From sabino at area.ba.cnr.it Mon Apr 2 11:02:08 2001 From: sabino at area.ba.cnr.it (Sabino Liuni) Date: Mon, 02 Apr 2001 17:02:08 +0200 Subject: Compseq error Message-ID: <5.0.2.1.0.20010402165534.00aa5cd0@area.ba.cnr.it> Hello everybody I have received this information from our user about the Compseq program. Any suggestion Regards, sabino Liuni --------------------------------- I have noticed that the EMBOSS program COMPSEQ calculates incorrectly w-mer nucleotide frequencies. For example the result obtained asking for mononuc composition is like the following: Total count 2846880 # # Word Obs Count Obs Frequency Exp Frequency Obs/Exp Frequency # A 968947 0.3403540 0.2500000 1.3614160 C 454493 0.1596460 0.2500000 0.6385840 G 454493 0.1596460 0.2500000 0.6385840 T 968947 0.3403540 0.2500000 1.3614160 It seems sum up A+T and C+G. ----------------------------------------------------------------- Bioinformatics and Genomic Group - C.N.R. Italian EMBnet Node Via Amendola 166/5 - 70126 Bari (Italy) Tel. +39-80-5482130 - Fax. +39-80-5484467 e_mail:sabino at area.ba.cnr.it From gwilliam at hgmp.mrc.ac.uk Mon Apr 2 11:12:08 2001 From: gwilliam at hgmp.mrc.ac.uk (Gary Williams, Tel 01223 494522) Date: Mon, 02 Apr 2001 16:12:08 +0100 Subject: Compseq error References: <5.0.2.1.0.20010402165534.00aa5cd0@area.ba.cnr.it> Message-ID: <3AC896C8.390F0FEA@hgmp.mrc.ac.uk> The default action with nucleic acid sequences is to do the composition analysis on both the forward and the reverse sense. This action was requested by a user when the program was first being written. In the case that you have, with a word size of 1, this does indeed give very strange-looking results where A = T and C = G. Try using 'compseq -noreverse' if you wish to only look at the forward sense. Gary Sabino Liuni wrote: > > Hello everybody > > I have received this information from our user about the Compseq program. > Any suggestion > > Regards, > > sabino Liuni > > --------------------------------- > I have noticed that the EMBOSS program COMPSEQ calculates incorrectly w-mer > nucleotide frequencies. For example the result obtained asking for mononuc > composition is like the following: > Total count 2846880 > # > # Word Obs Count Obs Frequency Exp Frequency Obs/Exp Frequency > # > A 968947 0.3403540 0.2500000 > 1.3614160 > C 454493 0.1596460 0.2500000 > 0.6385840 > G 454493 0.1596460 0.2500000 > 0.6385840 > T 968947 0.3403540 0.2500000 > 1.3614160 > > It seems sum up A+T and C+G. > ----------------------------------------------------------------- -- 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 mad at biol.unlp.edu.ar Fri Apr 6 15:01:50 2001 From: mad at biol.unlp.edu.ar (Sarachu Martin) Date: Fri, 6 Apr 2001 15:01:50 -0400 Subject: wEMBOSS - web interface for EMBOSS Message-ID: <200104061901.f36J1oD02783@nahuel.biol.unlp.edu.ar> Hi, I'm writing to announce wEMBOSS, a new web interface for EMBOSS. This interface was completely developed at the Argentinian EMBNet node Homepage at http://sol.biol.unlp.edu.ar/wEMBOSS You can test the interface at http://sol.biol.unlp.edu.ar/cgi-bin/embnet/wEMBOSS Mart?n From dmartin at davasg4.msiwtb.dundee.ac.uk Sat Apr 7 12:20:31 2001 From: dmartin at davasg4.msiwtb.dundee.ac.uk (David Martin) Date: Sat, 7 Apr 2001 17:20:31 +0100 Subject: wEMBOSS - web interface for EMBOSS In-Reply-To: <200104061901.f36J1oD02783@nahuel.biol.unlp.edu.ar> Message-ID: On Fri, 6 Apr 2001, Sarachu Martin wrote: > Hi, > > I'm writing to announce wEMBOSS, a new web interface for > EMBOSS. This interface was completely developed at the > Argentinian EMBNet node > Homepage at http://sol.biol.unlp.edu.ar/wEMBOSS > You can test the interface at > http://sol.biol.unlp.edu.ar/cgi-bin/embnet/wEMBOSS I get a 'not found' error.. I like the idea though.. ..d > > Mart?n > From bauer at genprofile.com Mon Apr 9 03:12:27 2001 From: bauer at genprofile.com (David Bauer) Date: Mon, 09 Apr 2001 09:12:27 +0200 Subject: wEMBOSS Message-ID: <3AD160DB.A5E0382C@genprofile.com> Hi, I'm just testing your web interface. I like it. It's easy to install and a good solution for use in an intranet. Here are some comments: 1) Under 'Installation' you should mention that the script requires the CGI.pm module and maybe put a link where to download it (CPAN or CSH). 2) Within the script it is not clear that the 'writeDIR' is an absolute path and the 'graphicsDir' is relative to the httpd document root because on top there is written that all names are full pathnames. 3) I had to add $ENV{"PATH"}="/bin:/usr/bin:/usr/local/bin"; to the script. Otherwise it did not find the EMBOSS executables. 4) Graphical output has a problem. It works nice with png. But if I select postscript, then the name of the graphical file is also written as 'IMG src' which then does not work. What about changing this to present as result a page with a link to the graphical file. If it can be rendered by the browser, it will showup within the browser. Postscript and other formats can be either processed by helper applications or saved for local use. David. -- Dr. David Bauer GenProfile AG, Max-Delbrueck-Center, Erwin-Negelein-Haus Robert-Roessle-Str. 10, D-13125 Berlin, Germany bauer at genprofile.com, Tel:49-30-94892165, FAX:49-30-94892151 From mad at biol.unlp.edu.ar Mon Apr 9 09:38:50 2001 From: mad at biol.unlp.edu.ar (Sarachu Martin) Date: Mon, 9 Apr 2001 09:38:50 -0400 Subject: wEMBOSS In-Reply-To: <3AD160DB.A5E0382C@genprofile.com> References: <3AD160DB.A5E0382C@genprofile.com> Message-ID: <200104091338.f39Dcov05646@nahuel.biol.unlp.edu.ar> Hi David, Thanks for your comments. Now for the specifics Mensaje citado por: David Bauer : > Hi, > > I'm just testing your web interface. I like it. It's easy to install and > a good solution for use in an