-format protein sequence files by using seqret on an EMBOSS protein sequence DB, then use these two files as the input to water or needle, I have to use "-sprotein1 -sprotein2" - otherwise they are treated as DNA sequences. In older versions of EMBOSS the files would automatically be treated as protein - I tried this out with a few legacy installations and the need to force the sequences to be protein appears to have been introduced in 4.1.0. I first noticed this problem when using 5.0.0, but version 4.0.0 automatically recognizes them as protein. Is this intentional? (i.e. to ensure that DNA sequences with lots of ambiguity codes don't get misinterpreted as protein). If not, then I'll post full details. best wishes, John Walshaw Department of Computational & Systems Biology John Innes Centre, Norwich Research Park, Colney, Norwich NR4 7UH, UK From pmr at ebi.ac.uk Fri Nov 23 12:48:13 2007 From: pmr at ebi.ac.uk (Peter Rice) Date: Fri, 23 Nov 2007 12:48:13 +0000 Subject: [EMBOSS] water/needle interpreting swiss-format protein sequence files as DNA In-Reply-To: References: Message-ID: <4746CC0D.8080902@ebi.ac.uk> john walshaw (JIC) wrote: > Hello, > > If I create two swiss-format protein sequence files by using seqret on > an EMBOSS protein sequence DB, then use these two files as the input to > water or needle, I have to use "-sprotein1 -sprotein2" - otherwise they > are treated as DNA sequences. Hmm ... so the ID line is being read as EMBL rather than SWISSPROT/UNIPROT. Can you send me the files and I will take a look. regards, Peter From golharam at umdnj.edu Wed Nov 28 19:51:56 2007 From: golharam at umdnj.edu (Ryan Golhar) Date: Wed, 28 Nov 2007 14:51:56 -0500 Subject: [EMBOSS] Vienna 1.6.5 Message-ID: <474DC6DC.9010104@umdnj.edu> Vienna 1.6.5 has been released. Right now, EMBOSS 5 uses 1.6.4. There are any plans on upgrading EMBOSS to use 1.6.5? Is all the needs to be done is updating the ACD files? Ryan From pmr at ebi.ac.uk Thu Nov 29 08:15:58 2007 From: pmr at ebi.ac.uk (Peter Rice) Date: Thu, 29 Nov 2007 08:15:58 +0000 Subject: [EMBOSS] Vienna 1.6.5 In-Reply-To: <474DC6DC.9010104@umdnj.edu> References: <474DC6DC.9010104@umdnj.edu> Message-ID: <474E753E.7070504@ebi.ac.uk> Ryan Golhar wrote: > Vienna 1.6.5 has been released. Right now, EMBOSS 5 uses 1.6.4. There > are any plans on upgrading EMBOSS to use 1.6.5? > > Is all the needs to be done is updating the ACD files? There will be more ... we modified the code for Vienna to cope with the RNA sequence/structure files. We would like to update Vienna ... I'll leave it up to Alan to take a look. Meanwhile, I am working through updating phylip to the latest release. A lot of minor code changes to check through, but whould be there in the next EMBOSS release. We changed out strategy for EMBASSY integration to work more with ACD files and simple wrapper applications - specifically to make updaing easier. regards, Peter From gatesmi at ninds.nih.gov Thu Nov 29 21:59:14 2007 From: gatesmi at ninds.nih.gov (Gates, Michael (NIH/NINDS) [F]) Date: Thu, 29 Nov 2007 16:59:14 -0500 Subject: [EMBOSS] Is a backport of emboss 5.0 to debian etch avalable? Message-ID: Hello I noticed in October there was a discussion of adding Emboss to backports for debian etch. Searching for emboss there did not yield any results. Has this in fact happened? If not, to whom can I plead to for it to happen? Is there -somewhere- a binary of emboss packaged the "debian way" for etch? Sadly "upgrading" to lenny/testing (where EMBOSS does exist) instead caused problems with R/Cran (or at least R interacting with Tcl/Tk). And for those of us whose bioinformatics consists of mainly of R and Emboss, this is .... a painful state of affairs. Alas. Or do I hear the gentle calls of "./configure make make install" in my near future? Michael Gates From golharam at umdnj.edu Fri Nov 30 01:31:15 2007 From: golharam at umdnj.edu (Ryan Golhar) Date: Thu, 29 Nov 2007 20:31:15 -0500 Subject: [EMBOSS] Is a backport of emboss 5.0 to debian etch avalable? In-Reply-To: References: Message-ID: <474F67E3.4020703@umdnj.edu> We have RPMs available for EMBOSS. If you know how to construct deb package, perhaps you can convert them...I've never tried myself. Gates, Michael (NIH/NINDS) [F] wrote: > Hello > > I noticed in October there was a discussion of adding Emboss to backports for debian etch. Searching for emboss there did not yield any results. Has this in fact happened? If not, to whom can I plead to for it to happen? Is there -somewhere- a binary of emboss packaged the "debian way" for etch? > > Sadly "upgrading" to lenny/testing (where EMBOSS does exist) instead caused problems with R/Cran (or at least R interacting with Tcl/Tk). And for those of us whose bioinformatics consists of mainly of R and Emboss, this is .... a painful state of affairs. Alas. > > Or do I hear the gentle calls of "./configure make make install" in my near future? > > Michael Gates > > _______________________________________________ > EMBOSS mailing list > EMBOSS at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/emboss > > From charles-listes-emboss at plessy.org Fri Nov 30 04:23:11 2007 From: charles-listes-emboss at plessy.org (charles-listes-emboss at plessy.org) Date: Fri, 30 Nov 2007 13:23:11 +0900 Subject: [EMBOSS] Is a backport of emboss 5.0 to debian etch avalable? In-Reply-To: References: Message-ID: <20071130042311.GA15647@kunpuu.plessy.org> Le Thu, Nov 29, 2007 at 04:59:14PM -0500, Gates, Michael (NIH/NINDS) [F] a ?crit : > > Hello > > I noticed in October there was a discussion of adding Emboss to > backports for debian etch. Searching for emboss there did not yield > any results. Has this in fact happened? If not, to whom can I plead to > for it to happen? Is there -somewhere- a binary of emboss packaged > the "debian way" for etch? Dear Michael, we definitely consider preparing official emboss packages for the backports.org facility. But in the meantime, you can use the backport I just prepared on my personnal website: http://charles.plessy.org/debian/emboss/ I prepared them in a minimal Etch chroot (with security updates), so I could not test them, but I do not see a reason why they should not work. These unofficial packages are unfortunately not GPG signed. Please tell me if it is a problem. The Debian source package (same for Sid/Lenny, and unofficial Etch) contain the psiphi patch: http://svn.debian.org/wsvn/pkg-emboss/emboss/trunk/debian/patches/psiphi-fix-2007-07-27.patch?op=file&rev=0&sc=0 (same as ftp://emboss.open-bio.org/pub/EMBOSS/fixes/patches ) Please report any problem or suggestion to me, or to the Debian-Med mailing list (CC'ed): http://lists.debian.org/debian-med/ Have a nice day, -- Charles Plessy Debian-Med packaging team Wak?, Saitama, Japan From gbottu at vub.ac.be Fri Nov 30 11:44:27 2007 From: gbottu at vub.ac.be (Guy Bottu) Date: Fri, 30 Nov 2007 12:44:27 +0100 Subject: [EMBOSS] wrappers4EMBOSS 2.0.0 released Message-ID: <474FF79B.9000804@vub.ac.be> Dear colleagues, You might have noticed that the wEMBOSS SourceForge site had not been updated for quite a while. The reason is the tragic disease and decease of our site manager and fellow developer Martin Sarachu from the Argentinean EMBnet Node (see http://www.embnet.org/files/shared/EMBnetNews/embnet_news13_3-high.pdf). The maintenance of the wEMBOSS project has now resumed and we can announce the release of a new version 2.0.0 of wrappers4EMBOSS. A new version of wEMBOSS (with version 2 of wrappers4EMBOSS included) is to be expected for begin 2008. An important change in wrappers4EMBOSS is that it now uses the EMBASSY module MYEMBOSS rather then EMBOSS itself for compiling and installing. This has two advantages : it goes much faster (which can be convenient if you need to redo it several times) and it avoids overwriting customizations you might have performed directly in the installed version of EMBOSS rather than in the source (addressing an issue raised by some users). Problem is that the manual in HTML format is now installed in .../share/EMBOSS/doc/html/embassy/myseq. A future version of wEMBOSS will fully address the problem of manual location ; for the moment users of wEMBOSS and some other GUI's might have to copy the manual entries "manually" to another location. There are two new modules : an interface to a local installation of the InterProScan server and an interface to a local installation of Maarten Hekkelman's MRS software for indexing databanks. The MRS module contains a program mrsindexsearch, which is much like the SRS based indexsearch. It also provides a tool for using a local MRS as sequence databank access mechanism for EMBOSS and a command line scripting tool. For a complete list of changes, you can consult the Changelog http://sourceforge.net/project/shownotes.php?group_id=170030&release_id=557931 As far as we know, wrappers4EMBOSS 2.0.0 and wEMBOSS 1.7.1 work well with all versions of EMBOSS from 3.0.0 to 5.0.0. If you however notice a bug, let us know. Also, since we do not have an SRS server anymore, we do not have the expertise for continuing supporting SRS beyond version 8.1 ; if you have a version 8.2 and notice a need for change in our SRS module, suggestions are welcome. Regards, Belgian EMBnet Node - wEMBOSS development team, Guy Bottu From pmr at ebi.ac.uk Fri Nov 30 12:36:14 2007 From: pmr at ebi.ac.uk (Peter Rice) Date: Fri, 30 Nov 2007 12:36:14 +0000 Subject: [EMBOSS] wrappers4EMBOSS 2.0.0 released In-Reply-To: <474FF79B.9000804@vub.ac.be> References: <474FF79B.9000804@vub.ac.be> Message-ID: <475003BE.5090608@ebi.ac.uk> Guy Bottu wrote: > An important change in wrappers4EMBOSS is that it now uses the EMBASSY module > MYEMBOSS rather then EMBOSS itself for compiling and installing. We are interested in any feedback from other using MYEMBOSS. We are preparing a book for programmers and all experiences (and requests for more information) are very useful. Martin Sarachu is greatly missed. A sad loss. Peter