From tcarver at hgmp.mrc.ac.uk Fri Nov 10 10:42:21 2000 From: tcarver at hgmp.mrc.ac.uk (Tim Carver) Date: Fri, 10 Nov 2000 15:42:21 +0000 Subject: trace file library Message-ID: <3A0C175D.5D73F6B@hgmp.mrc.ac.uk> Hi Just to let you know I am adding in some EMBOSS library fuctions to read in trace file formats (ABI/ALF). I have made a start on this for ABI trace files. If anyone has any suggestions/comments on how this would most usefully be implemented please let me know. Many Thanks Tim ------------------------------------ Tim Carver, PhD, Bioinformatics, MRC HGMP Resource Centre, Hinxton, Cambridge, CB10 1SB -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.open-bio.org/pipermail/emboss/attachments/20001110/3bc4ce02/attachment.html From milius at bscl.msi.umn.edu Wed Nov 15 19:01:31 2000 From: milius at bscl.msi.umn.edu (Robert Milius) Date: Wed, 15 Nov 2000 16:01:31 -0800 Subject: data files Message-ID: Hi, I just downloaded and installed the following databases for use with EMBOSS 1.7.0: rebase prints prosite transfac and used rebaseextract, printsextract, prosextract, and tfextract to extract them for use with EMBOSS. Everything seems to work, but the databases ended up being extracted to my original source directory, not my installation point. The respective programs (eg patmatmotifs) seem to work ok. I originally did my configure using "--prefix=/usr/local/EMBOSS" and my make install went without a hitch. Did I miss setting some environmental variable or something? I have the following set: setenv PLPLOT_LIB /usr/local/EMBOSS/share/EMBOSS setenv EMBOSS_ACDROOT /usr/local/EMBOSS/share/EMBOSS/acd thanks, bob Robert P. Milius, Ph.D. 612-626-2771 (office) Basic Sciences Computing Laboratory 612-625-4433 (fax) University of Minnesota Supercomputing Institute milius at msi.umn.edu for Digital Simulation and Advanced Computation From simon.andrews at bbsrc.ac.uk Thu Nov 16 06:17:31 2000 From: simon.andrews at bbsrc.ac.uk (simon andrews (BITS)) Date: Thu, 16 Nov 2000 11:17:31 -0000 Subject: PNG libraries for OSF / CTU Unix Message-ID: <41773CEF2B8FD411920200508BDCDC120D6A13@bits-exch1.bits.bbsrc.ac.uk> Apologies if you get this message twice - I tried sending it last week but never saw it appear in the group. I am trying to compile PNG support into EMBOSS on our CTU Unix system. This requires the z, png and gd libraries, which are not on our system at the moment. Does anyone know where I can get these libraries for either OSF or CTU Unix? All the references to them I have found on the web have been for Linux. Are these platform independent (so I can use the Linux libraries)? Or do I need specific versions for our unix version? Any and all help is appreciated TTFN Simon. ---- Simon Andrews PhD Molecular Biology Support BBSRC Bioscience IT Services e.mail: simon.andrews at bbsrc.ac.uk Tel:(+44) 1582 714900 Fax:(+44) 1582 714901 From johann at egenetics.com Thu Nov 16 06:35:46 2000 From: johann at egenetics.com (Johann Visagie) Date: Thu, 16 Nov 2000 13:35:46 +0200 Subject: PNG libraries for OSF / CTU Unix In-Reply-To: <41773CEF2B8FD411920200508BDCDC120D6A13@bits-exch1.bits.bbsrc.ac.uk>; from simon.andrews@bbsrc.ac.uk on Thu, Nov 16, 2000 at 11:17:31AM -0000 References: <41773CEF2B8FD411920200508BDCDC120D6A13@bits-exch1.bits.bbsrc.ac.uk> Message-ID: <20001116133546.A78540@fling.sanbi.ac.za> simon andrews (BITS) on 2000-11-16 (Thu) at 11:17:31 -0000: > > I am trying to compile PNG support into EMBOSS on our CTU Unix system. This > requires the z, png and gd libraries, which are not on our system at the > moment. > > Does anyone know where I can get these libraries for either OSF or CTU Unix? > All the references to them I have found on the web have been for Linux. Are > these platform independent (so I can use the Linux