From nycademon at spiralrealm.com Fri Aug 3 17:39:16 2007 From: nycademon at spiralrealm.com (Guido Vacano) Date: Fri, 03 Aug 2007 15:39:16 -0600 Subject: [EMBOSS] seqret error Message-ID: <46B3A084.1060904@spiralrealm.com> Hello-- I'm getting an error as follows: ------- $ seqret nt:EF348590 Reads and writes (returns) sequences EMBOSS An error in ajindex.c at line 2424: GetKeys: No keys in node -------- The nt database is a FASTA file from NCBI, and I used dbxfasta. My emboss.defaults entry for the database is: DB nt [ type: N dbalias: nt method: emboss format: fasta dir: /data/EMBOSS_data/nt file: nt.fasta indexdirectory: /data/EMBOSS_data/nt ] Any ideas what I'm doing wrong? Thanks, Guido From pmr at ebi.ac.uk Sun Aug 5 11:31:24 2007 From: pmr at ebi.ac.uk (Peter Rice) Date: Sun, 05 Aug 2007 16:31:24 +0100 Subject: [EMBOSS] seqret error In-Reply-To: <46B3A084.1060904@spiralrealm.com> References: <46B3A084.1060904@spiralrealm.com> Message-ID: <46B5ED4C.20906@ebi.ac.uk> Guido Vacano wrote: > Hello-- > > I'm getting an error as follows: > > ------- > $ seqret nt:EF348590 > Reads and writes (returns) sequences > > EMBOSS An error in ajindex.c at line 2424: > GetKeys: No keys in node > -------- > > The nt database is a FASTA file from NCBI, and I used dbxfasta. Does the database have accession numbers? There should be a count in the *.pxac file from the dbxfasta run. If you run seqret with -debug and send the seqret.dbg file to emboss-bug at emboss.open-bio.org it will help to trace the problem. regards, Peter From pmr at ebi.ac.uk Fri Aug 10 04:49:00 2007 From: pmr at ebi.ac.uk (Peter Rice) Date: Fri, 10 Aug 2007 09:49:00 +0100 Subject: [EMBOSS] help with Profit In-Reply-To: References: Message-ID: <46BC267C.7050406@ebi.ac.uk> Mehta, Perdeep wrote: > Hi, > > I am trying to search swissprot protein database with the "Profit" > program. Somehow after running for a while Profit produces following out > put that has no data in it. Here is the text in the generated output > file. > > # PROF scan using Henikoff profile pdz_henikoff.prf > # Scores >= threshold 75 (max score 88.53) > # > > Does any one have a clue what's wrong with it? I checked the > installation of swissprot database it works fine I could fetch a > sequence out with seqret. It appears there is a problem with profiles that cover complete sequences. When the profile (including gaps) is longer than a database sequence it fails to match that sequence. We will investigate. We will also add a note to the output to say how many hits were found and what the maximum score was. regards, Peter From pmr at ebi.ac.uk Fri Aug 10 05:05:24 2007 From: pmr at ebi.ac.uk (Peter Rice) Date: Fri, 10 Aug 2007 10:05:24 +0100 Subject: [EMBOSS] help with Profit In-Reply-To: References: Message-ID: <46BC2A54.9070205@ebi.ac.uk> Mehta, Perdeep wrote: > Hi, > > I am trying to search swissprot protein database with the "Profit" > program. Somehow after running for a while Profit produces following out > put that has no data in it. Here is the text in the generated output > file. > > # PROF scan using Henikoff profile pdz_henikoff.prf > # Scores >= threshold 75 (max score 88.53) > # Ah, now I see it .... You used profit, but that only uses ungapped profiles from prophecy. That is why it has the length limit. With gapped alignments as input to prophecy, you need to use prophet. A few things we could do to help: * Check for these cases and give a warning in profit for gapped input * Make profit and prophet use the same order of inputs (profile and database) * Add a threshold to prophet to report only scores above a threshold for alignments to a database rather than a single sequence regards, Peter From openlinuxsource at gmail.com Sat Aug 11 03:44:40 2007 From: openlinuxsource at gmail.com (Amy Lee) Date: Sat, 11 Aug 2007 15:44:40 +0800 Subject: [EMBOSS] Help: About Job Schedule Message-ID: <46BD68E8.6060402@gmail.com> Hello, I'm a Linux administrator. I build a Beowulf Cluster for our Bioinformatic Department. We use EMBOSS 4.1.0 in the cluster. In this cluster, we installed Sun Grid Engine as our job schedule tool. And I'm ONLY a system administrator, I'd like to know how to use SGE to control EMBOSS package. Is there any suggestions? Thanks~ Regards, Amy Lee From virtuellefestplatte at gmx.net Mon Aug 13 05:09:28 2007 From: virtuellefestplatte at gmx.net (Sascha Engel) Date: Mon, 13 Aug 2007 11:09:28 +0200 Subject: [EMBOSS] jEMBOSS doesn't start Message-ID: <20070813090928.275160@gmx.net> Hello, I try to run jEMBOSS with EMBOSS 5.0.0.1 on SUSE 9.3. I installed it using rpm-files. When I run, ./runJemboss.standalone I get following error message: Aug 13, 2007 10:59:28 AM org.apache.axis.utils.JavaUtils isAttachmentSupported WARNING: Unable to find required classes (javax.activation.DataHandler and javax.mail.internet.MimeMultipart). Attachment support is disabled. Exception in thread "Thread-3" java.lang.NoClassDefFoundError: javax/wsdl/OperationType at org.apache.axis.description.OperationDesc.(OperationDesc.java:58) at org.apache.axis.client.Call.setReturnType(Call.java:1102) at org.emboss.jemboss.soap.PublicRequest.