From Sean.Maceachern at dpi.vic.gov.au Thu Oct 2 03:04:23 2003 From: Sean.Maceachern at dpi.vic.gov.au (Sean.Maceachern at dpi.vic.gov.au) Date: Thu, 2 Oct 2003 17:04:23 +1000 Subject: [EMBOSS] Needle Message-ID: Hello, I am a novice at all things computer and i was hoping that someone might be able to give me some advice. I am working with two lynux machines with different versions of Emboss on them. I have noticed that in the most recent version of emboss the needle outputs have changed. I need to work with the 'old' fasta output that used to have trailing gaps/indels as white space and internal gaps/indels as periods '.' . I have found that the most recent version of emboss has changed the output format so now the fasta format looks more like a clustal output with gaps/indels represented as a ' -' whether thay are terminal or inserted within the sequence. I was hoping someone could point me towards a similar output for the new version of emboss or if it is not too much trouble to make a new format based on the fasta format from an older version of needle. Thank you Sean MacEachern From alex at compressweb.com Thu Oct 2 03:37:30 2003 From: alex at compressweb.com (alex at compressweb.com) Date: Thu, 2 Oct 2003 15:37:30 +0800 Subject: [EMBOSS] [Announce] EQ 1.0 version is available now! Message-ID: <41172-2200310427373097@redust> -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.open-bio.org/pipermail/emboss/attachments/20031002/2916420b/attachment.html -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: image/jpeg Size: 11542 bytes Desc: EQ.jpg Url : http://lists.open-bio.org/pipermail/emboss/attachments/20031002/2916420b/attachment.jpe From d.m.a.martin at dundee.ac.uk Thu Oct 2 04:17:42 2003 From: d.m.a.martin at dundee.ac.uk (David Martin) Date: Thu, 02 Oct 2003 09:17:42 +0100 Subject: [EMBOSS] Needle In-Reply-To: Message-ID: On 2/10/03 8:04 am, "Sean.Maceachern at dpi.vic.gov.au" wrote: > Hello, > > I am a novice at all things computer and i was hoping that someone might be > able to give me some advice. I am working with two lynux machines with > different versions of Emboss on them. I have noticed that in the most > recent version of emboss the needle outputs have changed. I need to work > with the 'old' fasta output that used to have trailing gaps/indels as white > space and internal gaps/indels as periods '.' . I have found that the most > recent version of emboss has changed the output format so now the fasta > format looks more like a clustal output with gaps/indels represented as a ' > -' whether thay are terminal or inserted within the sequence. I was hoping > someone could point me towards a similar output for the new version of > emboss or if it is not too much trouble to make a new format based on the > fasta format from an older version of needle. You will find that you can set the alignment format output by programs like needle using a command line flag. the EMBOSS website has full details of this at http://www.hgmp.mrc.ac.uk/Software/EMBOSS/Themes/AlignFormats.html regards ..d > > Thank you > > Sean MacEachern > > -- David Martin PhD Bioinformatics Scientific Officer Post-Genomics and Molecular Interactions Centre University of Dundee From martin_artist at yahoo.com Mon Oct 6 03:14:46 2003 From: martin_artist at yahoo.com (ENRON = Swarzenegger) Date: Mon, 6 Oct 2003 03:14:46 Subject: [EMBOSS] Stealing CA $9 billions = Recall Election Message-ID: <20031006101626.8E7767D206@mercury.hgmp.mrc.ac.uk> Bush bible PNAC Swarzeneger got money from ENRON to forgive 9 billions pay back I'm very worry, desperate PNAC may do 3rd Pearl Harbor to US. - Second is here: 1997 http://www.newamericancentury.org/RebuildingAmericasDefenses.pdf page 48 Clinton economy is good - page 51 on document or 63 / on Acrobat viewer.. - We have to have major attack on America first, to convince people OPEN YOUR MIND FOR YOURSELF AND YOUR KIDS LIFE; http://www.alternetnews.com/ Arnold or Adolph, what the different; D A N K E, will Terminate US all & California first Prescott help Adolph, George him & Enron; Gasoline $4 per gallon is just the beginning. Actor = skilled liar, how can we trust them ? I heard, his porno job is for sale; & He is ENRON BOY http://www.tarpley.net/bushb.htm http://www.bartcop.com/421102.htm http://www.bk2k.com/bushbodycount/prescott-bush/index.shtml http://hnn.us/comments/15105.html Hitler, Noriega, Hussein, bin Laden, Pinochet - did business with the Bush family. Now we do business with Bush as well; - $500 000 000 000 is gone, missing, and make US poor Perfect Taxpayers Rip Off - MONEY LAUNDRY - true Iraq repair kidding, - direct to own pocket, Isn't this a crime ?? + Lie of war reasons, and lie, and lie, and lie. Please look on this and think by yourself; where we are going ?? Or PNAC push us there, like stick to a blind sheep. - Start thinking on your own, please. http://pnac.tvnewslies.org http://www.tvnewslies.org START THINKING AGAIN !!! www.moveon.org/news/1577.html www.prisonplanet.com www.moveon.org www.votetoimpeach.com www.kgo810.com listen 810 AM; Bernie, Genie, Ray only (night time) How many Concentration Camps do they need today ? one for sure is on Cuba. If, after that news - you can't sleep too well -; get Warren book; " The Governor " try understand - how to blackmail Congress - Or movie films; " Enemy of the State" that most of us today " Spy like US " - abusing power by top managers " Air America " - how marihuana come to US It may happened, Pentagon will have to arrest White House and his own " Liar in Chief" to save USA On the base of George Washington Legacy War President & his bible "PNAC" inventing Terrorism & new Pearl Harbor: http://www.newamericancentury.org/RebuildingAmericasDefenses.pdf ) From Johanne.Duhaime at ircm.qc.ca Mon Oct 6 15:34:29 2003 From: Johanne.Duhaime at ircm.qc.ca (Duhaime Johanne) Date: Mon, 6 Oct 2003 15:34:29 -0400 Subject: [EMBOSS] citation for an Emboss program Message-ID: <75CDD43E62D698448ED86E23C290A2760A2C3F@pandore.ircm.priv> Hello If I use a program, Needle as an example, should I cite Emboss: Rice,P. Longden,I. and Bleasby,A. "EMBOSS: The European Molecular Biology Open Software Suite" Trends in Genetics June 2000, vol 16, No 6. pp.276-277 Or should I cite Alan Bleasby (ableasby ? hgmp.mrc.ac.uk) HGMP-RC, Genome Campus, Hinxton, Cambridge CB10 1SB, UK Thank you Johanne Duhaime IRCM -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.open-bio.org/pipermail/emboss/attachments/20031006/3d9ca881/attachment.html From sdyall at ucla.edu Mon Oct 6 23:42:33 2003 From: sdyall at ucla.edu (Sabrina Dyall) Date: Mon, 6 Oct 2003 20:42:33 -0700 Subject: [EMBOSS] orf Message-ID: Hi, Does anybody know if it is possible to select a maximum size open reading frame or a range of open reading frame sizes using getorf or another application? Sabrina From sdyall at ucla.edu Mon Oct 6 23:42:33 2003 From: sdyall at ucla.edu (Sabrina Dyall) Date: Mon, 6 Oct 2003 20:42:33 -0700 Subject: [EMBOSS] orf Message-ID: Hi, Does anybody know if it is possible to select a maximum size open reading frame or a range of open reading frame sizes using getorf or another application? Sabrina From gwilliam at hgmp.mrc.ac.uk Tue Oct 7 04:41:22 2003 From: gwilliam at hgmp.mrc.ac.uk (Gary Williams, Tel 01223 494522) Date: Tue, 07 Oct 2003 09:41:22 +0100 Subject: [EMBOSS] orf References: Message-ID: <3F827C32.792127C4@hgmp.mrc.ac.uk> I never thought of setting a maximum size! I've changed the code for the getorf program to allow maximum sizes. It will be available in the next release of EMBOSS, or you can get the program files from: ftp://ftp.hgmp.mrc.ac.uk/pub/EMBOSS/patchfiles/getorf.* Regards, Gary Sabrina Dyall wrote: > > Hi, > Does anybody know if it is possible to select a maximum size open > reading frame or a range of open reading frame sizes using getorf or > another application? > Sabrina -- 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, Hinxton, Cambridge, CB10 1SB, UK From nancyyu at imb.sinica.edu.tw Tue Oct 7 21:06:58 2003 From: nancyyu at imb.sinica.edu.tw (Nancy Yu) Date: Wed, 08 Oct 2003 09:06:58 +0800 Subject: [EMBOSS] How to Get Jemboss to display/save pictures Message-ID: <3F836332.4040801@imb.sinica.edu.tw> Hi, I can't seem to get Jemboss to produce pictures for Emboss programs like pepwheel or any other program that output pictures. I don't know if it is a simple setting problem or installation problem. Any suggestions? Nancy Yu From bounce-back at htmlemail.ca Wed Oct 8 05:02:28 2003 From: bounce-back at htmlemail.ca (Holiday Giveaways) Date: 08 Oct 2003 02:02:28 -0700 Subject: [EMBOSS] Draw for a Florida Holiday Message-ID: <20031008020228.BDAC8A76A40135D2@htmlemail.ca> Free Holiday Giveaways Sign-up for the FREE Holiday Giveaway Draw You must register to be eligible for the draw. Fill out this form to register and be eligible for our monthly draw. 5 days and 4 nights in Orlando, Florida 6 days and 5 nights in Ft. Lauderdale, Florida PLUS 7 day unlimited Car Rental PLUS 2 Tickets to Universal Studios or to Disney World You must register to be eligible for the draw. Fill out this form and we'll do the rest. Free Holiday Giveaways copyright 2003 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.open-bio.org/pipermail/emboss/attachments/20031008/73e063ba/attachment.html From tcarver at hgmp.mrc.ac.uk Wed Oct 8 04:43:06 2003 From: tcarver at hgmp.mrc.ac.uk (Dr T. Carver) Date: Wed, 8 Oct 2003 09:43:06 +0100 (BST) Subject: [EMBOSS] How to Get Jemboss to display/save pictures In-Reply-To: <3F836332.4040801@imb.sinica.edu.tw> Message-ID: Hi Nancy The first thing to do is to check you can run these applications from the command line and create graphics. That will then give you more of a clue. It may be a png library problem. Regards Tim Carver HGMP-RC On Wed, 8 Oct 2003, Nancy Yu wrote: > Hi, > > I can't seem to get Jemboss to produce pictures for Emboss programs like > pepwheel or any other program that output pictures. I don't know if it > is a simple setting problem or installation problem. Any suggestions? > > Nancy Yu > From nancyyu at imb.sinica.edu.tw Wed Oct 8 06:13:35 2003 From: nancyyu at imb.sinica.edu.tw (Nancy Yu) Date: Wed, 08 Oct 2003 18:13:35 +0800 Subject: [EMBOSS] Indexing databases and their updates/new releases Message-ID: <3F83E34F.2050200@imb.sinica.edu.tw> Hello, I have a bunch of questions about the indexing of the databases. First of all, what kind of computers are people using to run Emboss? I am running on a Athlon MP2000+ dual processor with 1GB RAM (on Linux Redhat 9.0). Running dbiflat for EMBL est*.dat has taken forever (about 5 days and still not done yet). Are people using 64-bit systems, cluster systems, or other high-end computing systems? Is Emboss designed to run on these technologies? I'm still confused about the dbiflat indexing process. I know it produces 4 files, acnum.hit, acnum.trg, division.lkp, entrynam.idx. As I read somewhere in the mail archive, division.lkp stores the location of the database directory. Doesn't this means that if we move our *.dat file to a different directory, we would have to re-index again? Hence, everytime we download a new database, a new release, or an update, we will have to re-index everything? Also, if dbiflat was interrupted half way through indexing, is it possible to continue where it left off? >From my experience, it seems like the whole process starts over again. Just wondering, are the included index files for databases like embl (eg. division.ndx and other *.ndx files) useful at all for Emboss, or are they more for other programs? Can I somehow use these index files, ie. is there a fast way of indexing a database that I missed, or am I too clueless to know what I'm talking about? My main concern is that at the speed it takes to index a new release of large databases like EMBL or Genbank, it would be difficult for me to try to keep my local databases up-to-date. Thanx in advance for any comments and explanations :) Best Regards, Nancy Yu From ableasby at hgmp.mrc.ac.uk Wed Oct 8 06:46:26 2003 From: ableasby at hgmp.mrc.ac.uk (Alan Bleasby) Date: Wed, 8 Oct 2003 11:46:26 +0100 (BST) Subject: [EMBOSS] Indexing databases and their updates/new releases Message-ID: <200310081046.h98AkQ85018479@bromine.hgmp.mrc.ac.uk> The current indexing system is a little long in the tooth. I am currently testing/configuring its replacement on the various platforms. The new indexing system will not be available in the next release but should be out within the next few months. It is intended that the next release of EMBOSS will, by default, compile with large file support on all platforms (although the old indexing system cannot support files >2Gb). So, 2.8.0 will have 64bit (aj)long integers. Features of the new indexing system are that it is a B+ tree structure and therefore can be dynamically updated (e.g. with EMBL updates), can handle large files and duplicate IDs. It also does not need any sorting operations (the major cause of slowness for the old indexing system). Timing for the new system to index the latest EMBL release on a Linux system with the same spec as yours is around 9hrs (8hrs of which is just reading the database over NFS). EMBOSS is not designed for parallel processing although we have identified the areas of code that would need attention should we go down that route in the future. It is not (in general) possible to restart the old indexing system where it left off. That is a feature that could be implemented in the new indexing system (but isn't yet). I'm sure others may answer anything I've missed. HTH Alan Bleasby HGMP From ranrub at md.huji.ac.il Wed Oct 8 07:22:48 2003 From: ranrub at md.huji.ac.il (Ran Rubinstein) Date: Wed, 8 Oct 2003 13:22:48 +0200 Subject: [EMBOSS] Indexing databases and their updates/new releases In-Reply-To: <3F83E34F.2050200@imb.sinica.edu.tw> Message-ID: <003001c38d8e$81482fd0$7ea74084@sauron> I am currently tacking similar problems. The solution I've worked out for now is to use SRS (www.lionbio.co.uk) as a database - it's free for academic institutions, has very strong indexing tools that can use parallel processing, and Emboss can be configured to work through it. It also has a very professional web interface that can launch EMBOSS tools. The downside is that it's a bit complicated to install and administer. I'll be glad to hear alternative suggestions, tho. The server I'm