libraries)? Or do I need > specific versions for our unix version? You should be able to compile them from the source on just about any Unix platform. http://www.info-zip.org/pub/infozip/zlib/ http://libpng.sourceforge.net/ http://www.boutell.com/gd/ -- Johann From LL at earthling.net Mon Nov 20 22:12:04 2000 From: LL at earthling.net (Long LIANG) Date: Tue, 21 Nov 2000 11:12:04 +0800 Subject: how to index the blast database formated by formatdb -v Message-ID: <3A19E804.70006@earthling.net> Hi, I have formated my htg blast database by formatdb -v to produce multiple volumes database, Could somebody tell me how to index such blast databases by using dbiblast. thanks! Long Liang, Ph.D. MD. From simon.andrews at bbsrc.ac.uk Tue Nov 21 09:43:40 2000 From: simon.andrews at bbsrc.ac.uk (simon andrews (BITS)) Date: Tue, 21 Nov 2000 14:43:40 -0000 Subject: Extracted data information Message-ID: <41773CEF2B8FD411920200508BDCDC120D6A23@bits-exch1.bits.bbsrc.ac.uk> Dear All, Firstly can I say thanks to those who pointed me in the right direction for the z, gd and png libraries - our Emboss install now makes beautiful (!?) pngs. Unfortunately I've now come up against another problem. I have Emboss installed on our development server and I'm preparing a dispatch which will send it out to about 20 remote sites. I ran the configure with the --prefix option to install to a private directory. I also collected all the data files (rebase, transfac etc.) to another directory and extracted the information from them with the relevant programs. My intention was to simply transfer the Emboss install directory and the Data directory to all sites, using symlinks where necessary so that the directory paths corresponded. However, when testing this I have found a couple of problems; 1) Although the Emboss programs work, I can't see any of the extracted data. For instance remap gives the error; EMBOSS An error in remap.c at line 167: Cannot locate enzyme file. Run REBASEEXTRACT This is despite the fact that I have both the Emboss install and the Data directories in the same place as on the development machine (which works). 2) The other major problem is that I can no longer see my databases defined in emboss.default. Again, the file exists, and is in the same place as on the development machine, but the box it is transferred to gives an empty list from showdb. Does anyone know where Emboss stores the information about the location of these files? It can't have installed anything outside the original installation directory (wasn't installed as root), so I'm guessing that the problem stems from the program resolving symlinks at some point. Again I would appreciate any help people can offer, and would be glad to report back to the group with whatever discoveries I make. Thanks in advance TTFN Simon. ---- Simon Andrews PhD Molecular Biology Support BBSRC Bioscience IT Services e.mail: simon.andrews at bbsrc.ac.uk Tel:(+44) 1582 714900 Fax:(+44) 1582 714901 From Peter.Rice at uk.lionbioscience.com Wed Nov 22 05:53:09 2000 From: Peter.Rice at uk.lionbioscience.com (Peter Rice) Date: Wed, 22 Nov 2000 10:53:09 +0000 Subject: Extracted data information References: <41773CEF2B8FD411920200508BDCDC120D6A23@bits-exch1.bits.bbsrc.ac.uk> Message-ID: <3A1BA595.E8A799DE@lionbio.co.uk> "simon andrews (BITS)" wrote: > 1) Although the Emboss programs work, I can't see any of the extracted data. > For instance remap gives the error; > > EMBOSS An error in remap.c at line 167: > Cannot locate enzyme file. Run REBASEEXTRACT > > This is despite the fact that I have both the Emboss install and the Data > directories in the same place as on the development machine (which works). > > 2) The other major problem is that I can no longer see my databases defined > in emboss.default. Again, the