(PublicRequest.java:133) at org.emboss.jemboss.soap.PublicRequest.(PublicRequest.java:84) at org.emboss.jemboss.soap.PublicRequest.(PublicRequest.java:56) at org.emboss.jemboss.soap.ShowDB.(ShowDB.java:60) at org.emboss.jemboss.gui.BuildProgramMenu$1$1.construct(BuildProgramMenu.java:154) at org.emboss.jemboss.gui.SwingWorker$2.run(SwingWorker.java:127) at java.lang.Thread.run(Unknown Source) Exception in thread "Thread-2" java.lang.NoClassDefFoundError: Could not initialize class org.apache.axis.description.OperationDesc at org.apache.axis.client.Call.setReturnType(Call.java:1102) at org.emboss.jemboss.soap.PublicRequest.(PublicRequest.java:133) at org.emboss.jemboss.soap.PublicRequest.(PublicRequest.java:84) at org.emboss.jemboss.soap.PublicRequest.(PublicRequest.java:56) at org.emboss.jemboss.soap.GetWossname.(GetWossname.java:51) at org.emboss.jemboss.gui.BuildProgramMenu$1.construct(BuildProgramMenu.java:228) at org.emboss.jemboss.gui.SwingWorker$2.run(SwingWorker.java:127) at java.lang.Thread.run(Unknown Source) Asking google I get the advice to copy "activation.jar" and "mailapi.jar" in some tomcat/.../lib directories. Unfortunately I can't get it fixed. Any ideas are heartly welcome Bye Sascha -- Ist Ihr Browser Vista-kompatibel? Jetzt die neuesten Browser-Versionen downloaden: http://www.gmx.net/de/go/browser From tjc at sanger.ac.uk Mon Aug 13 06:48:21 2007 From: tjc at sanger.ac.uk (Tim Carver) Date: Mon, 13 Aug 2007 11:48:21 +0100 Subject: [EMBOSS] jEMBOSS doesn't start In-Reply-To: <20070813090928.275160@gmx.net> Message-ID: Hi Sascha Ask the people who distribute the RPM but I suspect they do not support Jemboss. Regards Tim On 13/8/07 10:09, "Sascha Engel" wrote: > Hello, > > I try to run jEMBOSS with EMBOSS 5.0.0.1 on SUSE 9.3. I installed it using > rpm-files. > > When I run, ./runJemboss.standalone I get following error message: > > Aug 13, 2007 10:59:28 AM org.apache.axis.utils.JavaUtils isAttachmentSupported > WARNING: Unable to find required classes (javax.activation.DataHandler and > javax.mail.internet.MimeMultipart). Attachment support is disabled. > Exception in thread "Thread-3" java.lang.NoClassDefFoundError: > javax/wsdl/OperationType > at > org.apache.axis.description.OperationDesc.(OperationDesc.java:58) > at org.apache.axis.client.Call.setReturnType(Call.java:1102) > at > org.emboss.jemboss.soap.PublicRequest.(PublicRequest.java:133) > at org.emboss.jemboss.soap.PublicRequest.(PublicRequest.java:84) > at org.emboss.jemboss.soap.PublicRequest.(PublicRequest.java:56) > at org.emboss.jemboss.soap.ShowDB.(ShowDB.java:60) > at > org.emboss.jemboss.gui.BuildProgramMenu$1$1.construct(BuildProgramMenu.java:15 > 4) > at org.emboss.jemboss.gui.SwingWorker$2.run(SwingWorker.java:127) > at java.lang.Thread.run(Unknown Source) > Exception in thread "Thread-2" java.lang.NoClassDefFoundError: Could not > initialize class org.apache.axis.description.OperationDesc > at org.apache.axis.client.Call.setReturnType(Call.java:1102) > at > org.emboss.jemboss.soap.PublicRequest.(PublicRequest.java:133) > at org.emboss.jemboss.soap.PublicRequest.(PublicRequest.java:84) > at org.emboss.jemboss.soap.PublicRequest.(PublicRequest.java:56) > at org.emboss.jemboss.soap.GetWossname.(GetWossname.java:51) > at > org.emboss.jemboss.gui.BuildProgramMenu$1.construct(BuildProgramMenu.java:228) > at org.emboss.jemboss.gui.SwingWorker$2.run(SwingWorker.java:127) > at java.lang.Thread.run(Unknown Source) > > Asking google I get the advice to copy "activation.jar" and "mailapi.jar" in > some tomcat/.../lib directories. Unfortunately I can't get it fixed. > > Any ideas are heartly welcome > > Bye Sascha -- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE. From wenbinye at gmail.com Mon Aug 13 11:56:19 2007 From: wenbinye at gmail.com (Ye Wenbin) Date: Mon, 13 Aug 2007 23:56:19 +0800 Subject: [EMBOSS] An emacs mode to edit acd files Message-ID: Hi, I'm newbie to emboss, but it is really an interesting project. I spend sometime to implement a major mode to edit and view acd files for emacser. Hope it is useful. You can download it from: http://www.emacswiki.org/cgi-bin/emacs/acd.el Any comments are welcome! Enjoy. -- Best regards, Ye Wenbin From pmr at ebi.ac.uk Mon Aug 13 12:46:13 2007 From: pmr at ebi.ac.uk (Peter Rice) Date: Mon, 13 Aug 2007 17:46:13 +0100 Subject: [EMBOSS] An emacs mode to edit acd files In-Reply-To: References: Message-ID: <46C08AD5.7050801@ebi.ac.uk> Ye Wenbin wrote: > I'm newbie to emboss, but it is really an interesting project. > I spend sometime to implement a major mode to edit and view acd files for > emacser. > Hope it is useful. You can download it from: > http://www.emacswiki.org/cgi-bin/emacs/acd.el > > Any comments are welcome! Enjoy. Many thanks. I will try it out and let you know. From a first look I can see some interesting ways to extend it. Do you have a short user guide to explain what features it has? I discovered things like "appl" and "sec" which are nice. Which version of EMBOSS did you use? regards, Peter Rice From wenbinye at gmail.com Mon Aug 13 22:56:35 2007 From: wenbinye at gmail.com (Ye Wenbin) Date: Tue, 14 Aug 2007 10:56:35 +0800 Subject: [EMBOSS] An emacs mode