running SRS and EMBOSS on is a 4-processor Origin200, 270Mhz, with 1GB RAM. Indexing (using SRS) the latest GenBank release, with NO EST's, GSS, HTG, took approximately 24 hours, running in parallel on 4 processors. --? Ran Rubinstein Dept. of Molecular Biology Faculty of Medicine, Hebrew University, Ein Karem Tel +972-2-6757906 Fax +972-2-6758992 -----Original Message----- From: owner-emboss at hgmp.mrc.ac.uk [mailto:owner-emboss at hgmp.mrc.ac.uk] On Behalf Of Nancy Yu Sent: Wednesday, October 08, 2003 12:14 PM To: emboss at embnet.org Subject: [EMBOSS] Indexing databases and their updates/new releases Hello, I have a bunch of questions about the indexing of the databases. First of all, what kind of computers are people using to run Emboss? I am running on a Athlon MP2000+ dual processor with 1GB RAM (on Linux Redhat 9.0). Running dbiflat for EMBL est*.dat has taken forever (about 5 days and still not done yet). Are people using 64-bit systems, cluster systems, or other high-end computing systems? Is Emboss designed to run on these technologies? I'm still confused about the dbiflat indexing process. I know it produces 4 files, acnum.hit, acnum.trg, division.lkp, entrynam.idx. As I read somewhere in the mail archive, division.lkp stores the location of the database directory. Doesn't this means that if we move our *.dat file to a different directory, we would have to re-index again? Hence, everytime we download a new database, a new release, or an update, we will have to re-index everything? Also, if dbiflat was interrupted half way through indexing, is it possible to continue where it left off? >From my experience, it seems like the whole process starts over again. Just wondering, are the included index files for databases like embl (eg. division.ndx and other *.ndx files) useful at all for Emboss, or are they more for other programs? Can I somehow use these index files, ie. is there a fast way of indexing a database that I missed, or am I too clueless to know what I'm talking about? My main concern is that at the speed it takes to index a new release of large databases like EMBL or Genbank, it would be difficult for me to try to keep my local databases up-to-date. Thanx in advance for any comments and explanations :) Best Regards, Nancy Yu From aml at ica.cc Wed Oct 8 09:41:27 2003 From: aml at ica.cc (American Laboratory) Date: Wed, 8 Oct 2003 09:41:27 -0400 Subject: [EMBOSS] American Laboratory Message-ID: <78131748.20031008094127@ica.cc> To Subscribe Go To: http://www.icainfo.com/aml/appintro.asp?Priority=PEPAL3 Following are the themes to be featured in AL: November Microscopy, Optics, and Image Analysis December Pharmaceutical Analysis, Molecular Spectroscopy, EAS January Annual ISC Buyers' Guide,Thermal Analysis, Gas Chromatography February Pittcon 2004 New Analytical Instrumentation for Separation Science and Spectroscopy March Advances in Laboratory Software and Data Management April Microchemical Analysis, Sample Preparation Dear Colleague, Please accept my invitation to receive a free subscription to our journal, American Laboratory. American Laboratory covers the disciplines of analytical and bioanalytical chemistry, drug discovery, laboratory software and informatics. Each issue features articles from leading scientists from around the world reviewing applications of instrumentation and new measurement technology. For your FREE subscription to American Laboratory, please click on the following link. http://www.icainfo.com/aml/appintro.asp?Priority=PEPAL3 I am confident that you will enjoy our journal and find it to be of significant professional value. I look forward to hearing from you. Sincerely yours, Brian Howard, Ph.D. Editor International Scientific Communications, Inc. 30 Controls Drive, P.O. Box 870, Shelton, CT 06484 Tel.: 203-926-9300, Fax: 203-926-9310, www.iscpubs.com -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.open-bio.org/pipermail/emboss/attachments/20031008/6f8776bf/attachment.html From yann-francois.bizouerne at bayercropscience.com Wed Oct 8 11:32:55 2003 From: yann-francois.bizouerne at bayercropscience.com (yann-francois.bizouerne at bayercropscience.com) Date: Wed, 8 Oct 2003 17:32:55 +0200 Subject: [EMBOSS] Configuring EMBOSS to use getz Message-ID: Hi, I am trying to use the method "srs". I am using Emboss 2.7.1 and SRS 7.1. In my emboss.default file, I have : DB Nrl3dGetz [ methodquery: srs format: pir type: P comment: "NRL 3D using SRS" app: getz dbalias:NRL3D methodall: direct file: "*.seq" dir: $emboss_data_dir/nrl_3d ] When I execute the command "showdb", I obtain : user>showdb Displays information on the currently available databases # Name Type ID Qry All Comment # ==== ==== == === === ======= Nrl3dGetz P OK OK OK NRL 3D using SRS So I looks fine. But when I try to find an entry, I just obtain a error. user>entret Nrl3dGetz:11ASA -outfile stdout Reads and writes (returns) flatfile entries error: Unknown set or databank No set or library named "Nrl3dGetz" Error: Unable to read sequence 'Nrl3dGetz:11ASA' Died: entret terminated: Bad value for '-sequence' and no prompt I have read all the SRS and EMBOSS documentations related to this configuration and I don't know where the problem is. Do you have any clue ?? Thanks in advance. Yann-Fran?ois BIZOUERNE BioInformatic Team BAYER CropScience 1, rue Pierre Fontaine 91058 Evry Cedex FRANCE Phone: 33-(0) 1-69-47-61-56 FAX: 33-(0) 1-69-47-61-42 E-mail: yann-francois.bizouerne at bayercropscience.com Intranet: http://bioinfo.evry.fr.bayercropscience/ From ranrub at md.huji.ac.il Wed Oct 8 11:50:28 2003 From: ranrub at md.huji.ac.il (Ran Rubinstein) Date: Wed, 8 Oct 2003 17:50:28 +0200 Subject: [EMBOSS] Configuring EMBOSS to use getz In-Reply-To: Message-ID: <003301c38db3$e5cc26d0$7ea74084@sauron> Your dbalias parameter is probably wrong. It should be the name of the databank in SRS. Try to run getz directly with your query and see whether it works. --? Ran Rubinstein Dept. of Molecular Biology Faculty of Medicine, Hebrew University, Ein Karem, Jerusalem, Israel Tel +972-2-6757906 Fax +972-2-6758992 -----Original Message----- From: owner-emboss at hgmp.mrc.ac.uk [mailto:owner-emboss at hgmp.mrc.ac.uk] On Behalf Of yann-francois.bizouerne at bayercropscience.com Sent: Wednesday, October 08, 2003 5:33 PM To: emboss at embnet.org Subject: [EMBOSS] Configuring EMBOSS to use getz Hi, I am trying to use the method "srs". I am using Emboss 2.7.1 and SRS 7.1. In my emboss.default file, I have : DB Nrl3dGetz [ methodquery: srs format: pir type: P comment: "NRL 3D using SRS" app: getz dbalias:NRL3D methodall: direct file: "*.seq" dir: $emboss_data_dir/nrl_3d ] When I execute the command "showdb", I obtain : user>showdb Displays information on the currently available databases # Name Type ID Qry All Comment # ==== ==== == === === ======= Nrl3dGetz P OK OK OK NRL 3D using SRS So I looks fine. But when I try to find an entry, I just obtain a error. user>entret Nrl3dGetz:11ASA -outfile stdout Reads and writes (returns) flatfile entries error: Unknown set or databank No set or library named "Nrl3dGetz" Error: Unable to read sequence 'Nrl3dGetz:11ASA' Died: entret terminated: Bad value for '-sequence' and no prompt I have read all the SRS and EMBOSS documentations related to this configuration and I don't know where the problem is. Do you have any clue ?? Thanks in advance. Yann-Fran?ois BIZOUERNE BioInformatic Team BAYER CropScience 1, rue Pierre Fontaine 91058 Evry Cedex FRANCE Phone: 33-(0) 1-69-47-61-56 FAX: 33-(0) 1-69-47-61-42 E-mail: yann-francois.bizouerne at bayercropscience.com Intranet: http://bioinfo.evry.fr.bayercropscience/ From pmr at ebi.ac.uk Wed Oct 8 11:55:48 2003 From: pmr at ebi.ac.uk (Peter Rice) Date: Wed, 08 Oct 2003 16:55:48 +0100 Subject: [EMBOSS] Configuring EMBOSS to use getz References: Message-ID: <3F843384.9090609@ebi.ac.uk> yann-francois.bizouerne at bayercropscience.com wrote: > I am trying to use the method "srs". > I am using Emboss 2.7.1 and SRS 7.1. > > In my emboss.default file, I have : > > DB Nrl3dGetz [ > methodquery: srs > format: pir > type: P > comment: "NRL 3D using SRS" > app: getz > dbalias:NRL3D > methodall: direct > file: "*.seq" > dir: $emboss_data_dir/nrl_3d > ] Quick reply (it's a very busy day :_) From memory, SRS has a problem with PIR formatted databases. It does not report the entry in a format that EMBOSS recognizes (try getz -e to see what the entry looks like). You may find the SRSFASTA methodquery works better (use format fasta). Hope this helps - if not, ask me again!!! Peter Rice From gbottu at ben.vub.ac.be Wed Oct 8 14:10:33 2003 From: gbottu at ben.vub.ac.be (Guy Bottu) Date: Wed, 8 Oct 2003 20:10:33 +0200 (CEST) Subject: [EMBOSS] Configuring EMBOSS to use getz Message-ID: <200310081810.h98IAXrg1329213@black.vub.ac.be> from : BEN Dear friends, I have read the question of Yann-Francois and the replies by Ran and Peter. Allow me to add some further comments. - I think that the parameter "app: getz" is useless since "method: srs" already tells it is getz. By the way, is getz in your "path" ? (well, probably yes, since we would otherwise expect another error message) - To solve the problem Peter mentions you can in pir.i replace $Field:[$DF_ProtSequence token:sequence format:pir tableFormat:listing] by $Field:[$DF_ProtSequence token:sequence format:plain tableFormat:listing] Guy Bottu From felipb at eis.org Fri Oct 10 12:55:46 2003 From: felipb at eis.org (felipb at eis.org) Date: Fri, 10 Oct 2003 18:55:46 +0200 Subject: [EMBOSS] THE MULTIMEDIA WEB SOLUTION Message-ID: <001101c38f4f$70c67af0$1eef2350@EP> THE MULTIMEDIA WEB SOLUTION VISIT THE HUMAN ROBOT WEB SITE www.avantatge.com LA TEVA NOVA WEB MULTIMEDIA PROVA GRATU?TA 30 DIES -> PROVA GET YOUR NEW MULTIMEDIA WEB FREE TEST 30 DAYS -> TEST VOTRE NOUVELLE WEB MULTIMEDIA ESSAI GRATUIT 30 JOURS -> ESSAI LA TUA NUOVA WEB MULTIMEDIA PROVA GRATUITA 30 GIORNI -> PROVA Aquest missatge no es spam : es un missatge de resposta o perqu? ha visitat una de las nostres web . Si no vol mes rebre mes missatges o si l'ha rebut per error envi? una e-mail a stop at avantatge.com . Recordi que no perd el dret de tenir una web multimedia gratu?ta per 30 dies . You are currently subscribed to Avantatge news If you'd rather not receive e-mail about events, or product updates, send a message to stop at avantatge.com . However you will not lost the right to test for 30 days a full multimedia web ?2003 Avantatge? web studios by EP sl Andorra www.avantatge.com -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.open-bio.org/pipermail/emboss/attachments/20031010/714b6068/attachment.html -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: image/jpeg Size: 3681 bytes Desc: not available Url : http://lists.open-bio.org/pipermail/emboss/attachments/20031010/714b6068/attachment.jpe From nancyyu at imb.sinica.edu.tw Tue Oct 14 04:16:09 2003 From: nancyyu at imb.sinica.edu.tw (Nancy Yu) Date: Tue, 14 Oct 2003 16:16:09 +0800 Subject: [EMBOSS] How to Get Jemboss to display/save pictures In-Reply-To: References: Message-ID: <3F8BB0C9.1030506@imb.sinica.edu.tw> I can produce png graphic files from command line Emboss just fine, but it doesn't seem to work from Jemboss. Actually, a png file of 0 bytes is produced, and I don't know what that means. Does anyone else have similar problems? >Hi Nancy > >The first thing to do is to check you can run these applications from the >command line and create graphics. That will then give you more of a clue. >It may be a png library problem. > >Regards >Tim Carver > >HGMP-RC > >On Wed, 8 Oct 2003, Nancy Yu wrote: > > > >>Hi, >> >>I can't seem to get Jemboss to produce pictures for Emboss programs like >>pepwheel or any other program that output pictures. I don't know if it >>is a simple setting problem or installation problem. Any suggestions? >> >>Nancy Yu >> >> >> From ronald.yang at jakru.com Tue Oct 14 11:55:12 2003 From: ronald.yang at jakru.com (H.Ronald Yang) Date: Tue, 14 Oct 2003 11:55:12 -0400 Subject: [EMBOSS] EMBOSS GUI : mwcontam : unknown datatype 'filelist' Message-ID: <008201c3926b$8dcd16d0$02020a0a@rescentris.com> Hi, I have a problem using "mwcontam" and "mwfilter" through EMBOSS Web GUI. When I click on the one of "PROTEIN COMPOSITION" tool, "mwcontam", from the left side panel, there is error. Right after "input section", it says "ERROR" and "unknown datatype 'filelist'". Is this possible to fix? Thanks in advance, Ron From mccarthy at cs.usask.ca Tue Oct 14 12:25:17 2003 From: mccarthy at cs.usask.ca (Luke McCarthy) Date: 14 Oct 2003 10:25:17 -0600 Subject: [EMBOSS] EMBOSS GUI : mwcontam : unknown datatype 'filelist' In-Reply-To: <008201c3926b$8dcd16d0$02020a0a@rescentris.com> References: <008201c3926b$8dcd16d0$02020a0a@rescentris.com> Message-ID: <1066148717.933.17.camel@crazyharry.usask.ca> On Tue, 2003-10-14 at 09:55, H.Ronald Yang wrote: > Hi, > > I have a problem using "mwcontam" and "mwfilter" through EMBOSS Web GUI. > When I click on the one of "PROTEIN COMPOSITION" tool, "mwcontam", from the > left side panel, there is error. Right after "input section", it says > "ERROR" and "unknown datatype 'filelist'". Is this possible to fix? There's no support for that particular data type in the GUI -- I didn't know it existed... I'll put something together and make available an updated version of the GUI available hopefully later today. Check http://bioinfo.pbi.nrc.ca/~lukem/EMBOSS/ for the update. There's no mention of this particular data type in the ACD spec at http://www.hgmp.mrc.ac.uk/Software/EMBOSS/Acd/syntax.html#Acddata11 , but I assume it's just supposed to be a random list of files. Can someone on the list familiar with the internals confirm that this is true? If it is true, it's going to be particularly difficult to implement this type over the web as there is no standard control for uploading more than one file. I'll probably just treat this as an alias for 'datafile' unless there's some subtlety that I'm missing... Cheers, Luke -- Luke McCarthy Research Officer, Bioinformatics Department of Computer Science University of Saskatchewan mccarthy at cs.usask.ca From tcarver at hgmp.mrc.ac.uk Tue Oct 14 13:43:15 2003 From: tcarver at hgmp.mrc.ac.uk (Dr T. Carver) Date: Tue, 14 Oct 2003 18:43:15 +0100 (BST) Subject: [EMBOSS] How to Get Jemboss to display/save pictures In-Reply-To: <3F8BB0C9.1030506@imb.sinica.edu.tw> Message-ID: Hi Nancy Can you check the value in the file: $EMBOSS_INSTALL/share/EMBOSS/jemboss/resources/jemboss.properties of plplot? Also make sure there are no other jemboss.properties files on your file system. Regards Tim On Tue, 14 Oct 2003, Nancy Yu wrote: > I can produce png graphic files from command line Emboss just fine, but > it doesn't seem to work from Jemboss. Actually, a png file of 0 bytes > is produced, and I don't know what that means. Does anyone else have > similar problems? > > >Hi Nancy > > > >The first thing to do is to check you can run these applications from the > >command line and create graphics. That will then give you more of a clue. > >It may be a png library problem. > > > >Regards > >Tim Carver > > > >HGMP-RC > > > >On Wed, 8 Oct 2003, Nancy Yu wrote: > > > > > > > >>Hi, > >> > >>I can't seem to get Jemboss to produce pictures for Emboss programs like > >>pepwheel or any other program that output pictures. I don't know if it > >>is a simple setting problem or installation problem. Any suggestions? > >> > >>Nancy Yu > >> > >> > >> > From ronald.yang at jakru.com Tue Oct 14 13:58:00 2003 From: ronald.yang at jakru.com (H.Ronald Yang) Date: Tue, 14 Oct 2003 13:58:00 -0400 Subject: [EMBOSS] Re: EMBOSS GUI : mwcontam : unknown datatype 'filelist' References: <007001c39272$ceead790$862010ac@unisabanacli.unisabana.edu.co> Message-ID: <00d701c3927c$b591d820$02020a0a@rescentris.com> I am using Luke's EMBOSS-GUI. Maybe I should ask the question to Luke. If so, sorry to bother you with this. Ron ----- Original Message ----- From: "Leyla Jael Garc?a Castro" To: "'H.Ronald Yang'" Sent: Tuesday, October 14, 2003 12:47 PM Subject: RE: EMBOSS GUI : mwcontam : unknown datatype 'filelist' > Are you using JEmboss or another web GUI? > > -----Mensaje original----- > De: owner-emboss-dev at hgmp.mrc.ac.uk > [mailto:owner-emboss-dev at hgmp.mrc.ac.uk] En nombre de H.Ronald Yang > Enviado el: Martes, 14 de Octubre de 2003 10:55 a.m. > Para: emboss at embnet.org; emboss-dev at embnet.org > CC: R. Wolfgang Rumpf > Asunto: EMBOSS GUI : mwcontam : unknown datatype 'filelist' > > Hi, > > I have a problem using "mwcontam" and "mwfilter" through EMBOSS > Web GUI. > When I click on the one of "PROTEIN COMPOSITION" tool, "mwcontam", > from the > left side panel, there is error. Right after "input section", it > says > "ERROR" and "unknown datatype 'filelist'". Is this possible to > fix? > > Thanks in advance, > Ron > > From mccarthy at cs.usask.ca Tue Oct 14 16:46:03 2003 From: mccarthy at cs.usask.ca (Luke McCarthy) Date: 14 Oct 2003 14:46:03 -0600 Subject: [EMBOSS] EMBOSS GUI : mwcontam : unknown datatype 'filelist' In-Reply-To: <1066148717.933.17.camel@crazyharry.usask.ca> References: <008201c3926b$8dcd16d0$02020a0a@rescentris.com> <1066148717.933.17.camel@crazyharry.usask.ca> Message-ID: <1066164362.4910.33.camel@crazyharry.usask.ca> On Tue, 2003-10-14 at 10:25, Luke McCarthy wrote: > On Tue, 2003-10-14 at 09:55, H.Ronald Yang wrote: > > Hi, > > > > I have a problem using "mwcontam" and "mwfilter" through EMBOSS Web GUI. > > When I click on the one of "PROTEIN COMPOSITION" tool, "mwcontam", from the > > left side panel, there is error. Right after "input section", it says > > "ERROR" and "unknown datatype 'filelist'". Is this possible to fix? > > There's no support for that particular data type in the GUI -- I didn't > know it existed... I'll put something together and make available an > updated version of the GUI available hopefully later today. Check > http://bioinfo.pbi.nrc.ca/~lukem/EMBOSS/ for the update. The update is available at the above website. It fixes the error in displaying the input pages for 'mwcontam' and 'mwfilter', but it is only possible to upload a single file to each application. This means 'mwcontam' is all but useless when accessed through my web interface. I'll think more about this problem, but I don't think it will change any time soon. Cheers, Luke -- Luke McCarthy Research Officer, Bioinformatics Department of Computer Science University of Saskatchewan mccarthy at cs.usask.ca From ablavier at wanadoo.fr Wed Oct 15 06:25:07 2003 From: ablavier at wanadoo.fr (=?ISO-8859-1?Q?Andr=E9_Blavier?=) Date: Wed, 15 Oct 2003 12:25:07 +0200 Subject: [EMBOSS] EMBOSS for Windows: v. 2.7.1 available Message-ID: <3F8D2083.90903@wanadoo.fr> I have updated my Windows port of EMBOSS to version 2.7.1 It is available at http://perso.wanadoo.fr/ablavier/embosswin/embosswin.html Comments are welcome. -- Andr? Blavier From sebastian.bassi at ar.advantaseeds.com Wed Oct 15 23:05:01 2003 From: sebastian.bassi at ar.advantaseeds.com (Bassi, Sebastian) Date: Thu, 16 Oct 2003 05:05:01 +0200 Subject: [EMBOSS] Program for primer verification Message-ID: I would like to know what program should I use if I want to check a pair of primers for self annealing, for tm, for fitness for PCR, and so on. Does any of the EMBOSS program will do the job? Primer3 is usefull to find good primers, but what I want to do is the check primers I already have selected by another method. Is there a scriptable program to accomplish this? Sebastian Bassi. Advanta Seeds. Balcarce Research Station. From lmullan at hgmp.mrc.ac.uk Thu Oct 16 09:27:51 2003 From: lmullan at hgmp.mrc.ac.uk (Lisa Mullan) Date: Thu, 16 Oct 2003 14:27:51 +0100 Subject: [EMBOSS] Program for primer verification In-Reply-To: Message-ID: Hi Sebastian, AS far as I know, the only other program you could look at is "dan" which checks melting temperatures. However if you used Primer3 to pick primers in the first place, it should have checked all those things for you. HTH Lisa Mullan -----Original Message----- From: owner-emboss at hgmp.mrc.ac.uk [mailto:owner-emboss at hgmp.mrc.ac.uk]On Behalf Of Bassi, Sebastian Sent: Thursday, October 16, 2003 4:05 AM To: emboss at embnet.org Subject: [EMBOSS] Program for primer verification I would like to know what program should I use if I want to check a pair of primers for self annealing, for tm, for fitness for PCR, and so on. Does any of the EMBOSS program will do the job? Primer3 is usefull to find good primers, but what I want to do is the check primers I already have selected by another method. Is there a scriptable program to accomplish this? Sebastian Bassi. Advanta Seeds. Balcarce Research Station. From gwilliam at hgmp.mrc.ac.uk Thu Oct 16 09:42:12 2003 From: gwilliam at hgmp.mrc.ac.uk (Gary Williams, Tel 01223 494522) Date: Thu, 16 Oct 2003 14:42:12 +0100 Subject: [EMBOSS] Program for primer verification References: Message-ID: <3F8EA034.8FFC1AD9@hgmp.mrc.ac.uk> Lisa Mullan wrote: Use should eprimer3 and specify your existing primers in the -forwardinput and -reverseinput qualifiers. It will check that your primers are reasonable. Gary > -----Original Message----- > From: owner-emboss at hgmp.mrc.ac.uk [mailto:owner-emboss at hgmp.mrc.ac.uk]On > Behalf Of Bassi, Sebastian > Sent: Thursday, October 16, 2003 4:05 AM > To: emboss at embnet.org > Subject: [EMBOSS] Program for primer verification > > I would like to know what program should I use if I want to check a pair of > primers for self annealing, for tm, for fitness for PCR, and so on. Does any > of the EMBOSS program will do the job? Primer3 is usefull to find good > primers, but what I want to do is the check primers I already have selected > by another method. > Is there a scriptable program to accomplish this? > > Sebastian Bassi. > Advanta Seeds. Balcarce Research Station. -- 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, Hinxton, Cambridge, CB10 1SB, UK From grsvc at mucc.mahidol.ac.th Fri Oct 17 06:22:44 2003 From: grsvc at mucc.mahidol.ac.th (Suksiri Vichasri Grams) Date: Fri, 17 Oct 2003 17:22:44 +0700 Subject: [EMBOSS] embossRUNNER Message-ID: embossRUNNER is an interface for emboss 2.7.1 on MacOS 10.2. It is available for download at the MIT Mac Hyperarchive: http://hyperarchive.lcs.mit.edu/HyperArchive/Archive/sci/emboss-runner- 10.hqx Kindly, Rudi & Suksiri Dr. Suksiri Vichasri Grams Department of Biology Faculty of Science Mahidol University Rama VI Road Bangkok 10400 Thailand From R-8-721447-17263485-2-7807-US2-9F15919F at xmr3.com Fri Oct 17 13:08:17 2003 From: R-8-721447-17263485-2-7807-US2-9F15919F at xmr3.com (International Scientific Communications, Inc.) Date: Fri, 17 Oct 2003 13:08:17 -0400 Subject: [EMBOSS] Laboratory Instrumentation News - October 2003 Message-ID: An HTML attachment was scrubbed... URL: http://lists.open-bio.org/pipermail/emboss/attachments/20031017/93012ea4/attachment.html From idrummon at receptor.mgh.harvard.edu Fri Oct 17 21:33:01 2003 From: idrummon at receptor.mgh.harvard.edu (Iain Drummond) Date: Fri, 17 Oct 2003 21:33:01 -0400 Subject: [EMBOSS] maximum number of sequences for eprimer3 Message-ID: I am using eprimer3 and multiple fasta formatted dinucleotide containing sequences as input. I find that eprimer3/primer3_core will handle an input file containing up to 23 sequences; at 24 sequences, both eprimer3 and primer3_core ?sleep?. i.e. the processes never acheive run status when I watch what happens using top or prstat. I don?t know if this has something to do with limitations of my system (sun ultra5/1GB ram/500 MB free disk space) or intrinsic to eprimer3/primer3_core. I do know that it also happens on a Mac OS X system (640 MB ram/35 GB free disk space). Is there a config file that sets limits on eprimer3? (that i can change?) -- Iain Drummond, Ph.D. Assistant Professor Department of Medicine, Harvard Medical School and Renal Unit, Massachusetts General Hospital Mailing address: Renal Unit / MGH 149-8000 149 13th St. Charlestown, MA 02129 Tel: 617 726 5647 Fax: 617 726 5669 idrummond at partners.org idrummon at receptor.mgh.harvard.edu Lab Home Page: http://danio.mgh.harvard.edu -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.open-bio.org/pipermail/emboss/attachments/20031017/d4bc2713/attachment.html From areagp61 at yahoo.it Tue Oct 21 04:23:33 2003 From: areagp61 at yahoo.it (=?iso-8859-1?q?Gr=20Pa?=) Date: Tue, 21 Oct 2003 10:23:33 +0200 (CEST) Subject: [EMBOSS] "fasta" program Message-ID: <20031021082333.25496.qmail@web21005.mail.yahoo.com> Hi all, searching for "fasta and emboss", I have found this site http://ben.vub.ac.be/embosshelp/fasta.html reporting fasta as a program of the EMBOSS package, but it lacks in the EMBOSS official list of programs. Is this fasta program an old implementation or what? Regards Graziano ______________________________________________________________________ Yahoo! Mail: 6MB di spazio gratuito, 30MB per i tuoi allegati, l'antivirus, il filtro Anti-spam http://it.yahoo.com/mail_it/foot/?http://it.mail.yahoo.com/ From Marc.Logghe at devgen.com Tue Oct 21 07:53:12 2003 From: Marc.Logghe at devgen.com (Marc Logghe) Date: Tue, 21 Oct 2003 13:53:12 +0200 Subject: [EMBOSS] "fasta" program Message-ID: As far as I can see, fasta is a custom made application (or rather an EMBOSS wrapper around the fasta suite of programs) by Guy Bottu of BEN. Meaning it is not part of the 'official' EMBOSS suite. I don't find info whether they consider it as free software or not. Regards, Marc > -----Original Message----- > From: Gr Pa [mailto:areagp61 at yahoo.it] > Sent: Tuesday, October 21, 2003 10:24 AM > To: emboss at embnet.org > Subject: [EMBOSS] "fasta" program > > > Hi all, > searching for "fasta and emboss", I have found this > site http://ben.vub.ac.be/embosshelp/fasta.html > reporting fasta as a program of the EMBOSS package, > but it lacks in the EMBOSS official list of programs. > Is this fasta program an old implementation or what? > Regards > Graziano > > ______________________________________________________________________ > Yahoo! Mail: 6MB di spazio gratuito, 30MB per i tuoi > allegati, l'antivirus, il filtro Anti-spam > http://it.yahoo.com/mail_it/foot/?http://it.mail.yahoo.com/ > From rpg at mrc-lmb.cam.ac.uk Tue Oct 21 11:53:46 2003 From: rpg at mrc-lmb.cam.ac.uk (rpg at mrc-lmb.cam.ac.uk) Date: Tue, 21 Oct 2003 16:53:46 +0100 (BST) Subject: [EMBOSS] EMBASSY - mse Message-ID: <200310211553.h9LFrkn432808@alf1.lmb.internal> Anyone got mse compiled? I installed emboss on OS X using fink, and have the EMBASSY src code in a directory off that. % ./configure seems to work but then % make bombs out with Making all in ckit make[1]: Nothing to be done for `all'. Making all in source make[1]: *** No rule to make target `../../../ajax/libajax.la', needed by `mse'. Stop. make: *** [all-recursive] Error 1 I guess that means I need the ajax libraries. Where may I find them? thanks, r PS I do have a directory ../../ajax/ but nothing that looks like libajax. -- Richard P. Grant http://www2.mrc-lmb.cam.ac.uk/personal/rpg/ MRC-LMB, Cambridge, UK PGP: 0x5F9559B1 weblog: http://www.rg-d.com/BioLOG/ From idrummon at receptor.mgh.harvard.edu Tue Oct 21 12:41:06 2003 From: idrummon at receptor.mgh.harvard.edu (Iain Drummond) Date: Tue, 21 Oct 2003 12:41:06 -0400 Subject: [EMBOSS] eprimer3: max input file number? Message-ID: I have run into a limitation using eprimer3 as an interface for primer3. It seems that eprimer3 will accept up to 23 sequences (in a single fasta formatted text file) but not 24 or more; with 24 or more sequences, eprimer3 and primer3_core will just hang as ?sleeping? processes and never finish. My goal is to automate genomic sequence analysis (zebrafish) in order to generate new, potentially useful polymorphic markers from dinucleotide repeats. eprimer3 is the last step where a long list of ~500 bp sequences are sent to primer3 to make primers. I run into this problem both on a Sun ultra5 running solaris 8 (1GB ram) and on a mac G4 running OS X 10.2.8 (640 MB ram). To see whether the problem was in primer3_core or eprimer3, I prepared a list of 30 and 60 short sequences in Boulder io format and submitted them directly to primer3_core; no problem there, 30 or 60 primer pairs were returned. Does anyone know if there is a config file that would change the behavior of eprimer3, or is this a bug in the program? -- Iain Drummond, Ph.D. Assistant Professor Department of Medicine, Harvard Medical School and Renal Unit, Massachusetts General Hospital idrummond at partners.org idrummon at receptor.mgh.harvard.edu Lab Home Page: http://danio.mgh.harvard.edu -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.open-bio.org/pipermail/emboss/attachments/20031021/f02eeddb/attachment.html From abl at ica.cc Tue Oct 21 13:00:43 2003 From: abl at ica.cc (American Biotechnology Laboratory) Date: Tue, 21 Oct 2003 13:00:43 -0400 Subject: [EMBOSS] We thought you would be interested... Message-ID: <97921984.20031021130043@ica.cc> To Subscribe Go To: http://www.icainfo.com/aml/appintro.asp?Priority=PEPAB3 Following are the themes to be featured in AL: November Microscopy, Optics, and Image Analysis December Pharmaceutical Analysis, Molecular Spectroscopy, EAS January Annual ISC Buyers' Guide,Thermal Analysis, Gas Chromatography February Pittcon 2004 New Analytical Instrumentation for Separation Science and Spectroscopy March Advances in Laboratory Software and Data Management April Microchemical Analysis, Sample Preparation Dear Colleague, Please accept my invitation to receive a free subscription to our journal, American Laboratory. American Laboratory covers the disciplines of analytical and bioanalytical chemistry, drug discovery, laboratory software and informatics. Each issue features articles from leading scientists from around the world reviewing applications of instrumentation and new measurement technology. For your FREE subscription to American Laboratory, please click on the following link. http://www.icainfo.com/aml/appintro.asp?Priority=PEPAB3 I am confident that you will enjoy our journal and find it to be of significant professional value. I look forward to hearing from you. Sincerely yours, Brian Howard, Ph.D. Editor -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.open-bio.org/pipermail/emboss/attachments/20031021/fe83870e/attachment.html From yezq at mail.cbi.pku.edu.cn Wed Oct 22 05:52:10 2003 From: yezq at mail.cbi.pku.edu.cn (Zhiqiang Ye) Date: Wed, 22 Oct 2003 17:52:10 +0800 Subject: [EMBOSS] EMBASSY - mse Message-ID: <200310220944.h9M9iDAW029737@mail.cbi.pku.edu.cn> You should keep the source directory(eg. EMBOSS2.7.1) after you installed EMBOSS. then: cd EMBOSS2.7.1 mkdir embassy cp /path_to_mse/mse.tar.gz . gzip -dc mse.tar.gz | tar xf - cd mse; ./configure --prefix........ ( the parameters should be as the same as you build EMBOSS) make make install ???? >Anyone got mse compiled? > >I installed emboss on OS X using fink, and have the EMBASSY src code in a >directory off that. > >% ./configure > >seems to work but then > >% make > >bombs out with > >Making all in ckit >make[1]: Nothing to be done for `all'. >Making all in source >make[1]: *** No rule to make target `../../../ajax/libajax.la', needed by >`mse'. Stop. >make: *** [all-recursive] Error 1 > > >I guess that means I need the ajax libraries. Where may I find them? >thanks, > >r > >PS I do have a directory ../../ajax/ but nothing that looks like libajax. > > > >-- >Richard P. Grant http://www2.mrc-lmb.cam.ac.uk/personal/rpg/ >MRC-LMB, Cambridge, UK >PGP: 0x5F9559B1 weblog: http://www.rg-d.com/BioLOG/ = = = = = = = = = = = = = = = = = = = = Best Wishes! Zhiqiang Ye 2003-10-22 From rpg at mrc-lmb.cam.ac.uk Wed Oct 22 05:50:47 2003 From: rpg at mrc-lmb.cam.ac.uk (rpg at mrc-lmb.cam.ac.uk) Date: Wed, 22 Oct 2003 10:50:47 +0100 (BST) Subject: [EMBOSS] EMBASSY - mse In-Reply-To: <200310220944.h9M9iDAW029737@mail.cbi.pku.edu.cn> from Zhiqiang Ye at "Oct 22, 2003 05:52:10 pm" Message-ID: <200310220950.h9M9om1429913@alf1.lmb.internal> Nah, that loses track of ../../../depcomp. I suspect that David is right - it's trying to find a libajax.la when it should be looking for .dylib - it's a porting thing, apparently. -- Richard P. Grant http://www2.mrc-lmb.cam.ac.uk/personal/rpg/ MRC-LMB, Cambridge, UK PGP: 0x5F9559B1 weblog: http://www.rg-d.com/BioLOG/ From gbottu at ben.vub.ac.be Wed Oct 22 10:17:41 2003 From: gbottu at ben.vub.ac.be (Guy Bottu) Date: Wed, 22 Oct 2003 16:17:41 +0200 (CEST) Subject: [EMBOSS] "fasta" program Message-ID: <200310221417.h9MEHflw1266502@black.vub.ac.be> from : BEN Dear Graziano, At the BEN site we have BLAST, fastA and some other programs installed under an EMBOSS "wrapper" program. In their present form these programs are not readily installable elsewhere. When a year ago we dropped GCG (had become too expensive !) I rushed to replace the lost functionality for our users and did not consider portability. I think it would be a good idea to distribute our BLAST and fastA wrappers as an "Embassadir". I will start a conversation with the EMBOSS developement team about what is necessary to make it work. I know that M. Sarachu from the Argentina and J. Valverde from the Spanish EMBnet Nodes have our wrappers running at their site. J. Valverde had started to make it portable, but I do not know how far he got by know. If you are in a hurry, I can send you the files in their present state. To make it work you mainly need to edit the files and replace the paths of the programs and the names of the databanks by what you have at your site. Note that, since the EMBOSS programs are just "wrappers", you need in the first place the fastA programs themselves properly installed and configured with a collection of databanks in fastA format. Guy Bottu From ruediger at sanbi.ac.za Wed Oct 22 10:41:20 2003 From: ruediger at sanbi.ac.za (Ruediger Braeuning) Date: Wed, 22 Oct 2003 16:41:20 +0200 (SAST) Subject: [EMBOSS] "fasta" program In-Reply-To: <200310221417.h9MEHflw1266502@black.vub.ac.be> References: <200310221417.h9MEHflw1266502@black.vub.ac.be> Message-ID: <20031022163856.G2720@fling.sanbi.ac.za> Dear Guy, > I think it would be a good idea to distribute our BLAST and fastA wrappers as an > "Embassadir". I will start a conversation with the EMBOSS developement team > about what is necessary to make it work. Great, that would be a valuable addition. Thanks for sharing. > If you are in a hurry, I can send you the files in their present state. > To make it work you mainly need to edit the files and replace the paths > of the programs and the names of the databanks by what you have at your > site. Note that, since the EMBOSS programs are just "wrappers", you need > in the first place the fastA programs themselves properly installed and > configured with a collection of databanks in fastA format. If possible, I would like to have these wrappers as well. Thanks and best regards, Ruediger ------------------------------------------------------------------------- Ruediger Braeuning / South African National Bioinformatics Institute (=) University of the Western Cape Ph. +27 21 959 3645 / Private Bag X17 Fax +27 21 959 2512 (=) Bellville, 7535 www.sanbi.ac.za / South Africa From idrummon at receptor.mgh.harvard.edu Wed Oct 22 14:03:49 2003 From: idrummon at receptor.mgh.harvard.edu (Iain Drummond) Date: Wed, 22 Oct 2003 14:03:49 -0400 Subject: [EMBOSS] maximum number of sequences for eprimer3 In-Reply-To: Message-ID: Hi Sebastian, Interesting that you see the same problem with eprimer3 but the cutoff number varies; I wonder what the key variable is. I have used primer3 (primer3_core) and that has no cutoff; all the sequences are processed. I was hoping to use eprimer3 because the input and output files are easier to manage; I have limited perl scripting skills and I was trying to avoid converting the input to Boulder io format which for me would be laborious. Thanks, Iain Hello, I've been looking at the files you sent to me. Now I realize that I always used primer3, not eprimer3 and the input file is in different format. Anyway I made the test (with eprimer3) and the cut off value seems to be 10 sequences (more than that end into a sleep process). A workaround would be to send the job to eprimer3 in batch with the size it can handle. This will not correct the problem but at least you could get te results. Have you tried with the primer3 instead of eprimer3? Sebastian Bassi. Advanta Seeds. Balcarce Research Station. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.open-bio.org/pipermail/emboss/attachments/20031022/b79d5a91/attachment.html From maojn at hotmail.com Wed Oct 22 14:08:06 2003 From: maojn at hotmail.com (Jean Mao) Date: Wed, 22 Oct 2003 14:08:06 -0400 Subject: [EMBOSS] question about refseq database Message-ID: Hi, I would like to include the RefSeq database from NCBI into our databases collection. Is there any specific format of the database prefered (flat or fasta) or work better? is there any know bugs that I should be aware of? Any suggestion is appreciated. Thanks. ------------------------------------------------------------------- Jean Mao, Ph.D. Helix Systems Bldg 12B, Rm 2N207 National Institutes of Health Bethesda, MD 20895 Email:maoj at helix.nih.gov ------------------------------------------------------------------ From maojn at hotmail.com Wed Oct 22 14:08:06 2003 From: maojn at hotmail.com (Jean Mao) Date: Wed, 22 Oct 2003 14:08:06 -0400 Subject: [EMBOSS] question about refseq database Message-ID: Hi, I would like to include the RefSeq database from NCBI into our databases collection. Is there any specific format of the database prefered (flat or fasta) or work better? is there any know bugs that I should be aware of? Any suggestion is appreciated. Thanks. ------------------------------------------------------------------- Jean Mao, Ph.D. Helix Systems Bldg 12B, Rm 2N207 National Institutes of Health Bethesda, MD 20895 Email:maoj at helix.nih.gov ------------------------------------------------------------------ From idrummon at receptor.mgh.harvard.edu Wed Oct 22 14:03:49 2003 From: idrummon at receptor.mgh.harvard.edu (Iain Drummond) Date: Wed, 22 Oct 2003 14:03:49 -0400 Subject: [EMBOSS] maximum number of sequences for eprimer3 In-Reply-To: Message-ID: Hi Sebastian, Interesting that you see the same problem with eprimer3 but the cutoff number varies; I wonder what the key variable is. I have used primer3 (primer3_core) and that has no cutoff; all the sequences are processed. I was hoping to use eprimer3 because the input and output files are easier to manage; I have limited perl scripting skills and I was trying to avoid converting the input to Boulder io format which for me would be laborious. Thanks, Iain Hello, I've been looking at the files you sent to me. Now I realize that I always used primer3, not eprimer3 and the input file is in different format. Anyway I made the test (with eprimer3) and the cut off value seems to be 10 sequences (more than that end into a sleep process). A workaround would be to send the job to eprimer3 in batch with the size it can handle. This will not correct the problem but at least you could get te results. Have you tried with the primer3 instead of eprimer3? Sebastian Bassi. Advanta Seeds. Balcarce Research Station. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.open-bio.org/pipermail/emboss/attachments/20031022/b79d5a91/attachment-0001.html From ableasby at hgmp.mrc.ac.uk Wed Oct 22 15:06:03 2003 From: ableasby at hgmp.mrc.ac.uk (Alan Bleasby) Date: Wed, 22 Oct 2003 20:06:03 +0100 (BST) Subject: [EMBOSS] maximum number of sequences for eprimer3 Message-ID: <200310221906.h9MJ635K012628@bromine.hgmp.mrc.ac.uk> Having had a quick look at the code I suspect that it is not a variable involved (EMBOSS programs are designed not to be limited in that way, usually only by system resource available). The code uses pipes to redirect stdin and stdout to/from primer3_core. A possible cause is therefore blocking from a full buffer. I'll let the author of the eprimer3 program know about it. HTH Alan From maoj at mail.nih.gov Thu Oct 23 16:44:23 2003 From: maoj at mail.nih.gov (Jean Mao) Date: Thu, 23 Oct 2003 16:44:23 -0400 Subject: [EMBOSS] question about index refseq database Message-ID: <069201c399a6$7169dd10$494de780@CIT.NIH.GOV> Hi, I have the following 2 files for refseq nucleotide and protein databases from NCBI: ---------------------------------------------- rscu.gbff.Z GenBank flatfile view (nucleotide sequence with annotations) rscu.gnp.Z GenPept flatfile view (protein sequence with annotations) ----------------------------------------- When I run dbiflat, should I enter GB or REFSEQ when prompt 'Entry format'? Also, in the .embossrc file, is the following entry correct (method=emblcd and format=genbank)? ---------------------------------------- DB refseqnt [ type: N method: emblcd format: genbank dir: $emboss_db_dir/refseqnt indexdir: $emboss_db_dir/refseqnt file: "*.gbff" release: "1.0" comment: "update 23/Oct/03" ] Any suggestion is appreciated. Jean From henrikki.almusa at helsinki.fi Fri Oct 24 02:38:48 2003 From: henrikki.almusa at helsinki.fi (Henrikki Almusa) Date: Fri, 24 Oct 2003 09:38:48 +0300 Subject: [EMBOSS] question about index refseq database In-Reply-To: <069201c399a6$7169dd10$494de780@CIT.NIH.GOV> References: <069201c399a6$7169dd10$494de780@CIT.NIH.GOV> Message-ID: <200310240938.48134.henrikki.almusa@helsinki.fi> On Thursday 23 October 2003 23:44, Jean Mao wrote: > I have the following 2 files for refseq nucleotide and protein databases > from NCBI: > ---------------------------------------------- > rscu.gbff.Z GenBank flatfile view (nucleotide sequence with annotations) > rscu.gnp.Z GenPept flatfile view (protein sequence with annotations) > ----------------------------------------- > > When I run dbiflat, should I enter GB or REFSEQ when prompt 'Entry format'? I haven't used refseq files but. i'd suggest you use refseq (remember to unzip files first). > Also, in the .embossrc file, is the following entry correct (method=emblcd > and format=genbank)? > ---------------------------------------- > DB refseqnt [ type: N method: emblcd format: genbank dir: > $emboss_db_dir/refseqnt indexdir: $emboss_db_dir/refseqnt file: "*.gbff" > release: "1.0" comment: "update 23/Oct/03" ] Method might be refseq as well. Unfortunately this isn't covered by admin manual in emboss web site. I assume that you have two directories so that there is another entry in .embossrc for protein file. Hoope this helps, -- Henrikki Almusa From yann-francois.bizouerne at bayercropscience.com Fri Oct 24 07:10:56 2003 From: yann-francois.bizouerne at bayercropscience.com (yann-francois.bizouerne at bayercropscience.com) Date: Fri, 24 Oct 2003 13:10:56 +0200 Subject: [EMBOSS] question EMBOSS-GUI Message-ID: Hello, I don't know if you could help me with the little problem I have. I have installed your EMBOSS-GUI application on our server a few month ago. And it works great. Since I have installed SRS on our servern. I have mofified the emboss.default in order to use to the SRS indexes. Now it looks like : DB TREMBL [ methodquery: srs format: SWISS