file exists, and is in the same place as on > the development machine, but the box it is transferred to gives an empty > list from showdb. > > Does anyone know where Emboss stores the information about the location of > these files? It can't have installed anything outside the original > installation directory (wasn't installed as root), so I'm guessing that the > problem stems from the program resolving symlinks at some point. It is inside the binaries ... EMBOSS 'knows' the location of the files because it is picked up during the configure, when you build your copy, and included in the binaries. You can see it during compilation, especially of ajnam.c (where it is used): -DAJAX_FIXED_ROOT=\"/full/source/path\" -DPREFIX=\"/install/prefix/path\" To copy binaries, you need to define environment variable(s) to override the compile-time definitions, unless you can make the path (e.g. /usr/local) the same for the installations at each site. emboss.default can set environment variables too, but you need to tell EMBOSS where to find that file. setenv EMBOSS_ROOT /dir/for/default/file and then, in the emboss.default file you can set: SET EMBOSS_ACDROOT /install/dir/share/EMBOSS/acd or (this overrides it) you can use another environment variable: SET EMBOSS_ACDROOT /install/dir/share/EMBOSS/acd -- ------------------------------------------------ Peter Rice, LION Bioscience Ltd, Cambridge, UK peter.rice at uk.lionbioscience.com +44 1223 224723 From ableasby at hgmp.mrc.ac.uk Mon Nov 27 10:09:22 2000 From: ableasby at hgmp.mrc.ac.uk (ableasby at hgmp.mrc.ac.uk) Date: Mon, 27 Nov 2000 15:09:22 GMT Subject: EMBOSS 1.8.0 Message-ID: <200011271509.PAA09630@bromine.hgmp.mrc.ac.uk> CODERET: Assuming you have the embl (or GenBank) database in a form which allows access to the feature table information then this program will return all or some of the CDS, mRNA and translations. It caters for CDS sequences spread over different entries. The observant will note that some protein structure code has started appearing in the libraries. There is also some CORBA communication code. These are under active development but there are currently no supplied (nearly said distributed) applications. Alan PS: The MEME program is also supplied as an "embassy" gtar file on the ftp server and as part of the CVS tree. This awaits documentation. The program spots "conserved" regions in a set of sequences. From johann at egenetics.com Mon Nov 27 11:20:54 2000 From: johann at egenetics.com (Johann Visagie) Date: Mon, 27 Nov 2000 18:20:54 +0200 Subject: EMBOSS 1.8.0 In-Reply-To: <200011271509.PAA09630@bromine.hgmp.mrc.ac.uk>; from ableasby@hgmp.mrc.ac.uk on Mon, Nov 27, 2000 at 03:09:22PM +0000 References: <200011271509.PAA09630@bromine.hgmp.mrc.ac.uk> Message-ID: <20001127182054.D96727@fling.sanbi.ac.za> ableasby at hgmp.mrc.ac.uk on 2000-11-27 (Mon) at 15:09:22 +0000: > > PS: The MEME program is also supplied as an "embassy" gtar file on > the ftp server and as part of the CVS tree. > This awaits documentation. The program spots "conserved" > regions in a set of sequences. Great! Speaking of EMBASSY applications, some comments: On the EMBOSS web site... - the topmost link on /Software/EMBOSS/EMBASSY/index.html points to /Software/EMBOSS/EMBASSY/EMNU/index.html which does not exist. It should point to emnu.html in the same directory. On the EMBOSS FTP site... - EMNU-1.0.0.tar.gz does not exist in /pub/EMBOSS -- Johann From jrvalverde at cnb.uam.es Mon Nov 27 12:00:31 2000 From: jrvalverde at cnb.uam.es (jrvalverde at cnb.uam.es) Date: Mon, 27 Nov 2000 18:00:31 +0100 (MET) Subject: EMBOSS 1.8.0 In-Reply-To: <200011271509.PAA09630@bromine.hgmp.mrc.ac.uk> Message-ID: <200011271700.eARH0Yp9816290@embnet.cnb.uam.es> wrote: > CODERET: Assuming you have the embl (or