to edit acd files In-Reply-To: <46C08AD5.7050801@ebi.ac.uk> References: <46C08AD5.7050801@ebi.ac.uk> Message-ID: On Tue, 14 Aug 2007 00:46:13 +0800, Peter Rice wrote: > Do you have a short user guide to explain what features it has? I > discovered things like "appl" and "sec" which are nice. I wrote some simple description about features of acd-mode in the header of the files. Except keywords highlight and indentation as a major modes should do, I add some useful feature for editing: 1. support for imenu. You can use M-x imenu to move to other tokens 2. abbrevation using tempo.el. As you see, currently I add two abbrev "appl" and "sec", but you can add more as you like. That is easy, after load 'acd.el', you can use acd-define-tempo-template to add an new tempo template, for example: (acd-define-tempo-template "int" '("integer") '("default" "information")) The new abbrev cannot be used in a buffer opened before it defined, you have to M-x acd-mode to ask tempo install the new tempo-local-tags. Now you can type int and expand it to: integer: [ default: "" information: "" ] tempo can create marks when expand the template, so you move around using tempo-forward-marks and tempo-backward-marks, which are bound to C-c C-n and C-c C-p in acd-mode. This feature make me choose it rather than skeleton. And if you think you abbrev still to long, you can use M-x tempo-complete-tag to complete an abbrev, it is bound to C-c TAB. 3. Completion. Many things can be completed using TAB. For example, the name of data type bool can complete to boolean. And the attributes of the data type can be completed like: boolean feature [ def will get "default". The name of variable can be completed when it is declare before point: sequence: inseq [ features: $(fe will get "feature" if the variable "feature" is declare before. The calculated attributes also can be completed. $(inseq.le can get "length" if the "inseq" is declared as type "sequence" before. Today I add completions for standard groups because I think it is hard to remember so many groups. You can complete group name as: groups: " That all what acd-mode do. I want add a command acd-pretty that use command acdpretty to reformat code, but I don't know how to make the command read input from stdin, I use command: $ cat appl.acd | acdpretty -filter but failed. Is it possible to make the command read from stdin? > Which version of EMBOSS did you use? I check out the cvs version of emboss, and build it myself. This is some question about the document of library. I can find some scripts to generate documents for libraries under directory "scripts", but I can find command to build it. I try "make html" "make info", but get nothing. And run embossdoc.csh get errors: $ csh scripts/embossdoc.csh /home/ywb/downloads/emboss/emboss/ /home/ywb/downloads/emboss/emboss/doc touch: Cannot touch '/home/ywb/downloads/emboss/emboss/doc/ajax/dummy.html': No such file or directory foreach: No match. How can I use those scripts? Thanks! -- Best regards, Ye Wenbin From pmr at ebi.ac.uk Tue Aug 14 09:04:49 2007 From: pmr at ebi.ac.uk (Peter Rice) Date: Tue, 14 Aug 2007 14:04:49 +0100 Subject: [EMBOSS] An emacs mode to edit acd files In-Reply-To: References: <46C08AD5.7050801@ebi.ac.uk> Message-ID: <46C1A871.9010509@ebi.ac.uk> Ye Wenbin wrote: > I wrote some simple description about features of acd-mode in the header > of the files. Except keywords highlight and indentation as a major modes > should do, I add some useful feature for editing: > 1. support for imenu. You can use M-x imenu to move to other tokens Interesting. It understands sections. > And if you think you abbrev still to long, you can use > M-x tempo-complete-tag to complete an abbrev, it is bound to C-c TAB. Easy ... but it seems I have to use the exact abbreviation. Something that expands any abbreviation (if it is unique) and adds a set of attributes is very useful. This combines the abbreviation handling with the C-c TAB. Is that easy to implement? > 3. Completion. Many things can be completed using TAB. For example, > the name of data type bool can complete to boolean. And the > attributes of the data type can be completed like: > boolean feature [ > def > will get "default". Can it insert default and information (for example) as attributes? > The name of variable can be completed when it is declare before point: > sequence: inseq [ > features: $(fe > will get "feature" if the variable "feature" is declare before. > The calculated attributes also can be completed. $(inseq.le can get > "length" if the "inseq" is declared as type "sequence" before. > Today I add completions for standard groups because I think it is hard > to > remember so many groups. You can complete group name as: > groups: " That is useful. The current group names are stored in emboss/acd/groups.standard We validate them automatically. If we add acd.el to the EMBOSS CVS tree we can validate the list there and keep it updated. > I want add a command acd-pretty that use command acdpretty to reformat > code, but I don't know how to make the command read input from stdin, > I use command: > $ cat appl.acd | acdpretty -filter > but failed. Is