type: P comment: "TREMBL (SPTREMBL + TREMBLNEW) using SRS" app: getz dbalias: TREMBL methodall: direct file: "trembl.dat" dir: $emboss_data_dir/swall ] And that works quitr well on command line, when I need to retrieve a sequence with seqret for example. But if I am using the EMBOSS-GUI interface I just obtain the following errror message: EMBOSS An error in ajfile.c at line 145: execvp ('getz -e '[TREMBL-id:Q977L9]'', NULL) failed: 'No such file or directory' Error: Unable to read sequence 'TREMBL-id:Q977L9' Died: seqret terminated: Bad value for '-sequence' with -auto defined seqret exited with status 1... Do you have a clue for the problem ? Thanks in advance Best regards. Yann-Fran?ois BIZOUERNE BioInformatic Team BAYER CropScience 1, rue Pierre Fontaine 91058 Evry Cedex FRANCE Phone: 33-(0) 1-69-47-61-56 FAX: 33-(0) 1-69-47-61-42 E-mail: yann-francois.bizouerne at bayercropscience.com Intranet: http://bioinfo.evry.fr.bayercropscience/ From gbottu at ben.vub.ac.be Fri Oct 24 09:04:02 2003 From: gbottu at ben.vub.ac.be (Guy Bottu) Date: Fri, 24 Oct 2003 15:04:02 +0200 (CEST) Subject: [EMBOSS] question EMBOSS-GUI Message-ID: <200310241304.h9OD42XI1549926@black.vub.ac.be> from : BEN Dear Yann-Fran?ois, I had exactly the same problem when I first installed Jemoss. At the command line it works because getz is in the "path", but the GUI's often only look for programs in .../emboss/bin. The cure is to install in the directory with the EMBOSS programs a logical link pointing to getz. By the way, this applies also for clustalw and primer3_core. Guy Bottu From tcarver at hgmp.mrc.ac.uk Fri Oct 24 09:08:17 2003 From: tcarver at hgmp.mrc.ac.uk (Dr T. Carver) Date: Fri, 24 Oct 2003 14:08:17 +0100 (BST) Subject: [EMBOSS] question EMBOSS-GUI In-Reply-To: <200310241304.h9OD42XI1549926@black.vub.ac.be> Message-ID: The best way round is to alter the value of embossPath in: $EMBOSS_INSTALL/share/emboss/jemboss/resources/jemboss.properties by adding the path to getz, clustalw and primer3_core. For a description of jemboss.properties see: http://www.rfcgr.mrc.ac.uk/Software/EMBOSS/Jemboss/install/properties.html Regards Tim On Fri, 24 Oct 2003, Guy Bottu wrote: > from : BEN > > Dear Yann-Fran?ois, > > I had exactly the same problem when I first installed Jemoss. At the command > line it works because getz is in the "path", but the GUI's often only look for > programs in .../emboss/bin. The cure is to install in the directory with the > EMBOSS programs a logical link pointing to getz. By the way, this applies also > for clustalw and primer3_core. > > Guy Bottu > From stefanielager at fastmail.ca Fri Oct 24 09:24:03 2003 From: stefanielager at fastmail.ca (Stefanie Lager) Date: Fri, 24 Oct 2003 09:24:03 -0400 (EDT) Subject: [EMBOSS] question EMBOSS-GUI Message-ID: <3F9927F3.000085.66964@ns.interchange.ca> SRS is set up for the user that runs EMBOSS on command line, while SRS is NOT set up for the user (nobody) that runs through the web interface. If you have SRS running as web interface you can use method: srswww url: "http://the.adress.to local.SRS.com" Or write a script that calls getz, and sets up SRS and use the script with method: app app: "path/to/the/script " Stefanie > > > > > Hello, > > I don't know if you could help me with the little problem I have. > > I have installed your EMBOSS-GUI application on our server a few > month ago. And it works great. > Since I have installed SRS on our servern. I have mofified the > emboss.default in order to use to the SRS indexes. > Now it looks like : > > DB TREMBL [ > methodquery: srs > format: SWISS > type: P > comment: "TREMBL (SPTREMBL + TREMBLNEW) using SRS" > app: getz > dbalias: TREMBL > methodall: direct > file: "trembl.dat" > dir: $emboss_data_dir/swall > ] > > > > > And that works quitr well on command line, when I need to retrieve > a sequence with seqret for example. But if I am using the > EMBOSS-GUI interface I just obtain the following errror message: > > EMBOSS An error in ajfile.c at line 145: execvp ('getz -e > '[TREMBL-id:Q977L9]'', NULL) failed: 'No such file or directory' > Error: Unable to read sequence 'TREMBL-id:Q977L9' Died: seqret > terminated: Bad value for '-sequence' with -auto defined seqret > exited with status 1... > > Do you have a clue for the problem ? > > Thanks in advance > > Best regards. > > > > > > > > Yann-Fran?ois BIZOUERNE > BioInformatic Team > BAYER CropScience > 1, rue Pierre Fontaine > 91058 Evry Cedex > FRANCE > Phone: 33-(0) 1-69-47-61-56 > FAX: 33-(0) 1-69-47-61-42 > E-mail: yann-francois.bizouerne at bayercropscience.com > Intranet: http://bioinfo.evry.fr.bayercropscience/ _________________________________________________________________ http://fastmail.ca/ - Fast Secure Web Email for Canadians From mccarthy at cs.usask.ca Fri Oct 24 11:48:32 2003 From: mccarthy at cs.usask.ca (Luke McCarthy) Date: 24 Oct 2003 09:48:32 -0600 Subject: [EMBOSS] question EMBOSS-GUI In-Reply-To: References: Message-ID: <1067010512.8481.16.camel@crazyharry.usask.ca> On Fri, 2003-10-24 at 05:10, yann-francois.bizouerne at bayercropscience.com wrote: > EMBOSS An error in ajfile.c at line 145: execvp ('getz -e '[TREMBL-id:Q977L9]'', NULL) failed: 'No such file or directory' Error: > Unable to read sequence 'TREMBL-id:Q977L9' Died: seqret terminated: Bad value for '-sequence' with -auto defined seqret exited with > status 1.. I replied to this messages off-list, but it describes a fairly common problem (that will be dealt with when I bring the GUI up to speed for EMBOSS 2.8.0), so I thought I'd reply here, too. The problem in this case is that the getz application is not in the GUI's PATH. There are two solutions: 1) soft link whatever application you need to the directory containing the rest of the EMBOSS applications; 2) edit the statement on or about line 151 of GUI.pm and add the required directory to the GUI's PATH. The statement in question looks like this: $ENV{'PATH'} = "$EMBOSS_BIN:/bin"; To add another directory, simply append it to the colon-separated list on the right hand side of the assignment. For example, if getz were installed as /usr/bin/getz, you would edit the above statement to look like this: $ENV{'PATH'} = "$EMBOSS_BIN:/bin:/usr/bin"; This solution applies to the SRS problem mentioned by the OP above, as well as to a similar problem where emma fails to work because it can't find clustalw. Cheers, Luke -- Luke McCarthy Research Officer, Bioinformatics Department of Computer Science University of Saskatchewan mccarthy at cs.usask.ca From stefanielager at fastmail.ca Fri Oct 24 08:36:32 2003 From: stefanielager at fastmail.ca (Stefanie Lager) Date: Fri, 24 Oct 2003 08:36:32 -0400 (EDT) Subject: [EMBOSS] question EMBOSS-GUI Message-ID: <3F991CD0.000035.01708@ns.interchange.ca> SRS is set up for the user that runs EMBOSS on command line, while SRS is NOT set up for the user (nobody) that runs through the web interface. If you have SRS running as web interface you can use method: srswww url: "http://the.adress.to local.SRS.com" Or write a script that calls getz, and sets up SRS and use the script with method: app app: "path/to/the/script " Stefanie > > > > > Hello, > > I don't know if you could help me with the little problem I have. > > I have installed your EMBOSS-GUI application on our server a few > month ago. And it works great. > Since I have installed SRS on our servern. I have mofified the > emboss.default in order to use to the SRS indexes. > Now it looks like : > > DB TREMBL [ > methodquery: srs > format: SWISS > type: P > comment: "TREMBL (SPTREMBL + TREMBLNEW) using SRS" > app: getz > dbalias: TREMBL > methodall: direct > file: "trembl.dat" > dir: $emboss_data_dir/swall > ] > > > > > And that works quitr well on command line, when I need to retrieve > a sequence with seqret for example. But if I am using the > EMBOSS-GUI interface I just obtain the following errror message: > > EMBOSS An error in ajfile.c at line 145: execvp ('getz -e > '[TREMBL-id:Q977L9]'', NULL) failed: 'No such file or directory' > Error: Unable to read sequence 'TREMBL-id:Q977L9' Died: seqret > terminated: Bad value for '-sequence' with -auto defined seqret > exited with status 1... > > Do you have a clue for the problem ? > > Thanks in advance > > Best regards. > > > > > > > > Yann-Fran?ois BIZOUERNE > BioInformatic Team > BAYER CropScience > 1, rue Pierre Fontaine > 91058 Evry Cedex > FRANCE > Phone: 33-(0) 1-69-47-61-56 > FAX: 33-(0) 1-69-47-61-42 > E-mail: yann-francois.bizouerne at bayercropscience.com > Intranet: http://bioinfo.evry.fr.bayercropscience/ _________________________________________________________________ http://fastmail.ca/ - Fast Secure Web Email for Canadians From kmr at sanger.ac.uk Wed Oct 29 08:37:32 2003 From: kmr at sanger.ac.uk (Kim Rutherford) Date: Wed, 29 Oct 2003 13:37:32 +0000 Subject: [EMBOSS] Suggested change to seqretsplit Message-ID: <16287.49820.155450.529600@pcs2e.internal.sanger.ac.uk> Hi. Can I suggest this following change to seqretsplit.acd to allow features to be retained (with the -feature flag) when using seqretsplit: *** seqretsplit.acd 2003/10/06 08:52:50 1.9 --- seqretsplit.acd 2003/10/29 13:19:58 *************** *** 9,16 **** --- 9,22 ---- type: "page" ] + boolean: feature [ + default: "N" + information: "Use feature information" + ] + seqall: sequence [ parameter: "Y" + features: "$(feature)" type: "gapany" ] *************** *** 35,40 **** --- 41,47 ---- seqoutall: outseq [ parameter: "Y" ossingle: "Y" + features: "$(feature)" ] endsection: output It seems to work fine for me. Kim. From pmr at ebi.ac.uk Wed Oct 29 08:48:43 2003 From: pmr at ebi.ac.uk (pmr at ebi.ac.uk) Date: Wed, 29 Oct 2003 13:48:43 -0000 (GMT) Subject: [EMBOSS] Suggested change to seqretsplit In-Reply-To: <16287.49820.155450.529600@pcs2e.internal.sanger.ac.uk> References: <16287.49820.155450.529600@pcs2e.internal.sanger.ac.uk> Message-ID: <1228.217.134.9.58.1067435323.squirrel@webmail.ebi.ac.uk> > Hi. Can I suggest this following change to seqretsplit.acd to allow > features to be retained (with the -feature flag) when using > seqretsplit: Yes indeed!!! And we should look for any other programs that read in and write a sequence in case they could use features too. For some programs there is an issue in how the features get split, so it may not be until 2.9.0 that we have the full set. Seqretsplit is an easy one to do. regards, Peter Rice From Sean.Maceachern at dpi.vic.gov.au Thu Oct 2 07:04:23 2003 From: Sean.Maceachern at dpi.vic.gov.au (Sean.Maceachern at dpi.vic.gov.au) Date: Thu, 2 Oct 2003 17:04:23 +1000 Subject: [EMBOSS] Needle Message-ID: Hello, I am a novice at all things computer and i was hoping that someone might be able to give me some advice. I am working with two lynux machines with different versions of Emboss on them. I have noticed that in the most recent version of emboss the needle outputs have changed. I need to work with the 'old' fasta output that used to have trailing gaps/indels as white space and internal gaps/indels as periods '.' . I have found that the most recent version of emboss has changed the output format so now the fasta format looks more like a clustal output with gaps/indels represented as a ' -' whether thay are terminal or inserted within the sequence. I was hoping someone could point me towards a similar output for the new version of emboss or if it is not too much trouble to make a new format based on the fasta format from an older version of needle. Thank you Sean MacEachern From alex at compressweb.com Thu Oct 2 07:37:30 2003 From: alex at compressweb.com (alex at compressweb.com) Date: Thu, 2 Oct 2003 15:37:30 +0800 Subject: [EMBOSS] [Announce] EQ 1.0 version is available now! Message-ID: <41172-2200310427373097@redust> -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: EQ.jpg Type: image/jpeg Size: 11542 bytes Desc: EQ.jpg URL: From d.m.a.martin at dundee.ac.uk Thu Oct 2 08:17:42 2003 From: d.m.a.martin at dundee.ac.uk (David Martin) Date: Thu, 02 Oct 2003 09:17:42 +0100 Subject: [EMBOSS] Needle In-Reply-To: Message-ID: On 2/10/03 8:04 am, "Sean.Maceachern at dpi.vic.gov.au" wrote: > Hello, > > I am a novice at all things computer and i was hoping that someone might be > able to give me some advice. I am working with two lynux machines with > different versions of Emboss on them. I have noticed that in the most > recent version of emboss the needle outputs have changed. I need to work > with the 'old' fasta output that used to have trailing gaps/indels as white > space and internal gaps/indels as periods '.' . I have found that the most > recent version of emboss has changed the output format so now the fasta > format looks more like a clustal output with gaps/indels represented as a ' > -' whether thay are terminal or inserted within the sequence. I was hoping > someone could point me towards a similar output for the new version of > emboss or if it is not too much trouble to make a new format based on the > fasta format from an older version of needle. You will find that you can set the alignment format output by programs like needle using a command line flag. the EMBOSS website has full details of this at http://www.hgmp.mrc.ac.uk/Software/EMBOSS/Themes/AlignFormats.html regards ..d > > Thank you > > Sean MacEachern > > -- David Martin PhD Bioinformatics Scientific Officer Post-Genomics and Molecular Interactions Centre University of Dundee From martin_artist at yahoo.com Mon Oct 6 03:14:46 2003 From: martin_artist at yahoo.com (ENRON = Swarzenegger) Date: Mon, 6 Oct 2003 03:14:46 Subject: [EMBOSS] Stealing CA $9 billions = Recall Election Message-ID: <20031006101626.8E7767D206@mercury.hgmp.mrc.ac.uk> Bush bible PNAC Swarzeneger got money from ENRON to forgive 9 billions pay back I'm very worry, desperate PNAC may do 3rd Pearl Harbor to US. - Second is here: 1997 http://www.newamericancentury.org/RebuildingAmericasDefenses.pdf page 48 Clinton economy is good - page 51 on document or 63 / on Acrobat viewer.. - We have to have major attack on America first, to convince people OPEN YOUR MIND FOR YOURSELF AND YOUR KIDS LIFE; http://www.alternetnews.com/ Arnold or Adolph, what the different; D A N K E, will Terminate US all & California first Prescott help Adolph, George him & Enron; Gasoline $4 per gallon is just the beginning. Actor = skilled liar, how can we trust them ? I heard, his porno job is for sale; & He is ENRON BOY