intranet. > Here are some comments: > 1) > Under 'Installation' you should mention that the script requires the > CGI.pm module and maybe put a link where to download it (CPAN or CSH). Yes, I should mention that. Will correct > 2) > Within the script it is not clear that the 'writeDIR' is an absolute > path and the 'graphicsDir' is relative to the httpd document root > because on top there is written that all names are full pathnames. I have to make clearer comments... > 3) > I had to add > $ENV{"PATH"}="/bin:/usr/bin:/usr/local/bin"; > to the script. Otherwise it did not find the EMBOSS executables. I assumed that EMBOSS programs path will be in the PATH variable of the web server. What do you think about this? > 4) > Graphical output has a problem. It works nice with png. But if I select > postscript, then the name of the graphical file is also written as 'IMG > src' which then does not work. What about changing this to present as > result a page with a link to the graphical file. If it can be rendered > by the browser, it will showup within the browser. Postscript and other > formats can be either processed by helper applications or saved for > local use. Hmmm... I didn't thought of that. My first approach was to put all images into the tag so all the information would be "into" the page. You gave something to think about. Martin. From jrvalverde at cnb.uam.es Mon Apr 9 12:33:11 2001 From: jrvalverde at cnb.uam.es (jrvalverde at cnb.uam.es) Date: Mon, 9 Apr 2001 18:33:11 +0200 (DST) Subject: wEMBOSS In-Reply-To: <200104091338.f39Dcov05646@nahuel.biol.unlp.edu.ar> Message-ID: <200104091633.f39GXCb140642@embnet.cnb.uam.es> Sarachu Martin wrote: > > > 3) > > I had to add > > $ENV{"PATH"}="/bin:/usr/bin:/usr/local/bin"; > > to the script. Otherwise it did not find the EMBOSS > executables. > > I assumed that EMBOSS programs path will be in the PATH > variable of the web server. What do you think about > this? > Not everybody has it on the PATH. At least not me. We have a humongous amount of packages here, and including all their paths in PATH would exceed maximum allowable variable length. What we do have is a script that users run to add/remove packages to their environment as needed. I'd rather favour a perl variable $emboss_bin = "/your/path/to/emboss"; (which is How I'm modifying the script to make it work and then refer to applications as "$emboss_bin/$application" j From dmartin at davasg4.msiwtb.dundee.ac.uk Tue Apr 10 17:42:00 2001 From: dmartin at davasg4.msiwtb.dundee.ac.uk (David Martin) Date: Tue, 10 Apr 2001 22:42:00 +0100 Subject: EMBOSS on OS X Message-ID: Has anyone tried compiling and running EMBOSS on MacOS X yet? I can imagine this being very nice with the X interfaces (Colimate etc). ..d From johann at egenetics.com Wed Apr 11 03:35:11 2001 From: johann at egenetics.com (Johann Visagie) Date: Wed, 11 Apr 2001 09:35:11 +0200 Subject: EMBOSS on OS X In-Reply-To: ; from dmartin@davasg4.msiwtb.dundee.ac.uk on Tue, Apr 10, 2001 at 10:42:00PM +0100 References: Message-ID: <20010411093511.E44950@fling.sanbi.ac.za> David Martin wrote (to the EMBOSS list): > > Has anyone tried compiling and running EMBOSS on MacOS X yet? I can > imagine this being very nice with the X interfaces (Colimate etc). And Richard Phelps wrote (to me personally): > > How might I install emboss on Mac Os X?? Well, personally, I think I've touched the keyboard of a Mac maybe five times in my life (they're not common here at all), so it's highly unlikely I'll have the pleasure of using MacOS X any time soon. However: - It would be interesting to know how easily an application with a relatively GNUish installation process compiles and installs on OS X. I would personally be very interested in feedback. (Shouldn't be too difficult by all reports.) - Secondly, there is a project underway (though it's in its early stages yet) to unify packaging systems across a number of BSD-based operating systems, including OS X. In fact, Wilfredo Sanches, the former design lead on OS X, is a developer on this project. Should their work come to fruition, it's possible that the existing FreeBSD port could eventually serve as the basis for installing EMBOSS on OS X as well. :-) See: http://www.openpackages.org/ -- Johann From ame at esbs.u-strasbg.fr Wed Apr 11 04:59:38 2001 From: ame at esbs.u-strasbg.fr (Jean-Christophe Ame) Date: Wed, 11 Apr 2001 10:59:38 +0200 Subject: EMBOSS on OS X In-Reply-To: <20010411093511.E44950@fling.sanbi.ac.za> References: <20010411093511.E44950@fling.sanbi.ac.za> Message-ID: I have installed EMBOSS on MacOSX since the release of the public beta ant it works like a charm. There is no problem installing it, one needs just to remove -lnsl everywhere in the configure file. Jean-Christophe >David Martin wrote (to the EMBOSS list): >> >> Has anyone tried compiling and running EMBOSS on MacOS X yet? I can >> imagine this being very nice with the X interfaces (Colimate etc). > >And Richard Phelps wrote (to me personally): >> >> How might I install emboss on Mac Os X?? > >Well, personally, I think I've touched the keyboard of a Mac maybe five times >in my life (they're not common here at all), so it's highly unlikely I'll >have the pleasure of using MacOS X any time soon. > >However: > >- It would be interesting to know how easily an application with a relatively > GNUish installation process compiles and installs on OS X. I would > personally be very interested in feedback. (Shouldn't be too difficult by > all reports.) > >- Secondly, there is a project underway (though it's in its early stages yet) > to unify packaging systems across a number of BSD-based operating systems, > including OS X. In fact, Wilfredo Sanches, the former design lead on OS X, > is a developer on this project. Should