GenBank) database in a form > which allows access to the feature table information then this > program will return all or some of the CDS, mRNA and translations. > It caters for CDS sequences spread over different entries. > > The observant will note that some protein structure code has started > appearing in the libraries. There is also some CORBA communication > code. These are under active development but there are currently > no supplied (nearly said distributed) applications. One minor point I see in the distribution: there is effectively some "code", but it is all C code generted by ORB-it. This means one will need to install GNOME or at least ORB-it to be able to use it. Wouldn't it be better (or feasible) to distribute the IDL file and generate the hooks on the fly from the makefile using whichever ORB the user has available? j From jrvalverde at cnb.uam.es Mon Nov 27 12:09:19 2000 From: jrvalverde at cnb.uam.es (jrvalverde at cnb.uam.es) Date: Mon, 27 Nov 2000 18:09:19 +0100 (MET) Subject: MEME Message-ID: <200011271709.eARH9Kr9847484@embnet.cnb.uam.es> meme.h is missing in the distribution tar. j From gwilliam at hgmp.mrc.ac.uk Mon Nov 27 12:09:35 2000 From: gwilliam at hgmp.mrc.ac.uk (Gary Williams, Tel 01223 494522) Date: Mon, 27 Nov 2000 17:09:35 +0000 Subject: EMNU References: <200011271509.PAA09630@bromine.hgmp.mrc.ac.uk> <20001127182054.D96727@fling.sanbi.ac.za> Message-ID: <3A22954F.1D7F@hgmp.mrc.ac.uk> Johann Visagie wrote: > Great! Speaking of EMBASSY applications, some comments: > > On the EMBOSS web site... > > - the topmost link on /Software/EMBOSS/EMBASSY/index.html points to > /Software/EMBOSS/EMBASSY/EMNU/index.html which does not exist. It should > point to emnu.html in the same directory. > > On the EMBOSS FTP site... > > - EMNU-1.0.0.tar.gz does not exist in /pub/EMBOSS I'm just getting it ready to release.... watch this space! -- Gary Williams Tel: +44 1223 494522 Fax: +44 1223 494512 mailto:G.Williams at hgmp.mrc.ac.uk http://www.hgmp.mrc.ac.uk/ Bioinformatics,MRC HGMP Resource Centre,Hinxton,Cambridge, CB10 1SB,UK From ableasby at hgmp.mrc.ac.uk Mon Nov 27 12:56:07 2000 From: ableasby at hgmp.mrc.ac.uk (ableasby at hgmp.mrc.ac.uk) Date: Mon, 27 Nov 2000 17:56:07 GMT Subject: EMBOSS 1.8.0 Message-ID: <200011271756.RAA25940@tin.hgmp.mrc.ac.uk> >meme.h is missing in the distribution tar Rats! I'll fix that tonight. ORBit: Yes indeed, it will have to generate the hooks on the fly and not be tied to any particular orb. But I had to mention the code was there as someone was bound to comment :-) OK. Here is the reason that code is there..... We're rewriting the internal feature code at the moment to use a different internal representation. That representation must be able to deal with the biocorba idl. Peter is working on the features and its so we can all make sure everything meshes. The code that is there now will not be used by any applications. Structure: a very hairy problem. Ever tried downloading the SCOP flatfile and tried to find out what the numbers refer to? You end up parsing the html files. The numbers change between releases. PDB is another horrible problem. If the library is to be speedy and consistent it will have to use a partially cleaned PDB. We've constructed that but its sevral gigs. We will also be providing the ability to read most of the PDB files but there is only one parser in existence that can cope with all files (that I know of.. its by Kim Henrick) and that is enormous. Alan From ableasby at hgmp.mrc.ac.uk Mon Nov 27 16:41:54 2000 From: ableasby at hgmp.mrc.ac.uk (ableasby at hgmp.mrc.ac.uk) Date: Mon, 27 Nov 2000 21:41:54 GMT Subject: MEME Message-ID: <200011272141.VAA24803@bromine.hgmp.mrc.ac.uk> All the include files are now there in MEME-2.3.1.tar.gz on the ftp server. Apologies