http://www.tarpley.net/bushb.htm http://www.bartcop.com/421102.htm http://www.bk2k.com/bushbodycount/prescott-bush/index.shtml http://hnn.us/comments/15105.html Hitler, Noriega, Hussein, bin Laden, Pinochet - did business with the Bush family. Now we do business with Bush as well; - $500 000 000 000 is gone, missing, and make US poor Perfect Taxpayers Rip Off - MONEY LAUNDRY - true Iraq repair kidding, - direct to own pocket, Isn't this a crime ?? + Lie of war reasons, and lie, and lie, and lie. Please look on this and think by yourself; where we are going ?? Or PNAC push us there, like stick to a blind sheep. - Start thinking on your own, please. http://pnac.tvnewslies.org http://www.tvnewslies.org START THINKING AGAIN !!! www.moveon.org/news/1577.html www.prisonplanet.com www.moveon.org www.votetoimpeach.com www.kgo810.com listen 810 AM; Bernie, Genie, Ray only (night time) How many Concentration Camps do they need today ? one for sure is on Cuba. If, after that news - you can't sleep too well -; get Warren book; " The Governor " try understand - how to blackmail Congress - Or movie films; " Enemy of the State" that most of us today " Spy like US " - abusing power by top managers " Air America " - how marihuana come to US It may happened, Pentagon will have to arrest White House and his own " Liar in Chief" to save USA On the base of George Washington Legacy War President & his bible "PNAC" inventing Terrorism & new Pearl Harbor: http://www.newamericancentury.org/RebuildingAmericasDefenses.pdf ) From Johanne.Duhaime at ircm.qc.ca Mon Oct 6 19:34:29 2003 From: Johanne.Duhaime at ircm.qc.ca (Duhaime Johanne) Date: Mon, 6 Oct 2003 15:34:29 -0400 Subject: [EMBOSS] citation for an Emboss program Message-ID: <75CDD43E62D698448ED86E23C290A2760A2C3F@pandore.ircm.priv> Hello If I use a program, Needle as an example, should I cite Emboss: Rice,P. Longden,I. and Bleasby,A. "EMBOSS: The European Molecular Biology Open Software Suite" Trends in Genetics June 2000, vol 16, No 6. pp.276-277 Or should I cite Alan Bleasby (ableasby ? hgmp.mrc.ac.uk) HGMP-RC, Genome Campus, Hinxton, Cambridge CB10 1SB, UK Thank you Johanne Duhaime IRCM -------------- next part -------------- An HTML attachment was scrubbed... URL: From sdyall at ucla.edu Tue Oct 7 03:42:33 2003 From: sdyall at ucla.edu (Sabrina Dyall) Date: Mon, 6 Oct 2003 20:42:33 -0700 Subject: [EMBOSS] orf Message-ID: Hi, Does anybody know if it is possible to select a maximum size open reading frame or a range of open reading frame sizes using getorf or another application? Sabrina From sdyall at ucla.edu Tue Oct 7 03:42:33 2003 From: sdyall at ucla.edu (Sabrina Dyall) Date: Mon, 6 Oct 2003 20:42:33 -0700 Subject: [EMBOSS] orf Message-ID: Hi, Does anybody know if it is possible to select a maximum size open reading frame or a range of open reading frame sizes using getorf or another application? Sabrina From gwilliam at hgmp.mrc.ac.uk Tue Oct 7 08:41:22 2003 From: gwilliam at hgmp.mrc.ac.uk (Gary Williams, Tel 01223 494522) Date: Tue, 07 Oct 2003 09:41:22 +0100 Subject: [EMBOSS] orf References: Message-ID: <3F827C32.792127C4@hgmp.mrc.ac.uk> I never thought of setting a maximum size! I've changed the code for the getorf program to allow maximum sizes. It will be available in the next release of EMBOSS, or you can get the program files from: ftp://ftp.hgmp.mrc.ac.uk/pub/EMBOSS/patchfiles/getorf.* Regards, Gary Sabrina Dyall wrote: > > Hi, > Does anybody know if it is possible to select a maximum size open > reading frame or a range of open reading frame sizes using getorf or > another application? > Sabrina -- 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, Hinxton, Cambridge, CB10 1SB, UK From nancyyu at imb.sinica.edu.tw Wed Oct 8 01:06:58 2003 From: nancyyu at imb.sinica.edu.tw (Nancy Yu) Date: Wed, 08 Oct 2003 09:06:58 +0800 Subject: [EMBOSS] How to Get Jemboss to display/save pictures Message-ID: <3F836332.4040801@imb.sinica.edu.tw> Hi, I can't seem to get Jemboss to produce pictures for Emboss programs like pepwheel or any other program that output pictures. I don't know if it is a simple setting problem or installation problem. Any suggestions? Nancy Yu From bounce-back at htmlemail.ca Wed Oct 8 09:02:28 2003 From: bounce-back at htmlemail.ca (Holiday Giveaways) Date: 08 Oct 2003 02:02:28 -0700 Subject: [EMBOSS] Draw for a Florida Holiday Message-ID: <20031008020228.BDAC8A76A40135D2@htmlemail.ca> Free Holiday Giveaways Sign-up for the FREE Holiday Giveaway Draw You must register to be eligible for the draw. Fill out this form to register and be eligible for our monthly draw. 5 days and 4 nights in Orlando, Florida 6 days and 5 nights in Ft. Lauderdale, Florida PLUS 7 day unlimited Car Rental PLUS 2 Tickets to Universal Studios or to Disney World You must register to be eligible for the draw. Fill out this form and we'll do the rest. Free Holiday Giveaways copyright 2003 -------------- next part -------------- An HTML attachment was scrubbed... URL: From tcarver at hgmp.mrc.ac.uk Wed Oct 8 08:43:06 2003 From: tcarver at hgmp.mrc.ac.uk (Dr T. Carver) Date: Wed, 8 Oct 2003 09:43:06 +0100 (BST) Subject: [EMBOSS] How to Get Jemboss to display/save pictures In-Reply-To: <3F836332.4040801@imb.sinica.edu.tw> Message-ID: Hi Nancy The first thing to do is to check you can run these applications from the command line and create graphics. That will then give you more of a clue. It may be a png library problem. Regards Tim Carver HGMP-RC On Wed, 8 Oct 2003, Nancy Yu wrote: > Hi, > > I can't seem to get Jemboss to produce pictures for Emboss programs like > pepwheel or any other program that output pictures. I don't know if it > is a simple setting problem or installation problem. Any suggestions? > > Nancy Yu > From nancyyu at imb.sinica.edu.tw Wed Oct 8 10:13:35 2003 From: nancyyu at imb.sinica.edu.tw (Nancy Yu) Date: Wed, 08 Oct 2003 18:13:35 +0800 Subject: [EMBOSS] Indexing databases and their updates/new releases Message-ID: <3F83E34F.2050200@imb.sinica.edu.tw> Hello, I have a bunch of questions about the indexing of the databases. First of all, what kind of computers are people using to run Emboss? I am running on a Athlon MP2000+ dual processor with 1GB RAM (on Linux Redhat 9.0). Running dbiflat for EMBL est*.dat has taken forever (about 5 days and still not done yet). Are people using 64-bit systems, cluster systems, or other high-end computing systems? Is Emboss designed to run on these technologies? I'm still confused about the dbiflat indexing process. I know it produces 4 files, acnum.hit, acnum.trg, division.lkp, entrynam.idx. As I read somewhere in the mail archive, division.lkp stores the location of the database directory. Doesn't this means that if we move our *.dat file to a different directory, we would have to re-index again? Hence, everytime we download a new database, a new release, or an update, we will have to re-index everything? Also, if dbiflat was interrupted half way through indexing, is it possible to continue where it left off? >From my experience, it seems like the whole process starts over again. Just wondering, are the included index files for databases like embl (eg. division.ndx and other *.ndx files) useful at all for Emboss, or are they more for other programs? Can I somehow use these index files, ie. is there a fast way of indexing a database that I missed, or am I too clueless to know what I'm talking about? My main concern is that at the speed it takes to index a new release of large databases like EMBL or Genbank, it would be difficult for me to try to keep my local databases up-to-date. Thanx in advance for any comments and explanations :) Best Regards, Nancy Yu From ableasby at hgmp.mrc.ac.uk Wed Oct 8 10:46:26 2003 From: ableasby at hgmp.mrc.ac.uk (Alan Bleasby) Date: Wed, 8 Oct 2003 11:46:26 +0100 (BST) Subject: [EMBOSS] Indexing databases and their updates/new releases Message-ID: <200310081046.h98AkQ85018479@bromine.hgmp.mrc.ac.uk> The current indexing system is a little long in the tooth. I am currently testing/configuring its replacement on the various platforms. The new indexing system will not be available in the next release but should be out within the next few months. It is intended that the next release of EMBOSS will, by default, compile with large file support on all platforms (although the old indexing system cannot support files >2Gb). So, 2.8.0 will have 64bit (aj)long integers. Features of the new indexing system are that it is a B+ tree structure and therefore can be dynamically updated (e.g. with EMBL updates), can handle large files and duplicate IDs. It also does not need any sorting operations (the major cause of slowness for the old indexing system). Timing for the new system to index the latest EMBL release on a Linux system with the same spec as yours is around 9hrs (8hrs of which is just reading the database over NFS). EMBOSS is not designed for parallel processing although we have identified the areas of code that would need attention should we go down that route in the future. It is not (in general) possible to restart the old indexing system where it left off. That is a feature that could be implemented in the new indexing system (but isn't yet). I'm sure others may answer anything I've missed. HTH Alan Bleasby HGMP From ranrub at md.huji.ac.il Wed Oct 8 11:22:48 2003 From: ranrub at md.huji.ac.il (Ran Rubinstein) Date: Wed, 8 Oct 2003 13:22:48 +0200 Subject: [EMBOSS] Indexing databases and their updates/new releases In-Reply-To: <3F83E34F.2050200@imb.sinica.edu.tw> Message-ID: <003001c38d8e$81482fd0$7ea74084@sauron> I am currently tacking similar problems. The solution I've worked out for now is to use SRS (www.lionbio.co.uk) as a database - it's free for academic institutions, has very strong indexing tools that can use parallel processing, and Emboss can be configured to work through it. It also has a very professional web interface that can launch EMBOSS tools. The downside is that it's a bit complicated to install and administer. I'll be glad to hear alternative suggestions, tho. The server I'm running SRS and EMBOSS on is a 4-processor Origin200, 270Mhz, with 1GB RAM. Indexing (using SRS) the latest GenBank release, with NO EST's, GSS, HTG, took approximately 24 hours, running in parallel on 4 processors. --? Ran Rubinstein Dept. of Molecular Biology Faculty of Medicine, Hebrew University, Ein Karem Tel +972-2-6757906 Fax +972-2-6758992 -----Original Message----- From: owner-emboss at hgmp.mrc.ac.uk [mailto:owner-emboss at hgmp.mrc.ac.uk] On Behalf Of Nancy Yu Sent: Wednesday, October 08, 2003 12:14 PM To: emboss at embnet.org Subject: [EMBOSS] Indexing databases and their updates/new releases Hello, I have a bunch of questions about the indexing of the databases. First of all, what kind of computers are people using to run Emboss? I am running on a Athlon MP2000+ dual processor with 1GB RAM (on Linux Redhat 9.0). Running dbiflat for EMBL est*.dat has taken forever (about 5 days and still not done yet). Are people using 64-bit systems, cluster systems, or other high-end computing systems? Is Emboss designed to run on these technologies? I'm still confused about the dbiflat indexing process. I know it produces 4 files, acnum.hit, acnum.trg, division.lkp, entrynam.idx. As I read somewhere in the mail archive, division.lkp stores the location of the database directory. Doesn't this means that if we move our *.dat file to a different directory, we would have to re-index again? Hence, everytime we download a new database, a new release, or an update, we will have to re-index everything? Also, if dbiflat was interrupted half way through indexing, is it possible to continue where it left off? >From my experience, it seems like the whole process starts over again. Just wondering, are the included index files for databases like embl (eg. division.ndx and other *.ndx files) useful at all for Emboss, or are they more for other programs? Can I somehow use these index files, ie. is there a fast way of indexing a database that I missed, or am I too clueless to know what I'm talking about? My main concern is that at the speed it takes to index a new release of large databases like EMBL or Genbank, it would be difficult for me to try to keep my local databases up-to-date. Thanx in advance for any comments and explanations :) Best Regards, Nancy Yu From aml at ica.cc Wed Oct 8 13:41:27 2003 From: aml at ica.cc (American Laboratory) Date: Wed, 8 Oct 2003 09:41:27 -0400 Subject: [EMBOSS] American Laboratory Message-ID: <78131748.20031008094127@ica.cc> To Subscribe Go To: http://www.icainfo.com/aml/appintro.asp?Priority=PEPAL3 Following are the themes to be featured in AL: November Microscopy, Optics, and Image Analysis December Pharmaceutical Analysis, Molecular Spectroscopy, EAS January Annual ISC Buyers' Guide,Thermal Analysis, Gas Chromatography February Pittcon 2004 New Analytical Instrumentation for Separation Science and Spectroscopy March Advances in Laboratory Software and Data Management April Microchemical Analysis, Sample Preparation Dear Colleague, Please accept my invitation to receive a free subscription to our journal, American Laboratory. American Laboratory covers the disciplines of analytical and bioanalytical chemistry, drug discovery, laboratory software and informatics. Each issue features articles from leading scientists from around the world reviewing applications of instrumentation and new measurement technology. For your FREE subscription to American Laboratory, please click on the following link. http://www.icainfo.com/aml/appintro.asp?Priority=PEPAL3 I am confident that you will enjoy our journal and find it to be of significant professional value. I look forward to hearing from you. Sincerely yours, Brian Howard, Ph.D. Editor International Scientific Communications, Inc. 30 Controls Drive, P.O. Box 870, Shelton, CT 06484 Tel.: 203-926-9300, Fax: 203-926-9310, www.iscpubs.com -------------- next part -------------- An HTML attachment was scrubbed... URL: From yann-francois.bizouerne at bayercropscience.com Wed Oct 8 15:32:55 2003 From: yann-francois.bizouerne at bayercropscience.com (yann-francois.bizouerne at bayercropscience.com) Date: Wed, 8 Oct 2003 17:32:55 +0200 Subject: [EMBOSS] Configuring EMBOSS to use getz Message-ID: Hi, I am trying to use the method "srs". I am using Emboss 2.7.1 and SRS 7.1. In my emboss.default