their work come to fruition, it's > possible that the existing FreeBSD port could eventually serve as the basis > for installing EMBOSS on OS X as well. :-) See: > > http://www.openpackages.org/ > >-- Johann -- ________________________ Jean-Christophe Am?, PhD U.P.R. 9003 du CNRS - Canc?rog?n?se Et Mutag?n?se Mol?culaire Et Structurale ?cole Sup?rieure De Biotechnologie De Strasbourg P?le API Boulevard S?bastien-Brant 67400 Illkirch France tel.: 03 90 24 47 05 Fax.: 03 90 24 46 86 From CHOO_Keng_Wah at nyp.gov.sg Tue Apr 17 04:43:21 2001 From: CHOO_Keng_Wah at nyp.gov.sg (CHOO_Keng_Wah at nyp.gov.sg) Date: Tue, 17 Apr 2001 16:43:21 +0800 Subject: database access Message-ID: Deal all, I've just installed the EMBOSS-1.11.0 on my LINUX Red Hat 7.2 and I couldn't setup a connection to any database. Can soneone help me? Thank you. Jerome Choo From ableasby at hgmp.mrc.ac.uk Tue Apr 17 11:40:17 2001 From: ableasby at hgmp.mrc.ac.uk (ableasby at hgmp.mrc.ac.uk) Date: Tue, 17 Apr 2001 16:40:17 +0100 (BST) Subject: EMBOSS 1.12.0 Message-ID: <200104171540.QAA15078@tin.hgmp.mrc.ac.uk> EMBOSS 1.12.0 contains the following new programs in addition to the usual load of library mods/fixes/etc. Distmat: Creates a distance matrix from multiple alignments of nucleotide or protein sequences. The sequences need to be aligned before running this program. The quality of the alignment is of paramount importance in obtaining meaningful information from this analysis. Charge: Simple sliding window plot of charge vs position in a protein sequence. Cai: Codon adaptive index calculation. A measurement of the level of usage of the 64 codons in a sequence. Alan From btiwari at molbiol.ox.ac.uk Wed Apr 18 12:00:45 2001 From: btiwari at molbiol.ox.ac.uk (Bela Tiwari) Date: Wed, 18 Apr 2001 17:00:45 +0100 (BST) Subject: EMBOSS 1.12.0 Message-ID: Hello I hope this is the correct address to write to. I am writing from the Bioinformatics Centre at the University of Oxford. I just installed EMBOSS 1.12.0 and noticed that the applications in the emboss directory do not appear to get world r-x permissions set, which I'm pretty sure they did before. Just thought I'd mention it in case its not supposed to be this way. Cheers Bela .-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.- Dr. Bela Tiwari Bioinformatics Officer OU Bioinformatics Centre South Parks Road, 01865 (2)75507 Oxford OX1 3RE http://www.molbiol.ox.ac.uk .-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.- From ableasby at hgmp.mrc.ac.uk Wed Apr 18 12:45:46 2001 From: ableasby at hgmp.mrc.ac.uk (ableasby at hgmp.mrc.ac.uk) Date: Wed, 18 Apr 2001 17:45:46 +0100 (BST) Subject: EMBOSS 1.12.0 contacts.c Message-ID: <200104181645.RAA19931@tin.hgmp.mrc.ac.uk> Further to Bela's post we cannot reproduce the symptoms described. If anyone else notices this please send details to emboss-bug at embnet.org detailing your umask setting as well as usual version/system info. Bela has noticed a problem in the not-compiled-by-default applications you can get by typing "make check" in the applications directory. These applications are usually ones under development or examples and certainly come under a use at your peril heading etc. There is a typo in contacts.c in this section. A patch file has been put in the "patchfiles" directory of the ftp server. Again, this does not affect the workings of the main package you get from the recommended plain "make", it only affects the adventurous. Alan From charles at moulinette.dyndns.org Sun Apr 22 18:00:16 2001 From: charles at moulinette.dyndns.org (Charles) Date: Mon, 23 Apr 2001 00:00:16 +0200 (CEST) Subject: database access In-Reply-To: Message-ID: On Tue, 17 Apr 2001 CHOO_Keng_Wah at nyp.gov.sg wrote: > Deal all, > I've just installed the EMBOSS-1.11.0 on my LINUX Red Hat 7.2 and I > couldn't setup a connection to any database. > Can soneone help me? > I'm more or less at the same point than you : i've installed emboss on a debian woody (for self-training and satisfying curiosity), and could not get the time so sit down in front of the database installation manual, which is hard to understand for the unfamiliar reader. I copied the emboss.default file to .embossrc in my home directory, and uncommented the examples of genebank accassion by the internet. Well, if you have an unlimited internet access, i think it is the quicker way to proceed. However, i dont't even know if www.ca.embnet.org is designed to provide sequences to everybody, and i don't understand the syntax used. Hope this helps, Charles From ableasby at hgmp.mrc.ac.uk Sun Apr 22 18:52:02 2001 From: ableasby at hgmp.mrc.ac.uk (ableasby at hgmp.mrc.ac.uk) Date: Sun, 22 Apr 2001 23:52:02 +0100 (BST) Subject: database access Message-ID: <200104222252.XAA21974@tin.hgmp.mrc.ac.uk> In response to Charles: www.ca.embnet.org is designed to provide sequences to everybody this way. Like most EMBnet (European Molecular Biology network) sites it has an SRS server. The Canadian node is the only one I know that provides GenBank this way, most of us provide EMBL instead. You can play interactively with the Canadian server directly by using: http://www.ca.embnet.org/srs6.1/ It should then become clear what the DB entry is doing. As an addendum the original query was solved (typically) behind the scenes and was just an emboss.default file in the wrong place. I'm tempted to put this file in the emboss directory itself under a filename like: emboss.default.example . Historically the file is where it is to avoid new installations overwriting your own copy but the above would serve the same purpose. Alan (http://srs.hgmp.mrc.ac.uk/srs6/) From dessen at infobiogen.fr Mon Apr 23 02:42:05 2001 From: dessen at infobiogen.fr (Philippe Dessen) Date: Mon, 23 Apr 2001 08:42:05 +0200 (MET DST) Subject: database access GenBank In-Reply-To: <200104222252.XAA21974@tin.hgmp.mrc.ac.uk> from "ableasby@hgmp.mrc.ac.uk" at Apr 22, 2001 11:52:02 PM Message-ID: <200104230642.IAA12068@lovelace.infobiogen.fr> > > In response to Charles: > www.ca.embnet.org is designed to provide sequences to everybody this > way. Like most EMBnet (European Molecular Biology network) sites it > has an SRS server. The Canadian node is the only one I know that > provides GenBank this way, most of us provide EMBL instead. > You can play interactively with the Canadian server directly by using: > http://www.ca.embnet.org/srs6.1/ > It should then become clear what the DB entry is doing. > > As an addendum the original query was solved (typically) behind the scenes > and was just an emboss.default file in the wrong place. I'm tempted > to put this file in the emboss directory itself under a filename like: > emboss.default.example . Historically the file is where it is to > avoid new installations overwriting your own copy but the above would serve > the same purpose. > > Alan > > (http://srs.hgmp.mrc.ac.uk/srs6/) > > In the old EMBnet world, INFOBIOGEN offers GenBank on its SRS server since 1993 ... http://www.infobiogen.fr/srs6/. Regards Philippe Dessen From dmartin at gen67172.msiwtb.dundee.ac.uk Mon Apr 23 03:51:17 2001 From: dmartin at gen67172.msiwtb.dundee.ac.uk (David Martin) Date: Mon, 23 Apr 2001 08:51:17 +0100 (BST) Subject: database access In-Reply-To: Message-ID: On Mon, 23 Apr 2001, Charles wrote: > > > On Tue, 17 Apr 2001 CHOO_Keng_Wah at nyp.gov.sg wrote: > > > Deal all, > > I've just installed the EMBOSS-1.11.0 on my LINUX Red Hat 7.2 and I > > couldn't setup a connection to any database. > > Can soneone help me? > > > > I'm more or less at the same point than you : i've installed emboss on a > debian woody (for self-training and satisfying curiosity), and could not > get the time so sit down in front of the database installation manual, > which is hard to understand for the unfamiliar reader. OK.. if you have any suggestions on improving it I will see what I can do. When I wrote the manual it was because I wasn't clear how things were supposed to be set up, so I asked a lot of questions and hassled Peter Rice and Alan to give me the answers. Would a 'quick guide to setting up the EMBL database' section or similar help? > > I copied the emboss.default file to .embossrc in my home directory, and > uncommented the examples of genebank accassion by the internet. The example file isn't the best of examples. A case for better annotation. I'll add it to my list of 'things to do'. > > Well, if you have an unlimited internet access, i think it is the quicker > way to proceed. However, i dont't even know if www.ca.embnet.org is > designed to provide sequences to everybody, and i don't > understand the syntax used. > To be perfectly honest neither do I but it seems to work.. the syntax is the various arguments given to the wgetz script in the srs server. I notice looking through the admin guide that I have omitted www as a method for database retrieval. I'll add that in to the next version plus some notes on OS X and SuSE 7.1. If anyone else would care to contribute any installation quirks or workarounds they may have had to do (eg. a list of packages required for Debian to run EMBOSS and so on..) then I would be grateful for them. ..d > Hope this helps, > > Charles > From peter.rice at uk.lionbioscience.com Mon Apr 23 04:44:36 2001 From: peter.rice at uk.lionbioscience.com (Peter Rice) Date: Mon, 23 Apr 2001 09:44:36 +0100 Subject: database access References: <200104222252.XAA21974@tin.hgmp.mrc.ac.uk> Message-ID: <3AE3EB74.44E0B84D@uk.lionbioscience.com> ableasby at hgmp.mrc.ac.uk wrote: > > In response to Charles: > www.ca.embnet.org is designed to provide sequences to everybody this > way. Like most EMBnet (European Molecular Biology network) sites it > has an SRS server. The Canadian node is the only one I know that > provides GenBank this way, most of us provide EMBL instead. > You can play interactively with the Canadian server directly by using: > http://www.ca.embnet.org/srs6.1/ > It should then become clear what the DB entry is doing. There are a few others, all up to date: Denmark http://www.dk.embnet.org/srs6/ Finland http://srs.csc.fi:8002/srs6/ France http://www.fr.embnet.org/srs6/ Germany http://genius.embnet.dkfz-heidelberg.de/menu/srs/ The Netherlands EMBnet node has a Genbank database under SRS, but it only contains a few entries (under 250) that are not quite the same in EMBL, and is not the full database. The United Kingdom EMBnet node (Alan's own :-) used to run GenBank as well as EMBL until recently, and was the original source of Genbank in the emboss.defaults file. You can also use NCBI's Entrez for GenBank. regards, Peter Rice -- ------------------------------------------------ Peter Rice, LION Bioscience Ltd, Cambridge, UK peter.rice at uk.lionbioscience.com +44 1223 224723 From charles at moulinette.dyndns.org Mon Apr 30 13:20:34 2001 From: charles at moulinette.dyndns.org (Charles) Date: Mon, 30 Apr 2001 19:20:34 +0200 (CEST) Subject: Installing Database Message-ID: Hello, I'm using emboss for self-training, and I don't have tons of free disk space. I spent an hour this week-end, trying to see if one can install only a subset of a database. For example I would like to install a database containing only zebrafish ESTs. >From the admin guide it seems possible to install the whole database, and to configure a kind of alias, restricted to a section, like rodents for example. But that's not exactly what I want to do... I couldn't find a database subset isolated as a file, so I suspect that I'm trying to do an impossible thing. Can anybody confirm? Charles