for the oversight. Alan From tcarver at hgmp.mrc.ac.uk Fri Nov 10 15:42:21 2000 From: tcarver at hgmp.mrc.ac.uk (Tim Carver) Date: Fri, 10 Nov 2000 15:42:21 +0000 Subject: trace file library Message-ID: <3A0C175D.5D73F6B@hgmp.mrc.ac.uk> Hi Just to let you know I am adding in some EMBOSS library fuctions to read in trace file formats (ABI/ALF). I have made a start on this for ABI trace files. If anyone has any suggestions/comments on how this would most usefully be implemented please let me know. Many Thanks Tim ------------------------------------ Tim Carver, PhD, Bioinformatics, MRC HGMP Resource Centre, Hinxton, Cambridge, CB10 1SB -------------- next part -------------- An HTML attachment was scrubbed... URL: From milius at bscl.msi.umn.edu Thu Nov 16 00:01:31 2000 From: milius at bscl.msi.umn.edu (Robert Milius) Date: Wed, 15 Nov 2000 16:01:31 -0800 Subject: data files Message-ID: Hi, I just downloaded and installed the following databases for use with EMBOSS 1.7.0: rebase prints prosite transfac and used rebaseextract, printsextract, prosextract, and tfextract to extract them for use with EMBOSS. Everything seems to work, but the databases ended up being extracted to my original source directory, not my installation point. The respective programs (eg patmatmotifs) seem to work ok. I originally did my configure using "--prefix=/usr/local/EMBOSS" and my make install went without a hitch. Did I miss setting some environmental variable or something? I have the following set: setenv PLPLOT_LIB /usr/local/EMBOSS/share/EMBOSS setenv EMBOSS_ACDROOT /usr/local/EMBOSS/share/EMBOSS/acd thanks, bob Robert P. Milius, Ph.D. 612-626-2771 (office) Basic Sciences Computing Laboratory 612-625-4433 (fax) University of Minnesota Supercomputing Institute milius at msi.umn.edu for Digital Simulation and Advanced Computation From simon.andrews at bbsrc.ac.uk Thu Nov 16 11:17:31 2000 From: simon.andrews at bbsrc.ac.uk (simon andrews (BITS)) Date: Thu, 16 Nov 2000 11:17:31 -0000 Subject: PNG libraries for OSF / CTU Unix Message-ID: <41773CEF2B8FD411920200508BDCDC120D6A13@bits-exch1.bits.bbsrc.ac.uk> Apologies if you get this message twice - I tried sending it last week but never saw it appear in the group. I am trying to compile PNG support into EMBOSS on our CTU Unix system. This requires the z, png and gd libraries, which are not on our system at the moment. Does anyone know where I can get these libraries for either OSF or CTU Unix? All the references to them I have found on the web have been for Linux. Are these platform independent (so I can use the Linux libraries)? Or do I need specific versions for our unix version? Any and all help is appreciated TTFN Simon. ---- Simon Andrews PhD Molecular Biology Support BBSRC Bioscience IT Services e.mail: simon.andrews at bbsrc.ac.uk Tel:(+44) 1582 714900 Fax:(+44) 1582 714901 From johann at egenetics.com Thu Nov 16 11:35:46 2000 From: johann at egenetics.com (Johann Visagie) Date: Thu, 16 Nov 2000 13:35:46 +0200 Subject: PNG libraries for OSF / CTU Unix In-Reply-To: <41773CEF2B8FD411920200508BDCDC120D6A13@bits-exch1.bits.bbsrc.ac.uk>; from simon.andrews@bbsrc.ac.uk on Thu, Nov 16, 2000 at 11:17:31AM -0000 References: <41773CEF2B8FD411920200508BDCDC120D6A13@bits-exch1.bits.bbsrc.ac.uk> Message-ID: <20001116133546.A78540@fling.sanbi.ac.za> simon andrews (BITS) on 2000-11-16 (Thu) at 11:17:31 -0000: > > I am trying to compile PNG support into EMBOSS on our CTU Unix system. This > requires the z, png and gd libraries, which are not on our system at the > moment. > > Does anyone know where I can get these libraries for either OSF or CTU Unix? > All the references to them I have found on the web have been for Linux. Are > these platform independent (so I can use the Linux libraries)? Or do I need > specific