it possible to make the command read from stdin? No. The -filter option works for EMBOSS programs and the ACD file that acdpretty is reading (you can still use all the command line options of that ACD file). But it is easy to reformat code in emacs .. the indentation is not difficult. acdpretty also completes abbreviations and adds missing quotes. >> Which version of EMBOSS did you use? > I check out the cvs version of emboss, and build it myself. Thanks. So we can try it without having to make updates. > This is some question about the document of library. I can find some scripts > to generate documents for libraries under directory "scripts", but I can find > command to build it. > How can I use those scripts? Ah ... we make the documentation in another directory (because the documentation is on the sourceforge website, and sourceforge has restrictions on using CVS, we have to use a sourceforge CVS server). I run embossdoc.csh with two arguments - where to find the source code, and where to store the documentation. You can also pick up the documentation from emboss.cvs.sourceforge.net in directory sfdoc/developers and give the sfdoc.developers directory as the second argment to embossdoc.csh regards, Peter Rice From sum732 at mail.usask.ca Tue Aug 14 16:46:03 2007 From: sum732 at mail.usask.ca (Mehrotra, Sudeep) Date: Tue, 14 Aug 2007 14:46:03 -0600 Subject: [EMBOSS] MW in "Digest" -EMBOSS Message-ID: <1187124363.46c2148bf0808@webmail.usask.ca> Hello, I am trying to figure out how molecular weight of the peptide fragments in EMBOSS "DIGEST" is calculated? For example: given fragment AEK, "DIGEST" returns a MW = 346.378. Now if i look at the residual masses(monoisotopic) of A E K they are 71.03711, 129.04259, 128.09496, respectively, these dont add up to 346.378. I tried using Average mass, as well as normal mw of AA in question, but i am not to get a MW of 346.378. It would be very helpful if you can explain how MW is calculated in EMBOSS-DIGEST. Thanking You Sudeep From kvddrift at earthlink.net Sat Aug 18 16:11:41 2007 From: kvddrift at earthlink.net (Koen van der Drift) Date: Sat, 18 Aug 2007 16:11:41 -0400 Subject: [EMBOSS] MW in "Digest" -EMBOSS In-Reply-To: <1187124363.46c2148bf0808@webmail.usask.ca> References: <1187124363.46c2148bf0808@webmail.usask.ca> Message-ID: <9283D5A1-09F3-49BD-87C5-F40C0CBA7CB7@earthlink.net> You will have to add the mw of water (18) to get the total mw of your peptide. - Koen. On Aug 14, 2007, at 4:46 PM, Mehrotra, Sudeep wrote: > Hello, > > I am trying to figure out how molecular weight of the peptide > fragments in > EMBOSS > "DIGEST" is calculated? > > For example: given fragment AEK, "DIGEST" returns a MW = 346.378. > > Now if i look at the residual masses(monoisotopic) of A E K they > are 71.03711, > 129.04259, 128.09496, respectively, these dont add up to 346.378. I > tried using > Average mass, as well as normal mw of AA in question, but i am not > to get a MW > of > 346.378. > It would be very helpful if you can explain how MW is calculated in > EMBOSS-DIGEST. > > Thanking You > Sudeep > > _______________________________________________ > EMBOSS mailing list > EMBOSS at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/emboss From sum732 at mail.usask.ca Fri Aug 31 11:40:01 2007 From: sum732 at mail.usask.ca (Mehrotra, Sudeep) Date: Fri, 31 Aug 2007 09:40:01 -0600 Subject: [EMBOSS] Monoisotopic or Average mass Message-ID: <1188574801.46d83651b81ec@webmail.usask.ca> Hello, I am trying to figure out how molecular weight of the peptide fragments in EMBOSS program "DIGEST" is calculated if enzyme used for digestion is Trypsin. Monoisotopic mass of each constituent AA residues in a given peptide sequence+ monoisotopic mass of water or Average mass of each constituent AA residues in a given peptide sequence +average mass of water A quick response would be appreciated. Thanking You Sudeep From pmr at ebi.ac.uk Fri Aug 31 13:37:02 2007 From: pmr at ebi.ac.uk (Peter Rice) Date: Fri, 31 Aug 2007 18:37:02 +0100 Subject: [EMBOSS] Monoisotopic or Average mass In-Reply-To: <1188574801.46d83651b81ec@webmail.usask.ca> References: <1188574801.46d83651b81ec@webmail.usask.ca> Message-ID: <46D851BE.9010903@ebi.ac.uk> Hi Sudeep, > I am trying to figure out how molecular weight of the peptide fragments in > EMBOSS program "DIGEST" is calculated if enzyme used for digestion is Trypsin. > > Monoisotopic mass of each constituent AA residues in a given peptide sequence+ > monoisotopic mass of water > or > Average mass of each constituent AA residues in a given peptide sequence > +average mass of water Average mass. as far as I am aware ... but we do need more documentation of the molecular weights in Eamino.dat You can set the masses in a local data file if you want to use monoisotopic values. Add -aadata filename to the commandline or put a file Eamino.dat in your current directory. For the water the values are currently hardcoded in nucleus/embprop.c as: H 1.00782 OH 17.00274 But we could add values to Eamino.dat. If you can provide alternative values we can also add an alternative local data file to the EMBOSS distribution. Hope that helps. Peter