From sabino at area.ba.cnr.it Mon Apr 2 15:02:08 2001 From: sabino at area.ba.cnr.it (Sabino Liuni) Date: Mon, 02 Apr 2001 17:02:08 +0200 Subject: Compseq error Message-ID: <5.0.2.1.0.20010402165534.00aa5cd0@area.ba.cnr.it> Hello everybody I have received this information from our user about the Compseq program. Any suggestion Regards, sabino Liuni --------------------------------- I have noticed that the EMBOSS program COMPSEQ calculates incorrectly w-mer nucleotide frequencies. For example the result obtained asking for mononuc composition is like the following: Total count 2846880 # # Word Obs Count Obs Frequency Exp Frequency Obs/Exp Frequency # A 968947 0.3403540 0.2500000 1.3614160 C 454493 0.1596460 0.2500000 0.6385840 G 454493 0.1596460 0.2500000 0.6385840 T 968947 0.3403540 0.2500000 1.3614160 It seems sum up A+T and C+G. ----------------------------------------------------------------- Bioinformatics and Genomic Group - C.N.R. Italian EMBnet Node Via Amendola 166/5 - 70126 Bari (Italy) Tel. +39-80-5482130 - Fax. +39-80-5484467 e_mail:sabino at area.ba.cnr.it From gwilliam at hgmp.mrc.ac.uk Mon Apr 2 15:12:08 2001 From: gwilliam at hgmp.mrc.ac.uk (Gary Williams, Tel 01223 494522) Date: Mon, 02 Apr 2001 16:12:08 +0100 Subject: Compseq error References: <5.0.2.1.0.20010402165534.00aa5cd0@area.ba.cnr.it> Message-ID: <3AC896C8.390F0FEA@hgmp.mrc.ac.uk> The default action with nucleic acid sequences is to do the composition analysis on both the forward and the reverse sense. This action was requested by a user when the program was first being written. In the case that you have, with a word size of 1, this does indeed give very strange-looking results where A = T and C = G. Try using 'compseq -noreverse' if you wish to only look at the forward sense. Gary Sabino Liuni wrote: > > Hello everybody > > I have received this information from our user about the Compseq program. > Any suggestion > > Regards, > > sabino Liuni > > --------------------------------- > I have noticed that the EMBOSS program COMPSEQ calculates incorrectly w-mer > nucleotide frequencies. For example the result obtained asking for mononuc > composition is like the following: > Total count 2846880 > # > # Word Obs Count Obs Frequency Exp Frequency Obs/Exp Frequency > # > A 968947 0.3403540 0.2500000 > 1.3614160 > C 454493 0.1596460 0.2500000 > 0.6385840 > G 454493 0.1596460 0.2500000 > 0.6385840 > T 968947 0.3403540 0.2500000 > 1.3614160 > > It seems sum up A+T and C+G. > ----------------------------------------------------------------- -- 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 mad at biol.unlp.edu.ar Fri Apr 6 19:01:50 2001 From: mad at biol.unlp.edu.ar (Sarachu Martin) Date: Fri, 6 Apr 2001 15:01:50 -0400 Subject: wEMBOSS - web interface for EMBOSS Message-ID: <200104061901.f36J1oD02783@nahuel.biol.unlp.edu.ar> Hi, I'm writing to announce wEMBOSS, a new web interface for EMBOSS. This interface was completely developed at the Argentinian EMBNet node Homepage at http://sol.biol.unlp.edu.ar/wEMBOSS You can test the interface at http://sol.biol.unlp.edu.ar/cgi-bin/embnet/wEMBOSS Mart?n From dmartin at davasg4.msiwtb.dundee.ac.uk Sat Apr 7 16:20:31 2001 From: dmartin at davasg4.msiwtb.dundee.ac.uk (David Martin) Date: Sat, 7 Apr 2001 17:20:31 +0100 Subject: wEMBOSS - web interface for EMBOSS In-Reply-To: <200104061901.f36J1oD02783@nahuel.biol.unlp.edu.ar> Message-ID: On Fri, 6 Apr 2001, Sarachu Martin wrote: > Hi, > > I'm writing to announce wEMBOSS, a new web interface for > EMBOSS. This interface was completely developed at the > Argentinian EMBNet node > Homepage at http://sol.biol.unlp.edu.ar/wEMBOSS > You can test the interface at > http://sol.biol.unlp.edu.ar/cgi-bin/embnet/wEMBOSS I get a 'not found' error.. I like the idea though.. ..d > > Mart?n > From bauer at genprofile.com Mon Apr 9 07:12:27 2001 From: bauer at genprofile.com (David Bauer) Date: Mon, 09 Apr 2001 09:12:27 +0200 Subject: wEMBOSS Message-ID: <3AD160DB.A5E0382C@genprofile.com> Hi, I'm just testing your web interface. I like it. It's easy to install and a good solution for use in an intranet. Here are some comments: 1) Under 'Installation' you should mention that the script requires the CGI.pm module and maybe put a link where to download it (CPAN or CSH). 2) Within the script it is not clear that the 'writeDIR' is an absolute path and the 'graphicsDir' is relative to the httpd document root because on top there is written that all names are full pathnames. 3) I had to add $ENV{"PATH"}="/bin:/usr/bin:/usr/local/bin"; to the script. Otherwise it did not find the EMBOSS executables. 4) Graphical output has a problem. It works nice with png. But if I select postscript, then the name of the graphical file is also written as 'IMG src' which then does not work. What about changing this to present as result a page with a link to the graphical file. If it can be rendered by the browser, it will showup within the browser. Postscript and other formats can be either processed by helper applications or saved for local use. David. -- Dr. David Bauer GenProfile AG, Max-Delbrueck-Center, Erwin-Negelein-Haus Robert-Roessle-Str. 10, D-13125 Berlin, Germany bauer at genprofile.com, Tel:49-30-94892165, FAX:49-30-94892151 From mad at biol.unlp.edu.ar Mon Apr 9 13:38:50 2001 From: mad at biol.unlp.edu.ar (Sarachu Martin) Date: Mon, 9 Apr 2001 09:38:50 -0400 Subject: wEMBOSS In-Reply-To: <3AD160DB.A5E0382C@genprofile.com> References: <3AD160DB.A5E0382C@genprofile.com> Message-ID: <200104091338.f39Dcov05646@nahuel.biol.unlp.edu.ar> Hi David, Thanks for your comments. Now for the specifics Mensaje citado por: David Bauer : > Hi, > > I'm just testing your web interface. I like it. It's easy to install and > a good solution for use in an