versions for our unix version? You should be able to compile them from the source on just about any Unix platform. http://www.info-zip.org/pub/infozip/zlib/ http://libpng.sourceforge.net/ http://www.boutell.com/gd/ -- Johann From LL at earthling.net Tue Nov 21 03:12:04 2000 From: LL at earthling.net (Long LIANG) Date: Tue, 21 Nov 2000 11:12:04 +0800 Subject: how to index the blast database formated by formatdb -v Message-ID: <3A19E804.70006@earthling.net> Hi, I have formated my htg blast database by formatdb -v to produce multiple volumes database, Could somebody tell me how to index such blast databases by using dbiblast. thanks! Long Liang, Ph.D. MD. From simon.andrews at bbsrc.ac.uk Tue Nov 21 14:43:40 2000 From: simon.andrews at bbsrc.ac.uk (simon andrews (BITS)) Date: Tue, 21 Nov 2000 14:43:40 -0000 Subject: Extracted data information Message-ID: <41773CEF2B8FD411920200508BDCDC120D6A23@bits-exch1.bits.bbsrc.ac.uk> Dear All, Firstly can I say thanks to those who pointed me in the right direction for the z, gd and png libraries - our Emboss install now makes beautiful (!?) pngs. Unfortunately I've now come up against another problem. I have Emboss installed on our development server and I'm preparing a dispatch which will send it out to about 20 remote sites. I ran the configure with the --prefix option to install to a private directory. I also collected all the data files (rebase, transfac etc.) to another directory and extracted the information from them with the relevant programs. My intention was to simply transfer the Emboss install directory and the Data directory to all sites, using symlinks where necessary so that the directory paths corresponded. However, when testing this I have found a couple of problems; 1) Although the Emboss programs work, I can't see any of the extracted data. For instance remap gives the error; EMBOSS An error in remap.c at line 167: Cannot locate enzyme file. Run REBASEEXTRACT This is despite the fact that I have both the Emboss install and the Data directories in the same place as on the development machine (which works). 2) The other major problem is that I can no longer see my databases defined in emboss.default. Again, the file exists, and is in the same place as on the development machine, but the box it is transferred to gives an empty list from showdb. Does anyone know where Emboss stores the information about the location of these files? It can't have installed anything outside the original installation directory (wasn't installed as root), so I'm guessing that the problem stems from the program resolving symlinks at some point. Again I would appreciate any help people can offer, and would be glad to report back to the group with whatever discoveries I make. Thanks in advance TTFN Simon. ---- Simon Andrews PhD Molecular Biology Support BBSRC Bioscience IT Services e.mail: simon.andrews at bbsrc.ac.uk Tel:(+44) 1582 714900 Fax:(+44) 1582 714901 From Peter.Rice at uk.lionbioscience.com Wed Nov 22 10:53:09 2000 From: Peter.Rice at uk.lionbioscience.com (Peter Rice) Date: Wed, 22 Nov 2000 10:53:09 +0000 Subject: Extracted data information References: <41773CEF2B8FD411920200508BDCDC120D6A23@bits-exch1.bits.bbsrc.ac.uk> Message-ID: <3A1BA595.E8A799DE@lionbio.co.uk> "simon andrews (BITS)" wrote: > 1) Although the Emboss programs work, I can't see any of the extracted data. > For instance remap gives the error; > > EMBOSS An error in remap.c at line 167: > Cannot locate enzyme file. Run REBASEEXTRACT > > This is despite the fact that I have both the Emboss install and the Data > directories in the same place as on the development machine (which works). > > 2) The other major problem is that I can no longer see my databases defined > in emboss.default. Again, the file exists, and is in