From nycademon at spiralrealm.com Fri Aug 3 21:39:16 2007 From: nycademon at spiralrealm.com (Guido Vacano) Date: Fri, 03 Aug 2007 15:39:16 -0600 Subject: [EMBOSS] seqret error Message-ID: <46B3A084.1060904@spiralrealm.com> Hello-- I'm getting an error as follows: ------- $ seqret nt:EF348590 Reads and writes (returns) sequences EMBOSS An error in ajindex.c at line 2424: GetKeys: No keys in node -------- The nt database is a FASTA file from NCBI, and I used dbxfasta. My emboss.defaults entry for the database is: DB nt [ type: N dbalias: nt method: emboss format: fasta dir: /data/EMBOSS_data/nt file: nt.fasta indexdirectory: /data/EMBOSS_data/nt ] Any ideas what I'm doing wrong? Thanks, Guido From pmr at ebi.ac.uk Sun Aug 5 15:31:24 2007 From: pmr at ebi.ac.uk (Peter Rice) Date: Sun, 05 Aug 2007 16:31:24 +0100 Subject: [EMBOSS] seqret error In-Reply-To: <46B3A084.1060904@spiralrealm.com> References: <46B3A084.1060904@spiralrealm.com> Message-ID: <46B5ED4C.20906@ebi.ac.uk> Guido Vacano wrote: > Hello-- > > I'm getting an error as follows: > > ------- > $ seqret nt:EF348590 > Reads and writes (returns) sequences > > EMBOSS An error in ajindex.c at line 2424: > GetKeys: No keys in node > -------- > > The nt database is a FASTA file from NCBI, and I used dbxfasta. Does the database have accession numbers? There should be a count in the *.pxac file from the dbxfasta run. If you run seqret with -debug and send the seqret.dbg file to emboss-bug at emboss.open-bio.org it will help to trace the problem. regards, Peter From pmr at ebi.ac.uk Fri Aug 10 08:49:00 2007 From: pmr at ebi.ac.uk (Peter Rice) Date: Fri, 10 Aug 2007 09:49:00 +0100 Subject: [EMBOSS] help with Profit In-Reply-To: References: Message-ID: <46BC267C.7050406@ebi.ac.uk> Mehta, Perdeep wrote: > Hi, > > I am trying to search swissprot protein database with the "Profit" > program. Somehow after running for a while Profit produces following out > put that has no data in it. Here is the text in the generated output > file. > > # PROF scan using Henikoff profile pdz_henikoff.prf > # Scores >= threshold 75 (max score 88.53) > # > > Does any one have a clue what's wrong with it? I checked the > installation of swissprot database it works fine I could fetch a > sequence out with seqret. It appears there is a problem with profiles that cover complete sequences. When the profile (including gaps) is longer than a database sequence it fails to match that sequence. We will investigate. We will also add a note to the output to say how many hits were found and what the maximum score was. regards, Peter From pmr at ebi.ac.uk Fri Aug 10 09:05:24 2007 From: pmr at ebi.ac.uk (Peter Rice) Date: Fri, 10 Aug 2007 10:05:24 +0100 Subject: [EMBOSS] help with Profit In-Reply-To: References: Message-ID: <46BC2A54.9070205@ebi.ac.uk> Mehta, Perdeep wrote: > Hi, > > I am trying to search swissprot protein database with the "Profit" > program. Somehow after running for a while Profit produces following out > put that has no data in it. Here is the text in the generated output > file. > > # PROF scan using Henikoff profile pdz_henikoff.prf > # Scores >= threshold 75 (max score 88.53) > # Ah, now I see it .... You used profit, but that only uses ungapped profiles from prophecy. That is why it has the length limit. With gapped alignments as input to prophecy, you need to use prophet. A few things we could do to help: * Check for these cases and give a warning in profit for gapped input * Make profit and prophet use the same order of inputs (profile and database) * Add a threshold to prophet to report only scores above a threshold for alignments to a database rather than a single sequence regards, Peter From openlinuxsource at gmail.com Sat Aug 11 07:44:40 2007 From: openlinuxsource at gmail.com (Amy Lee) Date: Sat, 11 Aug 2007 15:44:40 +0800 Subject: [EMBOSS] Help: About Job Schedule Message-ID: <46BD68E8.6060402@gmail.com> Hello, I'm a Linux administrator. I build a Beowulf Cluster for our Bioinformatic Department. We use EMBOSS 4.1.0 in the cluster. In this cluster, we installed Sun Grid Engine as our job schedule tool. And I'm ONLY a system administrator, I'd like to know how to use SGE to control EMBOSS package. Is there any suggestions? Thanks~ Regards, Amy Lee From virtuellefestplatte at gmx.net Mon Aug 13 09:09:28 2007 From: virtuellefestplatte at gmx.net (Sascha Engel) Date: Mon, 13 Aug 2007 11:09:28 +0200 Subject: [EMBOSS] jEMBOSS doesn't start Message-ID: <20070813090928.275160@gmx.net> Hello, I try to run jEMBOSS with EMBOSS 5.0.0.1 on SUSE 9.3. I installed it using rpm-files. When I run, ./runJemboss.standalone I get following error message: Aug 13, 2007 10:59:28 AM org.apache.axis.utils.JavaUtils isAttachmentSupported WARNING: Unable to find required classes (javax.activation.DataHandler and javax.mail.internet.MimeMultipart). Attachment support is disabled. Exception in thread "Thread-3" java.lang.NoClassDefFoundError: javax/wsdl/OperationType at org.apache.axis.description.OperationDesc.(OperationDesc.java:58) at org.apache.axis.client.Call.setReturnType(Call.java:1102) at org.emboss.jemboss.soap.PublicRequest.