intranet. > Here are some comments: > 1) > Under 'Installation' you should mention that the script requires the > CGI.pm module and maybe put a link where to download it (CPAN or CSH). Yes, I should mention that. Will correct > 2) > Within the script it is not clear that the 'writeDIR' is an absolute > path and the 'graphicsDir' is relative to the httpd document root > because on top there is written that all names are full pathnames. I have to make clearer comments... > 3) > I had to add > $ENV{"PATH"}="/bin:/usr/bin:/usr/local/bin"; > to the script. Otherwise it did not find the EMBOSS executables. I assumed that EMBOSS programs path will be in the PATH variable of the web server. What do you think about this? > 4) > Graphical output has a problem. It works nice with png. But if I select > postscript, then the name of the graphical file is also written as 'IMG > src' which then does not work. What about changing this to present as > result a page with a link to the graphical file. If it can be rendered > by the browser, it will showup within the browser. Postscript and other > formats can be either processed by helper applications or saved for > local use. Hmmm... I didn't thought of that. My first approach was to put all images into the tag so all the information would be "into" the page. You gave something to think about. Martin. From jrvalverde at cnb.uam.es Mon Apr 9 16:33:11 2001 From: jrvalverde at cnb.uam.es (jrvalverde at cnb.uam.es) Date: Mon, 9 Apr 2001 18:33:11 +0200 (DST) Subject: wEMBOSS In-Reply-To: <200104091338.f39Dcov05646@nahuel.biol.unlp.edu.ar> Message-ID: <200104091633.f39GXCb140642@embnet.cnb.uam.es> Sarachu Martin wrote: > > > 3) > > I had to add > > $ENV{"PATH"}="/bin:/usr/bin:/usr/local/bin"; > > to the script. Otherwise it did not find the EMBOSS > executables. > > I assumed that EMBOSS programs path will be in the PATH > variable of the web server. What do you think about > this? > Not everybody has it on the PATH. At least not me. We have a humongous amount of packages here, and including all their paths in PATH would exceed maximum allowable variable length. What we do have is a script that users run to add/remove packages to their environment as needed. I'd rather favour a perl variable $emboss_bin = "/your/path/to/emboss"; (which is How I'm modifying the script to make it work and then refer to applications as "$emboss_bin/$application" j From dmartin at davasg4.msiwtb.dundee.ac.uk Tue Apr 10 21:42:00 2001 From: dmartin at davasg4.msiwtb.dundee.ac.uk (David Martin) Date: Tue, 10 Apr 2001 22:42:00 +0100 Subject: EMBOSS on OS X Message-ID: Has anyone tried compiling and running EMBOSS on MacOS X yet? I can imagine this being very nice with the X interfaces (Colimate etc). ..d From johann at egenetics.com Wed Apr 11 07:35:11 2001 From: johann at egenetics.com (Johann Visagie) Date: Wed, 11 Apr 2001 09:35:11 +0200 Subject: EMBOSS on OS X In-Reply-To: ; from dmartin@davasg4.msiwtb.dundee.ac.uk on Tue, Apr 10, 2001 at 10:42:00PM +0100 References: Message-ID: <20010411093511.E44950@fling.sanbi.ac.za> David Martin wrote (to the EMBOSS list): > > Has anyone tried compiling and running EMBOSS on MacOS X yet? I can > imagine this being very nice with the X interfaces (Colimate etc). And Richard Phelps wrote (to me personally): > > How might I install emboss on Mac Os X?? Well, personally, I think I've touched the keyboard of a Mac maybe five times in my life (they're not common here at all), so it's highly unlikely I'll have the pleasure of using MacOS X any time soon. However: - It would be interesting to know how easily an application with a relatively GNUish installation process compiles and installs on OS X. I would personally be very interested in feedback. (Shouldn't be too difficult by all reports.) - Secondly, there is a project underway (though it's in its early stages yet) to unify packaging systems across a number of BSD-based operating systems, including OS X. In fact, Wilfredo Sanches, the former design lead on OS X, is a developer on this project. Should their work come to fruition, it's possible that the existing FreeBSD port could eventually serve as the basis for installing EMBOSS on OS X as well. :-) See: http://www.openpackages.org/ -- Johann From ame at esbs.u-strasbg.fr Wed Apr 11 08:59:38 2001 From: ame at esbs.u-strasbg.fr (Jean-Christophe Ame) Date: Wed, 11 Apr 2001 10:59:38 +0200 Subject: EMBOSS on OS X In-Reply-To: <20010411093511.E44950@fling.sanbi.ac.za> References: <20010411093511.E44950@fling.sanbi.ac.za> Message-ID: I have installed EMBOSS on MacOSX since the release of the public beta ant it works like a charm. There is no problem installing it, one needs just to remove -lnsl everywhere in the configure file. Jean-Christophe >David Martin wrote (to the EMBOSS list): >> >> Has anyone tried compiling and running EMBOSS on MacOS X yet? I can >> imagine this being very nice with the X interfaces (Colimate etc). > >And Richard Phelps wrote (to me personally): >> >> How might I install emboss on Mac Os X?? > >Well, personally, I think I've touched the keyboard of a Mac maybe five times >in my life (they're not common here at all), so it's highly unlikely I'll >have the pleasure of using MacOS X any time soon. > >However: > >- It would be interesting to know how easily an application with a relatively > GNUish installation process compiles and installs on OS X. I would > personally be very interested in feedback. (Shouldn't be too difficult by > all reports.) > >- Secondly, there is a project underway (though it's in its early stages yet) > to unify packaging systems across a number of BSD-based operating systems, > including OS X. In fact, Wilfredo Sanches, the former design lead on OS X, > is a developer on this project. Should