file, I have : DB Nrl3dGetz [ methodquery: srs format: pir type: P comment: "NRL 3D using SRS" app: getz dbalias:NRL3D methodall: direct file: "*.seq" dir: $emboss_data_dir/nrl_3d ] When I execute the command "showdb", I obtain : user>showdb Displays information on the currently available databases # Name Type ID Qry All Comment # ==== ==== == === === ======= Nrl3dGetz P OK OK OK NRL 3D using SRS So I looks fine. But when I try to find an entry, I just obtain a error. user>entret Nrl3dGetz:11ASA -outfile stdout Reads and writes (returns) flatfile entries error: Unknown set or databank No set or library named "Nrl3dGetz" Error: Unable to read sequence 'Nrl3dGetz:11ASA' Died: entret terminated: Bad value for '-sequence' and no prompt I have read all the SRS and EMBOSS documentations related to this configuration and I don't know where the problem is. Do you have any clue ?? Thanks in advance. Yann-Fran?ois BIZOUERNE BioInformatic Team BAYER CropScience 1, rue Pierre Fontaine 91058 Evry Cedex FRANCE Phone: 33-(0) 1-69-47-61-56 FAX: 33-(0) 1-69-47-61-42 E-mail: yann-francois.bizouerne at bayercropscience.com Intranet: http://bioinfo.evry.fr.bayercropscience/ From ranrub at md.huji.ac.il Wed Oct 8 15:50:28 2003 From: ranrub at md.huji.ac.il (Ran Rubinstein) Date: Wed, 8 Oct 2003 17:50:28 +0200 Subject: [EMBOSS] Configuring EMBOSS to use getz In-Reply-To: Message-ID: <003301c38db3$e5cc26d0$7ea74084@sauron> Your dbalias parameter is probably wrong. It should be the name of the databank in SRS. Try to run getz directly with your query and see whether it works. --? Ran Rubinstein Dept. of Molecular Biology Faculty of Medicine, Hebrew University, Ein Karem, Jerusalem, Israel Tel +972-2-6757906 Fax +972-2-6758992 -----Original Message----- From: owner-emboss at hgmp.mrc.ac.uk [mailto:owner-emboss at hgmp.mrc.ac.uk] On Behalf Of yann-francois.bizouerne at bayercropscience.com Sent: Wednesday, October 08, 2003 5:33 PM To: emboss at embnet.org Subject: [EMBOSS] Configuring EMBOSS to use getz Hi, I am trying to use the method "srs". I am using Emboss 2.7.1 and SRS 7.1. In my emboss.default file, I have : DB Nrl3dGetz [ methodquery: srs format: pir type: P comment: "NRL 3D using SRS" app: getz dbalias:NRL3D methodall: direct file: "*.seq" dir: $emboss_data_dir/nrl_3d ] When I execute the command "showdb", I obtain : user>showdb Displays information on the currently available databases # Name Type ID Qry All Comment # ==== ==== == === === ======= Nrl3dGetz P OK OK OK NRL 3D using SRS So I looks fine. But when I try to find an entry, I just obtain a error. user>entret Nrl3dGetz:11ASA -outfile stdout Reads and writes (returns) flatfile entries error: Unknown set or databank No set or library named "Nrl3dGetz" Error: Unable to read sequence 'Nrl3dGetz:11ASA' Died: entret terminated: Bad value for '-sequence' and no prompt I have read all the SRS and EMBOSS documentations related to this configuration and I don't know where the problem is. Do you have any clue ?? Thanks in advance. Yann-Fran?ois BIZOUERNE BioInformatic Team BAYER CropScience 1, rue Pierre Fontaine 91058 Evry Cedex FRANCE Phone: 33-(0) 1-69-47-61-56 FAX: 33-(0) 1-69-47-61-42 E-mail: yann-francois.bizouerne at bayercropscience.com Intranet: http://bioinfo.evry.fr.bayercropscience/ From pmr at ebi.ac.uk Wed Oct 8 15:55:48 2003 From: pmr at ebi.ac.uk (Peter Rice) Date: Wed, 08 Oct 2003 16:55:48 +0100 Subject: [EMBOSS] Configuring EMBOSS to use getz References: Message-ID: <3F843384.9090609@ebi.ac.uk> yann-francois.bizouerne at bayercropscience.com wrote: > I am trying to use the method "srs". > I am using Emboss 2.7.1 and SRS 7.1. > > In my emboss.default file, I have : > > DB Nrl3dGetz [ > methodquery: srs > format: pir > type: P > comment: "NRL 3D using SRS" > app: getz > dbalias:NRL3D > methodall: direct > file: "*.seq" > dir: $emboss_data_dir/nrl_3d > ] Quick reply (it's a very busy day :_) From memory, SRS has a problem with PIR formatted databases. It does not report the entry in a format that EMBOSS recognizes (try getz -e to see what the entry looks like). You may find the SRSFASTA methodquery works better (use format fasta). Hope this helps - if not, ask me again!!! Peter Rice From gbottu at ben.vub.ac.be Wed Oct 8 18:10:33 2003 From: gbottu at ben.vub.ac.be (Guy Bottu) Date: Wed, 8 Oct 2003 20:10:33 +0200 (CEST) Subject: [EMBOSS] Configuring EMBOSS to use getz Message-ID: <200310081810.h98IAXrg1329213@black.vub.ac.be> from : BEN Dear friends, I have read the question of Yann-Francois and the replies by Ran and Peter. Allow me to add some further comments. - I think that the parameter "app: getz" is useless since "method: srs" already tells it is getz. By the way, is getz in your "path" ? (well, probably yes, since we would otherwise expect another error message) - To solve the problem Peter mentions you can in pir.i replace $Field:[$DF_ProtSequence token:sequence format:pir tableFormat:listing] by $Field:[$DF_ProtSequence token:sequence format:plain tableFormat:listing] Guy Bottu From felipb at eis.org Fri Oct 10 16:55:46 2003 From: felipb at eis.org (felipb at eis.org) Date: Fri, 10 Oct 2003 18:55:46 +0200 Subject: [EMBOSS] THE MULTIMEDIA WEB SOLUTION Message-ID: <001101c38f4f$70c67af0$1eef2350@EP> THE MULTIMEDIA WEB SOLUTION VISIT THE HUMAN ROBOT WEB SITE www.avantatge.com LA TEVA NOVA WEB MULTIMEDIA PROVA GRATU?TA 30 DIES -> PROVA GET YOUR NEW MULTIMEDIA WEB FREE TEST 30 DAYS -> TEST VOTRE NOUVELLE WEB MULTIMEDIA ESSAI GRATUIT 30 JOURS -> ESSAI LA TUA NUOVA WEB MULTIMEDIA PROVA GRATUITA 30 GIORNI -> PROVA Aquest missatge no es spam : es un missatge de resposta o perqu? ha visitat una de las nostres web . Si no vol mes rebre mes missatges o si l'ha rebut per error envi? una e-mail a stop at avantatge.com . Recordi que no perd el dret de tenir una web multimedia gratu?ta per 30 dies . You are currently subscribed to Avantatge news If you'd rather not receive e-mail about events, or product updates, send a message to stop at avantatge.com . However you will not lost the right to test for 30 days a full multimedia web ?2003 Avantatge? web studios by EP sl Andorra www.avantatge.com -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: FOTOROBOT01.jpg Type: image/jpeg Size: 3681 bytes Desc: not available URL: From nancyyu at imb.sinica.edu.tw Tue Oct 14 08:16:09 2003 From: nancyyu at imb.sinica.edu.tw (Nancy Yu) Date: Tue, 14 Oct 2003 16:16:09 +0800 Subject: [EMBOSS] How to Get Jemboss to display/save pictures In-Reply-To: References: Message-ID: <3F8BB0C9.1030506@imb.sinica.edu.tw> I can produce png graphic files from command line Emboss just fine, but it doesn't seem to work from Jemboss. Actually, a png file of 0 bytes is produced, and I don't know what that means. Does anyone else have similar problems? >Hi Nancy > >The first thing to do is to check you can run these applications from the >command line and create graphics. That will then give you more of a clue. >It may be a png library problem. > >Regards >Tim Carver > >HGMP-RC > >On Wed, 8 Oct 2003, Nancy Yu wrote: > > > >>Hi, >> >>I can't seem to get Jemboss to produce pictures for Emboss programs like >>pepwheel or any other program that output pictures. I don't know if it >>is a simple setting problem or installation problem. Any suggestions? >> >>Nancy Yu >> >> >> From ronald.yang at jakru.com Tue Oct 14 15:55:12 2003 From: ronald.yang at jakru.com (H.Ronald Yang) Date: Tue, 14 Oct 2003 11:55:12 -0400 Subject: [EMBOSS] EMBOSS GUI : mwcontam : unknown datatype 'filelist' Message-ID: <008201c3926b$8dcd16d0$02020a0a@rescentris.com> Hi, I have a problem using "mwcontam" and "mwfilter" through EMBOSS Web GUI. When I click on the one of "PROTEIN COMPOSITION" tool, "mwcontam", from the left side panel, there is error. Right after "input section", it says "ERROR" and "unknown datatype 'filelist'". Is this possible to fix? Thanks in advance, Ron From mccarthy at cs.usask.ca Tue Oct 14 16:25:17 2003 From: mccarthy at cs.usask.ca (Luke McCarthy) Date: 14 Oct 2003 10:25:17 -0600 Subject: [EMBOSS] EMBOSS GUI : mwcontam : unknown datatype 'filelist' In-Reply-To: <008201c3926b$8dcd16d0$02020a0a@rescentris.com> References: <008201c3926b$8dcd16d0$02020a0a@rescentris.com> Message-ID: <1066148717.933.17.camel@crazyharry.usask.ca> On Tue, 2003-10-14 at 09:55, H.Ronald Yang wrote: > Hi, > > I have a problem using "mwcontam" and "mwfilter" through EMBOSS Web GUI. > When I click on the one of "PROTEIN COMPOSITION" tool, "mwcontam", from the > left side panel, there is error. Right after "input section", it says > "ERROR" and "unknown datatype 'filelist'". Is this possible to fix? There's no support for that particular data type in the GUI -- I didn't know it existed... I'll put something together and make available an updated version of the GUI available hopefully later today. Check http://bioinfo.pbi.nrc.ca/~lukem/EMBOSS/ for the update. There's no mention of this particular data type in the ACD spec at http://www.hgmp.mrc.ac.uk/Software/EMBOSS/Acd/syntax.html#Acddata11 , but I assume it's just supposed to be a random list of files. Can someone on the list familiar with the internals confirm that this is true? If it is true, it's going to be particularly difficult to implement this type over the web as there is no standard control for uploading more than one file. I'll probably just treat this as an alias for 'datafile' unless there's some subtlety that I'm missing... Cheers, Luke -- Luke McCarthy Research Officer, Bioinformatics Department of Computer Science University of Saskatchewan mccarthy at cs.usask.ca From tcarver at hgmp.mrc.ac.uk Tue Oct 14 17:43:15 2003 From: tcarver at hgmp.mrc.ac.uk (Dr T. Carver) Date: Tue, 14 Oct 2003 18:43:15 +0100 (BST) Subject: [EMBOSS] How to Get Jemboss to display/save pictures In-Reply-To: <3F8BB0C9.1030506@imb.sinica.edu.tw> Message-ID: Hi Nancy Can you check the value in the file: $EMBOSS_INSTALL/share/EMBOSS/jemboss/resources/jemboss.properties of plplot? Also make sure there are no other jemboss.properties files on your file system. Regards Tim On Tue, 14 Oct 2003, Nancy Yu wrote: > I can produce png graphic files from command line Emboss just fine, but > it doesn't seem to work from Jemboss. Actually, a png file of 0 bytes > is produced, and I don't know what that means. Does anyone else have > similar problems? > > >Hi Nancy > > > >The first thing to do is to check you can run these applications from the > >command line and create graphics. That will then give you more of a clue. > >It may be a png library problem. > > > >Regards > >Tim Carver > > > >HGMP-RC > > > >On Wed, 8 Oct 2003, Nancy Yu wrote: > > > > > > > >>Hi, > >> > >>I can't seem to get Jemboss to produce pictures for Emboss programs like > >>pepwheel or any other program that output pictures. I don't know if it > >>is a simple setting problem or installation problem. Any suggestions? > >> > >>Nancy Yu > >> > >> > >> > From ronald.yang at jakru.com Tue Oct 14 17:58:00 2003 From: ronald.yang at jakru.com (H.Ronald Yang) Date: Tue, 14 Oct 2003 13:58:00 -0400 Subject: [EMBOSS] Re: EMBOSS GUI : mwcontam : unknown datatype 'filelist' References: <007001c39272$ceead790$862010ac@unisabanacli.unisabana.edu.co> Message-ID: <00d701c3927c$b591d820$02020a0a@rescentris.com> I am using Luke's EMBOSS-GUI. Maybe I should ask the question to Luke. If so, sorry to bother you with this. Ron ----- Original Message ----- From: "Leyla Jael Garc?a Castro" To: "'H.Ronald Yang'" Sent: Tuesday, October 14, 2003 12:47 PM Subject: RE: EMBOSS GUI : mwcontam : unknown datatype 'filelist' > Are you using JEmboss or another web GUI? > > -----Mensaje original----- > De: owner-emboss-dev at hgmp.mrc.ac.uk > [mailto:owner-emboss-dev at hgmp.mrc.ac.uk] En nombre de H.Ronald Yang > Enviado el: Martes, 14 de Octubre de 2003 10:55 a.m. > Para: emboss at embnet.org; emboss-dev at embnet.org > CC: R. Wolfgang Rumpf > Asunto: EMBOSS GUI : mwcontam : unknown datatype 'filelist' > > Hi, > > I have a problem using "mwcontam" and "mwfilter" through EMBOSS > Web GUI. > When I click on the one of "PROTEIN COMPOSITION" tool, "mwcontam", > from the > left side panel, there is error. Right after "input section", it > says > "ERROR" and "unknown datatype 'filelist'". Is this possible to > fix? > > Thanks in advance, > Ron > > From mccarthy at cs.usask.ca Tue Oct 14 20:46:03 2003 From: mccarthy at cs.usask.ca (Luke McCarthy) Date: 14 Oct 2003 14:46:03 -0600 Subject: [EMBOSS] EMBOSS GUI : mwcontam : unknown datatype 'filelist' In-Reply-To: <1066148717.933.17.camel@crazyharry.usask.ca> References: <008201c3926b$8dcd16d0$02020a0a@rescentris.com> <1066148717.933.17.camel@crazyharry.usask.ca> Message-ID: <1066164362.4910.33.camel@crazyharry.usask.ca> On Tue, 2003-10-14 at 10:25, Luke McCarthy wrote: > On Tue, 2003-10-14 at 09:55, H.Ronald Yang wrote: > > Hi, > > > > I have a problem using "mwcontam" and "mwfilter" through EMBOSS Web GUI. > > When I click on the one of "PROTEIN COMPOSITION" tool, "mwcontam", from the > > left side panel, there is error. Right after "input section", it says > > "ERROR" and "unknown datatype 'filelist'". Is this possible to fix? > > There's no support for that particular data type in the GUI -- I didn't > know it existed... I'll put something together and make available an > updated version of the GUI available hopefully later today. Check > http://bioinfo.pbi.nrc.ca/~lukem/EMBOSS/ for the update. The update is available at the above website. It fixes the error in displaying the input pages for 'mwcontam' and 'mwfilter', but it is only possible to upload a single file to each application. This means 'mwcontam' is all but useless when accessed through my web interface. I'll think more about this problem, but I don't think it will change any time soon. Cheers, Luke -- Luke McCarthy Research Officer, Bioinformatics Department of Computer Science University of Saskatchewan mccarthy at cs.usask.ca From ablavier at wanadoo.fr Wed Oct 15 10:25:07 2003 From: ablavier at wanadoo.fr (=?ISO-8859-1?Q?Andr=E9_Blavier?