the same place as on > the development machine, but the box it is transferred to gives an empty > list from showdb. > > Does anyone know where Emboss stores the information about the location of > these files? It can't have installed anything outside the original > installation directory (wasn't installed as root), so I'm guessing that the > problem stems from the program resolving symlinks at some point. It is inside the binaries ... EMBOSS 'knows' the location of the files because it is picked up during the configure, when you build your copy, and included in the binaries. You can see it during compilation, especially of ajnam.c (where it is used): -DAJAX_FIXED_ROOT=\"/full/source/path\" -DPREFIX=\"/install/prefix/path\" To copy binaries, you need to define environment variable(s) to override the compile-time definitions, unless you can make the path (e.g. /usr/local) the same for the installations at each site. emboss.default can set environment variables too, but you need to tell EMBOSS where to find that file. setenv EMBOSS_ROOT /dir/for/default/file and then, in the emboss.default file you can set: SET EMBOSS_ACDROOT /install/dir/share/EMBOSS/acd or (this overrides it) you can use another environment variable: SET EMBOSS_ACDROOT /install/dir/share/EMBOSS/acd -- ------------------------------------------------ Peter Rice, LION Bioscience Ltd, Cambridge, UK peter.rice at uk.lionbioscience.com +44 1223 224723 From ableasby at hgmp.mrc.ac.uk Mon Nov 27 15:09:22 2000 From: ableasby at hgmp.mrc.ac.uk (ableasby at hgmp.mrc.ac.uk) Date: Mon, 27 Nov 2000 15:09:22 GMT Subject: EMBOSS 1.8.0 Message-ID: <200011271509.PAA09630@bromine.hgmp.mrc.ac.uk> CODERET: Assuming you have the embl (or GenBank) database in a form which allows access to the feature table information then this program will return all or some of the CDS, mRNA and translations. It caters for CDS sequences spread over different entries. The observant will note that some protein structure code has started appearing in the libraries. There is also some CORBA communication code. These are under active development but there are currently no supplied (nearly said distributed) applications. Alan PS: The MEME program is also supplied as an "embassy" gtar file on the ftp server and as part of the CVS tree. This awaits documentation. The program spots "conserved" regions in a set of sequences. From johann at egenetics.com Mon Nov 27 16:20:54 2000 From: johann at egenetics.com (Johann Visagie) Date: Mon, 27 Nov 2000 18:20:54 +0200 Subject: EMBOSS 1.8.0 In-Reply-To: <200011271509.PAA09630@bromine.hgmp.mrc.ac.uk>; from ableasby@hgmp.mrc.ac.uk on Mon, Nov 27, 2000 at 03:09:22PM +0000 References: <200011271509.PAA09630@bromine.hgmp.mrc.ac.uk> Message-ID: <20001127182054.D96727@fling.sanbi.ac.za> ableasby at hgmp.mrc.ac.uk on 2000-11-27 (Mon) at 15:09:22 +0000: > > PS: The MEME program is also supplied as an "embassy" gtar file on > the ftp server and as part of the CVS tree. > This awaits documentation. The program spots "conserved" > regions in a set of sequences. Great! Speaking of EMBASSY applications, some comments: On the EMBOSS web site... - the topmost link on /Software/EMBOSS/EMBASSY/index.html points to /Software/EMBOSS/EMBASSY/EMNU/index.html which does not exist. It should point to emnu.html in the same directory. On the EMBOSS FTP site... - EMNU-1.0.0.tar.gz does not exist in /pub/EMBOSS -- Johann From jrvalverde at cnb.uam.es Mon Nov 27 17:00:31 2000 From: jrvalverde at cnb.uam.es (jrvalverde at cnb.uam.es) Date: Mon, 27 Nov 2000 18:00:31 +0100 (MET) Subject: EMBOSS 1.8.0 In-Reply-To: <200011271509.PAA09630@bromine.hgmp.mrc.ac.uk> Message-ID: <200011271700.eARH0Yp9816290@embnet.cnb.uam.es> wrote: > CODERET: Assuming you have the embl (or GenBank) database in a form > which