their work come to fruition, it's > possible that the existing FreeBSD port could eventually serve as the basis > for installing EMBOSS on OS X as well. :-) See: > > http://www.openpackages.org/ > >-- Johann -- ________________________ Jean-Christophe Am?, PhD U.P.R. 9003 du CNRS - Canc?rog?n?se Et Mutag?n?se Mol?culaire Et Structurale ?cole Sup?rieure De Biotechnologie De Strasbourg P?le API Boulevard S?bastien-Brant 67400 Illkirch France tel.: 03 90 24 47 05 Fax.: 03 90 24 46 86 From CHOO_Keng_Wah at nyp.gov.sg Tue Apr 17 08:43:21 2001 From: CHOO_Keng_Wah at nyp.gov.sg (CHOO_Keng_Wah at nyp.gov.sg) Date: Tue, 17 Apr 2001 16:43:21 +0800 Subject: database access Message-ID: Deal all, I've just installed the EMBOSS-1.11.0 on my LINUX Red Hat 7.2 and I couldn't setup a connection to any database. Can soneone help me? Thank you. Jerome Choo From ableasby at hgmp.mrc.ac.uk Tue Apr 17 15:40:17 2001 From: ableasby at hgmp.mrc.ac.uk (ableasby at hgmp.mrc.ac.uk) Date: Tue, 17 Apr 2001 16:40:17 +0100 (BST) Subject: EMBOSS 1.12.0 Message-ID: <200104171540.QAA15078@tin.hgmp.mrc.ac.uk> EMBOSS 1.12.0 contains the following new programs in addition to the usual load of library mods/fixes/etc. Distmat: Creates a distance matrix from multiple alignments of nucleotide or protein sequences. The sequences need to be aligned before running this program. The quality of the alignment is of paramount importance in obtaining meaningful information from this analysis. Charge: Simple sliding window plot of charge vs position in a protein sequence. Cai: Codon adaptive index calculation. A measurement of the level of usage of the 64 codons in a sequence. Alan From btiwari at molbiol.ox.ac.uk Wed Apr 18 16:00:45 2001 From: btiwari at molbiol.ox.ac.uk (Bela Tiwari) Date: Wed, 18 Apr 2001 17:00:45 +0100 (BST) Subject: EMBOSS 1.12.0 Message-ID: Hello I hope this is the correct address to write to. I am writing from the Bioinformatics Centre at the University of Oxford. I just installed EMBOSS 1.12.0 and noticed that the applications in the emboss directory do not appear to get world r-x permissions set, which I'm pretty sure they did before. Just thought I'd mention it in case its not supposed to be this way. Cheers Bela .-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.- Dr. Bela Tiwari Bioinformatics Officer OU Bioinformatics Centre South Parks Road, 01865 (2)75507 Oxford OX1 3RE http://www.molbiol.ox.ac.uk .-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.- From ableasby at hgmp.mrc.ac.uk Wed Apr 18 16:45:46 2001 From: ableasby at hgmp.mrc.ac.uk (ableasby at hgmp.mrc.ac.uk) Date: Wed, 18 Apr 2001 17:45:46 +0100 (BST) Subject: EMBOSS 1.12.0 contacts.c Message-ID: <200104181645.RAA19931@tin.hgmp.mrc.ac.uk> Further to Bela's post we cannot reproduce the symptoms described. If anyone else notices this please send details to emboss-bug at embnet.org detailing your umask setting as well as usual version/system info. Bela has noticed a problem in the not-compiled-by-default applications you can get by typing "make check" in the applications directory. These applications are usually ones under development or examples and certainly come under a use at your peril heading etc. There is a typo in contacts.c in this section. A patch file has been put in the "patchfiles" directory of the ftp server. Again, this does not affect the workings of the main package you get from the recommended plain "make", it only affects the adventurous. Alan From charles at moulinette.dyndns.org Sun Apr 22 22:00:16 2001 From: charles at moulinette.dyndns.org (Charles) Date: Mon, 23 Apr 2001 00:00:16 +0200 (CEST) Subject: database access In-Reply-To: Message-ID: On Tue, 17 Apr 2001 CHOO_Keng_Wah at nyp.gov.sg wrote: > Deal all, > I've just installed the EMBOSS-1.11.0 on my LINUX Red Hat 7.2 and I > couldn't setup a connection to any database. > Can soneone help me? > I'm more or less at the same point than you : i've installed emboss on a debian woody (for self-training and satisfying curiosity), and could not get the time so sit down in front of the database installation manual, which is hard to understand for the unfamiliar reader. I copied the emboss.default file to .embossrc in my home directory, and uncommented the examples of genebank accassion by the internet. Well, if you have an unlimited internet access, i think it is the quicker way to proceed. However, i dont't even know if www.ca.embnet.org is designed to provide sequences to everybody, and i don't understand the syntax used. Hope this helps, Charles From ableasby at hgmp.mrc.ac.uk Sun Apr 22 22:52:02 2001 From: ableasby at hgmp.mrc.ac.uk (ableasby at hgmp.mrc.ac.uk) Date: Sun, 22 Apr 2001 23:52:02 +0100 (BST) Subject: database access Message-ID: <200104222252.XAA21974@tin.hgmp.mrc.ac.uk> In response to Charles: www.ca.embnet.org is designed to provide sequences to everybody this way. Like most EMBnet (European Molecular Biology network) sites it has an SRS server. The Canadian node is the only one I know that provides GenBank this way, most of us provide EMBL instead. You can play interactively with the Canadian server directly by using: http://www.ca.embnet.org/srs6.1/ It should then become clear what the DB entry is doing. As an addendum the original query was solved (typically) behind the scenes and was just an emboss.default file in the wrong place. I'm tempted to put this file in the emboss directory itself under a filename like: emboss.default.example . Historically the file is where it is to avoid new installations overwriting your own copy but the above would serve the same purpose. Alan (http://srs.hgmp.mrc.ac.uk/srs6/) From dessen at infobiogen.fr Mon Apr 23 06:42:05 2001 From: dessen at infobiogen.fr (Philippe Dessen) Date: Mon, 23 Apr 2001 08:42:05 +0200 (MET DST) Subject: database access GenBank In-Reply-To: <200104222252.XAA21974@tin.hgmp.mrc.ac.uk> from "ableasby@hgmp.mrc.ac.uk" at Apr 22, 2001 11:52:02 PM Message-ID: <200104230642.IAA12068@lovelace.infobiogen.fr> > > In response to Charles: > www.ca.embnet.org is designed to provide sequences to everybody this > way. Like most EMBnet (European Molecular Biology network) sites it > has an SRS server. The Canadian node is the only one I know that > provides GenBank this way, most of us provide EMBL instead. > You can play interactively with the Canadian server directly by using: > http://www.ca.embnet.org/srs6.1/ > It should then become clear what the DB entry is doing. > > As an addendum the original query was solved (typically) behind the scenes > and was just an emboss.default file in the wrong place. I'm tempted > to put this file in the emboss directory itself under a filename like: > emboss.default.example . Historically the file is where it is to > avoid new installations overwriting your own copy but the above would serve > the same purpose. > > Alan > > (http://srs.hgmp.mrc.ac.uk/srs6/) > > In the old EMBnet world, INFOBIOGEN offers GenBank on its SRS server since 1993 ... http://www.infobiogen.fr/srs6/. Regards Philippe Dessen From dmartin at gen67172.msiwtb.dundee.ac.uk Mon Apr 23 07:51:17 2001 From: dmartin at gen67172.msiwtb.dundee.ac.uk (David Martin) Date: Mon, 23 Apr 2001 08:51:17 +0100 (BST) Subject: database access In-Reply-To: Message-ID: On Mon, 23 Apr 2001, Charles wrote: > > > On Tue, 17 Apr 2001 CHOO_Keng_Wah at nyp.gov.sg wrote: > > > Deal all, > > I've just installed the EMBOSS-1.11.0 on my LINUX Red Hat 7.2 and I > > couldn't setup a connection to any database. > > Can soneone help me? > > > > I'm more or less at the same point than you : i've installed emboss on a > debian woody (for self-training and satisfying curiosity), and could not > get the time so sit down in front of the database installation manual, > which is hard to understand for the unfamiliar reader. OK.. if you have any suggestions on improving it I will see what I can do. When I wrote the manual it was because I wasn't clear how things were supposed to be set up, so I asked a lot of questions and hassled Peter Rice and Alan to give me the answers. Would a 'quick guide to setting up the EMBL database' section or similar help? > > I copied the emboss.default file to .embossrc in my home directory, and > uncommented the examples of genebank accassion by the internet. The example file isn't the best of examples. A case for better annotation. I'll add it to my list of 'things to do'. > > Well, if you have an unlimited internet access, i think it is the quicker > way to proceed. However, i dont't even know if www.ca.embnet.org is > designed to provide sequences to everybody, and i don't > understand the syntax used. > To be perfectly honest neither do I but it seems to work.. the syntax is the various arguments given to the wgetz script in the srs server. I notice looking through the admin guide that I have omitted www as a method for database retrieval. I'll add that in to the next version plus some notes on OS X and SuSE 7.1. If anyone else would care to contribute any installation quirks or workarounds they may have had to do (eg. a list of packages required for Debian to run EMBOSS and so on..) then I would be grateful for them. ..d > Hope this helps, > > Charles > From peter.rice at uk.lionbioscience.com Mon Apr 23 08:44:36 2001 From: peter.rice at uk.lionbioscience.com (Peter Rice) Date: Mon, 23 Apr 2001 09:44:36 +0100 Subject: database access References: <200104222252.XAA21974@tin.hgmp.mrc.ac.uk> Message-ID: <3AE3EB74.44E0B84D@uk.lionbioscience.com> ableasby at hgmp.mrc.ac.uk wrote: > > In response to Charles: > www.ca.embnet.org is designed to provide sequences to everybody this > way. Like most EMBnet (European Molecular Biology network) sites it > has an SRS server. The Canadian node is the only one I know that > provides GenBank this way, most of us provide EMBL instead. > You can play interactively with the Canadian server directly by using: > http://www.ca.embnet.org/srs6.1/ > It should then become clear what the DB entry is doing. There are a few others, all up to date: Denmark http://www.dk.embnet.org/srs6/ Finland http://srs.csc.fi:8002/srs6/ France http://www.fr.embnet.org/srs6/ Germany http://genius.embnet.dkfz-heidelberg.de/menu/srs/ The Netherlands EMBnet node has a Genbank database under SRS, but it only contains a few entries (under 250) that are not quite the same in EMBL, and is not the full database. The United Kingdom EMBnet node (Alan's own :-) used to run GenBank as well as EMBL until recently, and was the original source of Genbank in the emboss.defaults file. You can also use NCBI's Entrez for GenBank. regards, Peter Rice -- ------------------------------------------------ Peter Rice, LION Bioscience Ltd, Cambridge, UK peter.rice at uk.lionbioscience.com +44 1223 224723 From charles at moulinette.dyndns.org Mon Apr 30 17:20:34 2001 From: charles at moulinette.dyndns.org (Charles) Date: Mon, 30 Apr 2001 19:20:34 +0200 (CEST) Subject: Installing Database Message-ID: Hello, I'm using emboss for self-training, and I don't have tons of free disk space. I spent an hour this week-end, trying to see if one can install only a subset of a database. For example I would like to install a database containing only zebrafish ESTs. >From the admin guide it seems possible to install the whole database, and to configure a kind of alias, restricted to a section, like rodents for example. But that's not exactly what I want to do... I couldn't find a database subset isolated as a file, so I suspect that I'm trying to do an impossible thing. Can anybody confirm? Charles