(PublicRequest.java:133) at org.emboss.jemboss.soap.PublicRequest.(PublicRequest.java:84) at org.emboss.jemboss.soap.PublicRequest.(PublicRequest.java:56) at org.emboss.jemboss.soap.ShowDB.(ShowDB.java:60) at org.emboss.jemboss.gui.BuildProgramMenu$1$1.construct(BuildProgramMenu.java:154) at org.emboss.jemboss.gui.SwingWorker$2.run(SwingWorker.java:127) at java.lang.Thread.run(Unknown Source) Exception in thread "Thread-2" java.lang.NoClassDefFoundError: Could not initialize class org.apache.axis.description.OperationDesc at org.apache.axis.client.Call.setReturnType(Call.java:1102) at org.emboss.jemboss.soap.PublicRequest.(PublicRequest.java:133) at org.emboss.jemboss.soap.PublicRequest.(PublicRequest.java:84) at org.emboss.jemboss.soap.PublicRequest.(PublicRequest.java:56) at org.emboss.jemboss.soap.GetWossname.(GetWossname.java:51) at org.emboss.jemboss.gui.BuildProgramMenu$1.construct(BuildProgramMenu.java:228) at org.emboss.jemboss.gui.SwingWorker$2.run(SwingWorker.java:127) at java.lang.Thread.run(Unknown Source) Asking google I get the advice to copy "activation.jar" and "mailapi.jar" in some tomcat/.../lib directories. Unfortunately I can't get it fixed. Any ideas are heartly welcome Bye Sascha -- Ist Ihr Browser Vista-kompatibel? Jetzt die neuesten Browser-Versionen downloaden: http://www.gmx.net/de/go/browser From tjc at sanger.ac.uk Mon Aug 13 10:48:21 2007 From: tjc at sanger.ac.uk (Tim Carver) Date: Mon, 13 Aug 2007 11:48:21 +0100 Subject: [EMBOSS] jEMBOSS doesn't start In-Reply-To: <20070813090928.275160@gmx.net> Message-ID: Hi Sascha Ask the people who distribute the RPM but I suspect they do not support Jemboss. Regards Tim On 13/8/07 10:09, "Sascha Engel" wrote: > Hello, > > I try to run jEMBOSS with EMBOSS 5.0.0.1 on SUSE 9.3. I installed it using > rpm-files. > > When I run, ./runJemboss.standalone I get following error message: > > Aug 13, 2007 10:59:28 AM org.apache.axis.utils.JavaUtils isAttachmentSupported > WARNING: Unable to find required classes (javax.activation.DataHandler and > javax.mail.internet.MimeMultipart). Attachment support is disabled. > Exception in thread "Thread-3" java.lang.NoClassDefFoundError: > javax/wsdl/OperationType > at > org.apache.axis.description.OperationDesc.(OperationDesc.java:58) > at org.apache.axis.client.Call.setReturnType(Call.java:1102) > at > org.emboss.jemboss.soap.PublicRequest.(PublicRequest.java:133) > at org.emboss.jemboss.soap.PublicRequest.(PublicRequest.java:84) > at org.emboss.jemboss.soap.PublicRequest.(PublicRequest.java:56) > at org.emboss.jemboss.soap.ShowDB.(ShowDB.java:60) > at > org.emboss.jemboss.gui.BuildProgramMenu$1$1.construct(BuildProgramMenu.java:15 > 4) > at org.emboss.jemboss.gui.SwingWorker$2.run(SwingWorker.java:127) > at java.lang.Thread.run(Unknown Source) > Exception in thread "Thread-2" java.lang.NoClassDefFoundError: Could not > initialize class org.apache.axis.description.OperationDesc > at org.apache.axis.client.Call.setReturnType(Call.java:1102) > at > org.emboss.jemboss.soap.PublicRequest.(PublicRequest.java:133) > at org.emboss.jemboss.soap.PublicRequest.(PublicRequest.java:84) > at org.emboss.jemboss.soap.PublicRequest.(PublicRequest.java:56) > at org.emboss.jemboss.soap.GetWossname.(GetWossname.java:51) > at > org.emboss.jemboss.gui.BuildProgramMenu$1.construct(BuildProgramMenu.java:228) > at org.emboss.jemboss.gui.SwingWorker$2.run(SwingWorker.java:127) > at java.lang.Thread.run(Unknown Source) > > Asking google I get the advice to copy "activation.jar" and "mailapi.jar" in > some tomcat/.../lib directories. Unfortunately I can't get it fixed. > > Any ideas are heartly welcome > > Bye Sascha -- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE. From wenbinye at gmail.com Mon Aug 13 15:56:19 2007 From: wenbinye at gmail.com (Ye Wenbin) Date: Mon, 13 Aug 2007 23:56:19 +0800 Subject: [EMBOSS] An emacs mode to edit acd files Message-ID: Hi, I'm newbie to emboss, but it is really an interesting project. I spend sometime to implement a major mode to edit and view acd files for emacser. Hope it is useful. You can download it from: http://www.emacswiki.org/cgi-bin/emacs/acd.el Any comments are welcome! Enjoy. -- Best regards, Ye Wenbin From pmr at ebi.ac.uk Mon Aug 13 16:46:13 2007 From: pmr at ebi.ac.uk (Peter Rice) Date: Mon, 13 Aug 2007 17:46:13 +0100 Subject: [EMBOSS] An emacs mode to edit acd files In-Reply-To: References: Message-ID: <46C08AD5.7050801@ebi.ac.uk> Ye Wenbin wrote: > I'm newbie to emboss, but it is really an interesting project. > I spend sometime to implement a major mode to edit and view acd files for > emacser. > Hope it is useful. You can download it from: > http://www.emacswiki.org/cgi-bin/emacs/acd.el > > Any comments are welcome! Enjoy. Many thanks. I will try it out and let you know. From a first look I can see some interesting ways to extend it. Do you have a short user guide to explain what features it has? I discovered things like "appl" and "sec" which are nice. Which version of EMBOSS did you use? regards, Peter Rice From wenbinye at gmail.com Tue Aug 14 02:56:35 2007 From: wenbinye at gmail.com (Ye Wenbin) Date: Tue, 14 Aug 2007 10:56:35 +0800 Subject: [EMBOSS] An emacs mode