allows access to the feature table information then this > program will return all or some of the CDS, mRNA and translations. > It caters for CDS sequences spread over different entries. > > The observant will note that some protein structure code has started > appearing in the libraries. There is also some CORBA communication > code. These are under active development but there are currently > no supplied (nearly said distributed) applications. One minor point I see in the distribution: there is effectively some "code", but it is all C code generted by ORB-it. This means one will need to install GNOME or at least ORB-it to be able to use it. Wouldn't it be better (or feasible) to distribute the IDL file and generate the hooks on the fly from the makefile using whichever ORB the user has available? j From jrvalverde at cnb.uam.es Mon Nov 27 17:09:19 2000 From: jrvalverde at cnb.uam.es (jrvalverde at cnb.uam.es) Date: Mon, 27 Nov 2000 18:09:19 +0100 (MET) Subject: MEME Message-ID: <200011271709.eARH9Kr9847484@embnet.cnb.uam.es> meme.h is missing in the distribution tar. j From gwilliam at hgmp.mrc.ac.uk Mon Nov 27 17:09:35 2000 From: gwilliam at hgmp.mrc.ac.uk (Gary Williams, Tel 01223 494522) Date: Mon, 27 Nov 2000 17:09:35 +0000 Subject: EMNU References: <200011271509.PAA09630@bromine.hgmp.mrc.ac.uk> <20001127182054.D96727@fling.sanbi.ac.za> Message-ID: <3A22954F.1D7F@hgmp.mrc.ac.uk> Johann Visagie wrote: > Great! Speaking of EMBASSY applications, some comments: > > On the EMBOSS web site... > > - the topmost link on /Software/EMBOSS/EMBASSY/index.html points to > /Software/EMBOSS/EMBASSY/EMNU/index.html which does not exist. It should > point to emnu.html in the same directory. > > On the EMBOSS FTP site... > > - EMNU-1.0.0.tar.gz does not exist in /pub/EMBOSS I'm just getting it ready to release.... watch this space! -- Gary Williams Tel: +44 1223 494522 Fax: +44 1223 494512 mailto:G.Williams at hgmp.mrc.ac.uk http://www.hgmp.mrc.ac.uk/ Bioinformatics,MRC HGMP Resource Centre,Hinxton,Cambridge, CB10 1SB,UK From ableasby at hgmp.mrc.ac.uk Mon Nov 27 17:56:07 2000 From: ableasby at hgmp.mrc.ac.uk (ableasby at hgmp.mrc.ac.uk) Date: Mon, 27 Nov 2000 17:56:07 GMT Subject: EMBOSS 1.8.0 Message-ID: <200011271756.RAA25940@tin.hgmp.mrc.ac.uk> >meme.h is missing in the distribution tar Rats! I'll fix that tonight. ORBit: Yes indeed, it will have to generate the hooks on the fly and not be tied to any particular orb. But I had to mention the code was there as someone was bound to comment :-) OK. Here is the reason that code is there..... We're rewriting the internal feature code at the moment to use a different internal representation. That representation must be able to deal with the biocorba idl. Peter is working on the features and its so we can all make sure everything meshes. The code that is there now will not be used by any applications. Structure: a very hairy problem. Ever tried downloading the SCOP flatfile and tried to find out what the numbers refer to? You end up parsing the html files. The numbers change between releases. PDB is another horrible problem. If the library is to be speedy and consistent it will have to use a partially cleaned PDB. We've constructed that but its sevral gigs. We will also be providing the ability to read most of the PDB files but there is only one parser in existence that can cope with all files (that I know of.. its by Kim Henrick) and that is enormous. Alan From ableasby at hgmp.mrc.ac.uk Mon Nov 27 21:41:54 2000 From: ableasby at hgmp.mrc.ac.uk (ableasby at hgmp.mrc.ac.uk) Date: Mon, 27 Nov 2000 21:41:54 GMT Subject: MEME Message-ID: <200011272141.VAA24803@bromine.hgmp.mrc.ac.uk> All the include files are now there in MEME-2.3.1.tar.gz on the ftp server. Apologies for the oversight. Alan