to edit acd files In-Reply-To: <46C08AD5.7050801@ebi.ac.uk> References: <46C08AD5.7050801@ebi.ac.uk> Message-ID: On Tue, 14 Aug 2007 00:46:13 +0800, Peter Rice wrote: > Do you have a short user guide to explain what features it has? I > discovered things like "appl" and "sec" which are nice. I wrote some simple description about features of acd-mode in the header of the files. Except keywords highlight and indentation as a major modes should do, I add some useful feature for editing: 1. support for imenu. You can use M-x imenu to move to other tokens 2. abbrevation using tempo.el. As you see, currently I add two abbrev "appl" and "sec", but you can add more as you like. That is easy, after load 'acd.el', you can use acd-define-tempo-template to add an new tempo template, for example: (acd-define-tempo-template "int" '("integer") '("default" "information")) The new abbrev cannot be used in a buffer opened before it defined, you have to M-x acd-mode to ask tempo install the new tempo-local-tags. Now you can type int and expand it to: integer: [ default: "" information: "" ] tempo can create marks when expand the template, so you move around using tempo-forward-marks and tempo-backward-marks, which are bound to C-c C-n and C-c C-p in acd-mode. This feature make me choose it rather than skeleton. And if you think you abbrev still to long, you can use M-x tempo-complete-tag to complete an abbrev, it is bound to C-c TAB. 3. Completion. Many things can be completed using TAB. For example, the name of data type bool can complete to boolean. And the attributes of the data type can be completed like: boolean feature [ def will get "default". The name of variable can be completed when it is declare before point: sequence: inseq [ features: $(fe will get "feature" if the variable "feature" is declare before. The calculated attributes also can be completed. $(inseq.le can get "length" if the "inseq" is declared as type "sequence" before. Today I add completions for standard groups because I think it is hard to remember so many groups. You can complete group name as: groups: " That all what acd-mode do. I want add a command acd-pretty that use command acdpretty to reformat code, but I don't know how to make the command read input from stdin, I use command: $ cat appl.acd | acdpretty -filter but failed. Is it possible to make the command read from stdin? > Which version of EMBOSS did you use? I check out the cvs version of emboss, and build it myself. This is some question about the document of library. I can find some scripts to generate documents for libraries under directory "scripts", but I can find command to build it. I try "make html" "make info", but get nothing. And run embossdoc.csh get errors: $ csh scripts/embossdoc.csh /home/ywb/downloads/emboss/emboss/ /home/ywb/downloads/emboss/emboss/doc touch: Cannot touch '/home/ywb/downloads/emboss/emboss/doc/ajax/dummy.html': No such file or directory foreach: No match. How can I use those scripts? Thanks! -- Best regards, Ye Wenbin From pmr at ebi.ac.uk Tue Aug 14 13:04:49 2007 From: pmr at ebi.ac.uk (Peter Rice) Date: Tue, 14 Aug 2007 14:04:49 +0100 Subject: [EMBOSS] An emacs mode to edit acd files In-Reply-To: References: <46C08AD5.7050801@ebi.ac.uk> Message-ID: <46C1A871.9010509@ebi.ac.uk> Ye Wenbin wrote: > I wrote some simple description about features of acd-mode in the header > of the files. Except keywords highlight and indentation as a major modes > should do, I add some useful feature for editing: > 1. support for imenu. You can use M-x imenu to move to other tokens Interesting. It understands sections. > And if you think you abbrev still to long, you can use > M-x tempo-complete-tag to complete an abbrev, it is bound to C-c TAB. Easy ... but it seems I have to use the exact abbreviation. Something that expands any abbreviation (if it is unique) and adds a set of attributes is very useful. This combines the abbreviation handling with the C-c TAB. Is that easy to implement? > 3. Completion. Many things can be completed using TAB. For example, > the name of data type bool can complete to boolean. And the > attributes of the data type can be completed like: > boolean feature [ > def > will get "default". Can it insert default and information (for example) as attributes? > The name of variable can be completed when it is declare before point: > sequence: inseq [ > features: $(fe > will get "feature" if the variable "feature" is declare before. > The calculated attributes also can be completed. $(inseq.le can get > "length" if the "inseq" is declared as type "sequence" before. > Today I add completions for standard groups because I think it is hard > to > remember so many groups. You can complete group name as: > groups: " That is useful. The current group names are stored in emboss/acd/groups.standard We validate them automatically. If we add acd.el to the EMBOSS CVS tree we can validate the list there and keep it updated. > I want add a command acd-pretty that use command acdpretty to reformat > code, but I don't know how to make the command read input from stdin, > I use command: > $ cat appl.acd | acdpretty -filter > but failed. Is it possible to make the command read from stdin? No. The -filter option works for EMBOSS programs and the ACD file that acdpretty is reading (you can still use all the command line options of that ACD file). But it is easy to reformat code in emacs .. the indentation is not difficult. acdpretty also completes abbreviations and adds missing quotes. >> Which version of EMBOSS did you use? > I check out the cvs version of emboss, and build it myself. Thanks. So we can try it without having to make updates. > This is some question about the document of library. I can find some scripts > to generate documents for libraries under directory "scripts", but I can find > command to build it. > How can I use those scripts? Ah ... we make the documentation in another directory (because the documentation is on the sourceforge website, and sourceforge has restrictions on using CVS, we have to use a sourceforge CVS server). I run embossdoc.csh with two arguments - where to find the source code, and where to store the documentation. You can also pick up the documentation from emboss.cvs.sourceforge.net in directory sfdoc/developers and give the sfdoc.developers directory as the second argment to embossdoc.csh regards, Peter Rice From sum732 at mail.usask.ca Tue Aug 14 20:46:03 2007 From: sum732 at mail.usask.ca (Mehrotra, Sudeep) Date: Tue, 14 Aug 2007 14:46:03 -0600 Subject: [EMBOSS] MW in "Digest" -EMBOSS Message-ID: <1187124363.46c2148bf0808@webmail.usask.ca> Hello, I am trying to figure out how molecular weight of the peptide fragments in EMBOSS "DIGEST" is calculated? For example: given fragment AEK, "DIGEST" returns a MW = 346.378. Now if i look at the residual masses(monoisotopic) of A E K they are 71.03711, 129.04259, 128.09496, respectively, these dont add up to 346.378. I tried using Average mass, as well as normal mw of AA in question, but i am not to get a MW of 346.378. It would be very helpful if you can explain how MW is calculated in EMBOSS-DIGEST. Thanking You Sudeep From kvddrift at earthlink.net Sat Aug 18 20:11:41 2007 From: kvddrift at earthlink.net (Koen van der Drift) Date: Sat, 18 Aug 2007 16:11:41 -0400 Subject: [EMBOSS] MW in "Digest" -EMBOSS In-Reply-To: <1187124363.46c2148bf0808@webmail.usask.ca> References: <1187124363.46c2148bf0808@webmail.usask.ca> Message-ID: <9283D5A1-09F3-49BD-87C5-F40C0CBA7CB7@earthlink.net> You will have to add the mw of water (18) to get the total mw of your peptide. - Koen. On Aug 14, 2007, at 4:46 PM, Mehrotra, Sudeep wrote: > Hello, > > I am trying to figure out how molecular weight of the peptide > fragments in > EMBOSS > "DIGEST" is calculated? > > For example: given fragment AEK, "DIGEST" returns a MW = 346.378. > > Now if i look at the residual masses(monoisotopic) of A E K they > are 71.03711, > 129.04259, 128.09496, respectively, these dont add up to 346.378. I > tried using > Average mass, as well as normal mw of AA in question, but i am not > to get a MW > of > 346.378. > It would be very helpful if you can explain how MW is calculated in > EMBOSS-DIGEST. > > Thanking You > Sudeep > > _______________________________________________ > EMBOSS mailing list > EMBOSS at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/emboss From sum732 at mail.usask.ca Fri Aug 31 15:40:01 2007 From: sum732 at mail.usask.ca (Mehrotra, Sudeep) Date: Fri, 31 Aug 2007 09:40:01 -0600 Subject: [EMBOSS] Monoisotopic or Average mass Message-ID: <1188574801.46d83651b81ec@webmail.usask.ca> Hello, I am trying to figure out how molecular weight of the peptide fragments in EMBOSS program "DIGEST" is calculated if enzyme used for digestion is Trypsin. Monoisotopic mass of each constituent AA residues in a given peptide sequence+ monoisotopic mass of water or Average mass of each constituent AA residues in a given peptide sequence +average mass of water A quick response would be appreciated. Thanking You Sudeep From pmr at ebi.ac.uk Fri Aug 31 17:37:02 2007 From: pmr at ebi.ac.uk (Peter Rice) Date: Fri, 31 Aug 2007 18:37:02 +0100 Subject: [EMBOSS] Monoisotopic or Average mass In-Reply-To: <1188574801.46d83651b81ec@webmail.usask.ca> References: <1188574801.46d83651b81ec@webmail.usask.ca> Message-ID: <46D851BE.9010903@ebi.ac.uk> Hi Sudeep, > I am trying to figure out how molecular weight of the peptide fragments in > EMBOSS program "DIGEST" is calculated if enzyme used for digestion is Trypsin. > > Monoisotopic mass of each constituent AA residues in a given peptide sequence+ > monoisotopic mass of water > or > Average mass of each constituent AA residues in a given peptide sequence > +average mass of water Average mass. as far as I am aware ... but we do need more documentation of the molecular weights in Eamino.dat You can set the masses in a local data file if you want to use monoisotopic values. Add -aadata filename to the commandline or put a file Eamino.dat in your current directory. For the water the values are currently hardcoded in nucleus/embprop.c as: H 1.00782 OH 17.00274 But we could add values to Eamino.dat. If you can provide alternative values we can also add an alternative local data file to the EMBOSS distribution. Hope that helps. Peter