=) Date: Wed, 15 Oct 2003 12:25:07 +0200 Subject: [EMBOSS] EMBOSS for Windows: v. 2.7.1 available Message-ID: <3F8D2083.90903@wanadoo.fr> I have updated my Windows port of EMBOSS to version 2.7.1 It is available at http://perso.wanadoo.fr/ablavier/embosswin/embosswin.html Comments are welcome. -- Andr? Blavier From sebastian.bassi at ar.advantaseeds.com Thu Oct 16 03:05:01 2003 From: sebastian.bassi at ar.advantaseeds.com (Bassi, Sebastian) Date: Thu, 16 Oct 2003 05:05:01 +0200 Subject: [EMBOSS] Program for primer verification Message-ID: I would like to know what program should I use if I want to check a pair of primers for self annealing, for tm, for fitness for PCR, and so on. Does any of the EMBOSS program will do the job? Primer3 is usefull to find good primers, but what I want to do is the check primers I already have selected by another method. Is there a scriptable program to accomplish this? Sebastian Bassi. Advanta Seeds. Balcarce Research Station. From lmullan at hgmp.mrc.ac.uk Thu Oct 16 13:27:51 2003 From: lmullan at hgmp.mrc.ac.uk (Lisa Mullan) Date: Thu, 16 Oct 2003 14:27:51 +0100 Subject: [EMBOSS] Program for primer verification In-Reply-To: Message-ID: Hi Sebastian, AS far as I know, the only other program you could look at is "dan" which checks melting temperatures. However if you used Primer3 to pick primers in the first place, it should have checked all those things for you. HTH Lisa Mullan -----Original Message----- From: owner-emboss at hgmp.mrc.ac.uk [mailto:owner-emboss at hgmp.mrc.ac.uk]On Behalf Of Bassi, Sebastian Sent: Thursday, October 16, 2003 4:05 AM To: emboss at embnet.org Subject: [EMBOSS] Program for primer verification I would like to know what program should I use if I want to check a pair of primers for self annealing, for tm, for fitness for PCR, and so on. Does any of the EMBOSS program will do the job? Primer3 is usefull to find good primers, but what I want to do is the check primers I already have selected by another method. Is there a scriptable program to accomplish this? Sebastian Bassi. Advanta Seeds. Balcarce Research Station. From gwilliam at hgmp.mrc.ac.uk Thu Oct 16 13:42:12 2003 From: gwilliam at hgmp.mrc.ac.uk (Gary Williams, Tel 01223 494522) Date: Thu, 16 Oct 2003 14:42:12 +0100 Subject: [EMBOSS] Program for primer verification References: Message-ID: <3F8EA034.8FFC1AD9@hgmp.mrc.ac.uk> Lisa Mullan wrote: Use should eprimer3 and specify your existing primers in the -forwardinput and -reverseinput qualifiers. It will check that your primers are reasonable. Gary > -----Original Message----- > From: owner-emboss at hgmp.mrc.ac.uk [mailto:owner-emboss at hgmp.mrc.ac.uk]On > Behalf Of Bassi, Sebastian > Sent: Thursday, October 16, 2003 4:05 AM > To: emboss at embnet.org > Subject: [EMBOSS] Program for primer verification > > I would like to know what program should I use if I want to check a pair of > primers for self annealing, for tm, for fitness for PCR, and so on. Does any > of the EMBOSS program will do the job? Primer3 is usefull to find good > primers, but what I want to do is the check primers I already have selected > by another method. > Is there a scriptable program to accomplish this? > > Sebastian Bassi. > Advanta Seeds. Balcarce Research Station. -- 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, Hinxton, Cambridge, CB10 1SB, UK From grsvc at mucc.mahidol.ac.th Fri Oct 17 10:22:44 2003 From: grsvc at mucc.mahidol.ac.th (Suksiri Vichasri Grams) Date: Fri, 17 Oct 2003 17:22:44 +0700 Subject: [EMBOSS] embossRUNNER Message-ID: embossRUNNER is an interface for emboss 2.7.1 on MacOS 10.2. It is available for download at the MIT Mac Hyperarchive: http://hyperarchive.lcs.mit.edu/HyperArchive/Archive/sci/emboss-runner- 10.hqx Kindly, Rudi & Suksiri Dr. Suksiri Vichasri Grams Department of Biology Faculty of Science Mahidol University Rama VI Road Bangkok 10400 Thailand From R-8-721447-17263485-2-7807-US2-9F15919F at xmr3.com Fri Oct 17 17:08:17 2003 From: R-8-721447-17263485-2-7807-US2-9F15919F at xmr3.com (International Scientific Communications, Inc.) Date: Fri, 17 Oct 2003 13:08:17 -0400 Subject: [EMBOSS] Laboratory Instrumentation News - October 2003 Message-ID: An HTML attachment was scrubbed... URL: From idrummon at receptor.mgh.harvard.edu Sat Oct 18 01:33:01 2003 From: idrummon at receptor.mgh.harvard.edu (Iain Drummond) Date: Fri, 17 Oct 2003 21:33:01 -0400 Subject: [EMBOSS] maximum number of sequences for eprimer3 Message-ID: I am using eprimer3 and multiple fasta formatted dinucleotide containing sequences as input. I find that eprimer3/primer3_core will handle an input file containing up to 23 sequences; at 24 sequences, both eprimer3 and primer3_core ?sleep?. i.e. the processes never acheive run status when I watch what happens using top or prstat. I don?t know if this has something to do with limitations of my system (sun ultra5/1GB ram/500 MB free disk space) or intrinsic to eprimer3/primer3_core. I do know that it also happens on a Mac OS X system (640 MB ram/35 GB free disk space). Is there a config file that sets limits on eprimer3? (that i can change?) -- Iain Drummond, Ph.D. Assistant Professor Department of Medicine, Harvard Medical School and Renal Unit, Massachusetts General Hospital Mailing address: Renal Unit / MGH 149-8000 149 13th St. Charlestown, MA 02129 Tel: 617 726 5647 Fax: 617 726 5669 idrummond at partners.org idrummon at receptor.mgh.harvard.edu Lab Home Page: http://danio.mgh.harvard.edu -------------- next part -------------- An HTML attachment was scrubbed... URL: From areagp61 at yahoo.it Tue Oct 21 08:23:33 2003 From: areagp61 at yahoo.it (=?iso-8859-1?q?Gr=20Pa?=) Date: Tue, 21 Oct 2003 10:23:33 +0200 (CEST) Subject: [EMBOSS] "fasta" program Message-ID: <20031021082333.25496.qmail@web21005.mail.yahoo.com> Hi all, searching for "fasta and emboss", I have found this site http://ben.vub.ac.be/embosshelp/fasta.html reporting fasta as a program of the EMBOSS package, but it lacks in the EMBOSS official list of programs. Is this fasta program an old implementation or what? Regards Graziano ______________________________________________________________________ Yahoo! Mail: 6MB di spazio gratuito, 30MB per i tuoi allegati, l'antivirus, il filtro Anti-spam http://it.yahoo.com/mail_it/foot/?http://it.mail.yahoo.com/ From Marc.Logghe at devgen.com Tue Oct 21 11:53:12 2003 From: Marc.Logghe at devgen.com (Marc Logghe) Date: Tue, 21 Oct 2003 13:53:12 +0200 Subject: [EMBOSS] "fasta" program Message-ID: As far as I can see, fasta is a custom made application (or rather an EMBOSS wrapper around the fasta suite of programs) by Guy Bottu of BEN. Meaning it is not part of the 'official' EMBOSS suite. I don't find info whether they consider it as free software or not. Regards, Marc > -----Original Message----- > From: Gr Pa [mailto:areagp61 at yahoo.it] > Sent: Tuesday, October 21, 2003 10:24 AM > To: emboss at embnet.org > Subject: [EMBOSS] "fasta" program > > > Hi all, > searching for "fasta and emboss", I have found this > site http://ben.vub.ac.be/embosshelp/fasta.html > reporting fasta as a program of the EMBOSS package, > but it lacks in the EMBOSS official list of programs. > Is this fasta program an old implementation or what? > Regards > Graziano > > ______________________________________________________________________ > Yahoo! Mail: 6MB di spazio gratuito, 30MB per i tuoi > allegati, l'antivirus, il filtro Anti-spam > http://it.yahoo.com/mail_it/foot/?http://it.mail.yahoo.com/ > From rpg at mrc-lmb.cam.ac.uk Tue Oct 21 15:53:46 2003 From: rpg at mrc-lmb.cam.ac.uk (rpg at mrc-lmb.cam.ac.uk) Date: Tue, 21 Oct 2003 16:53:46 +0100 (BST) Subject: [EMBOSS] EMBASSY - mse Message-ID: <200310211553.h9LFrkn432808@alf1.lmb.internal> Anyone got mse compiled? I installed emboss on OS X using fink, and have the EMBASSY src code in a directory off that. % ./configure seems to work but then % make bombs out with Making all in ckit make[1]: Nothing to be done for `all'. Making all in source make[1]: *** No rule to make target `../../../ajax/libajax.la', needed by `mse'. Stop. make: *** [all-recursive] Error 1 I guess that means I need the ajax libraries. Where may I find them? thanks, r PS I do have a directory ../../ajax/ but nothing that looks like libajax. -- Richard P. Grant http://www2.mrc-lmb.cam.ac.uk/personal/rpg/ MRC-LMB, Cambridge, UK PGP: 0x5F9559B1 weblog: http://www.rg-d.com/BioLOG/ From idrummon at receptor.mgh.harvard.edu Tue Oct 21 16:41:06 2003 From: idrummon at receptor.mgh.harvard.edu (Iain Drummond) Date: Tue, 21 Oct 2003 12:41:06 -0400 Subject: [EMBOSS] eprimer3: max input file number? Message-ID: I have run into a limitation using eprimer3 as an interface for primer3. It seems that eprimer3 will accept up to 23 sequences (in a single fasta formatted text file) but not 24 or more; with 24 or more sequences, eprimer3 and primer3_core will just hang as ?sleeping? processes and never finish. My goal is to automate genomic sequence analysis (zebrafish) in order to generate new, potentially useful polymorphic markers from dinucleotide repeats. eprimer3 is the last step where a long list of ~500 bp sequences are sent to primer3 to make primers. I run into this problem both on a Sun ultra5 running solaris 8 (1GB ram) and on a mac G4 running OS X 10.2.8 (640 MB ram). To see whether the problem was in primer3_core or eprimer3, I prepared a list of 30 and 60 short sequences in Boulder io format and submitted them directly to primer3_core; no problem there, 30 or 60 primer pairs were returned. Does anyone know if there is a config file that would change the behavior of eprimer3, or is this a bug in the program? -- Iain Drummond, Ph.D. Assistant Professor Department of Medicine, Harvard Medical School and Renal Unit, Massachusetts General Hospital idrummond at partners.org idrummon at receptor.mgh.harvard.edu Lab Home Page: http://danio.mgh.harvard.edu -------------- next part -------------- An HTML attachment was scrubbed... URL: From abl at ica.cc Tue Oct 21 17:00:43 2003 From: abl at ica.cc (American Biotechnology Laboratory) Date: Tue, 21 Oct 2003 13:00:43 -0400 Subject: [EMBOSS] We thought you would be interested... Message-ID: <97921984.20031021130043@ica.cc> To Subscribe Go To: http://www.icainfo.com/aml/appintro.asp?Priority=PEPAB3 Following are the themes to be featured in AL: November Microscopy, Optics, and Image Analysis December Pharmaceutical Analysis, Molecular Spectroscopy, EAS January Annual ISC Buyers' Guide,Thermal Analysis, Gas Chromatography February Pittcon 2004 New Analytical Instrumentation for Separation Science and Spectroscopy March Advances in Laboratory Software and Data Management April Microchemical Analysis, Sample Preparation Dear Colleague, Please accept my invitation to receive a free subscription to our journal, American Laboratory. American Laboratory covers the disciplines of analytical and bioanalytical chemistry, drug discovery, laboratory software and informatics. Each issue features articles from leading scientists from around the world reviewing applications of instrumentation and new measurement technology. For your FREE subscription to American Laboratory, please click on the following link. http://www.icainfo.com/aml/appintro.asp?Priority=PEPAB3 I am confident that you will enjoy our journal and find it to be of significant professional value. I look forward to hearing from you. Sincerely yours, Brian Howard, Ph.D. Editor -------------- next part -------------- An HTML attachment was scrubbed... URL: From yezq at mail.cbi.pku.edu.cn Wed Oct 22 09:52:10 2003 From: yezq at mail.cbi.pku.edu.cn (Zhiqiang Ye) Date: Wed, 22 Oct 2003 17:52:10 +0800 Subject: [EMBOSS] EMBASSY - mse Message-ID: <200310220944.h9M9iDAW029737@mail.cbi.pku.edu.cn> You should keep the source directory(eg. EMBOSS2.7.1) after you installed EMBOSS. then: cd EMBOSS2.7.1 mkdir embassy cp /path_to_mse/mse.tar.gz . gzip -dc mse.tar.gz | tar xf - cd mse; ./configure --prefix........ ( the parameters should be as the same as you build EMBOSS) make make install ?? >Anyone got mse compiled? > >I installed emboss on OS X using fink, and have the EMBASSY src code in a >directory off that. > >% ./configure > >seems to work but then > >% make > >bombs out with > >Making all in ckit >make[1]: Nothing to be done for `all'. >Making all in source >make[1]: *** No rule to make target `../../../ajax/libajax.la', needed by >`mse'. Stop. >make: *** [all-recursive] Error 1 > > >I guess that means I need the ajax libraries. Where may I find them? >thanks, > >r > >PS I do have a directory ../../ajax/ but nothing that looks like libajax. > > > >-- >Richard P. Grant http://www2.mrc-lmb.cam.ac.uk/personal/rpg/ >MRC-LMB, Cambridge, UK >PGP: 0x5F9559B1 weblog: http://www.rg-d.com/BioLOG/ = = = = = = = = = = = = = = = = = = = = Best Wishes! Zhiqiang Ye 2003-10-22 From rpg at mrc-lmb.cam.ac.uk Wed Oct 22 09:50:47 2003 From: rpg at mrc-lmb.cam.ac.uk (rpg at mrc-lmb.cam.ac.uk) Date: Wed, 22 Oct 2003 10:50:47 +0100 (BST) Subject: [EMBOSS] EMBASSY - mse In-Reply-To: <200310220944.h9M9iDAW029737@mail.cbi.pku.edu.cn> from Zhiqiang Ye at "Oct 22, 2003 05:52:10 pm" Message-ID: <200310220950.h9M9om1429913@alf1.lmb.internal> Nah, that loses track of ../../../depcomp. I suspect that David is right - it's trying to find a libajax.la when it should be looking for .dylib - it's a porting thing, apparently. -- Richard P. Grant http://www2.mrc-lmb.cam.ac.uk/personal/rpg/ MRC-LMB, Cambridge, UK PGP: 0x5F9559B1 weblog: http://www.rg-d.com/BioLOG/ From gbottu at ben.vub.ac.be Wed Oct 22 14:17:41 2003 From: gbottu at ben.vub.ac.be (Guy Bottu) Date: Wed, 22 Oct 2003 16:17:41 +0200 (CEST) Subject: [EMBOSS] "fasta" program Message-ID: <200310221417.h9MEHflw1266502@black.vub.ac.be> from : BEN Dear Graziano, At the BEN site we have BLAST, fastA and some other programs installed under an EMBOSS "wrapper" program. In their present form these programs are not readily installable elsewhere. When a year ago we dropped GCG (had become too expensive !) I rushed to replace the lost functionality for our users and did not consider portability. I think it would be a good idea to distribute our BLAST and fastA wrappers as an "Embassadir". I will start a conversation with the EMBOSS developement team about what is necessary to make it work. I know that M. Sarachu from the Argentina and J. Valverde from the Spanish EMBnet Nodes have our wrappers running at their site. J. Valverde had started to make it portable, but I do not know how far he got by know. If you are in a hurry, I can send you the files in their present state. To make it work you mainly need to edit the files and replace the paths of the programs and the names of the databanks by what you have at your site. Note that, since the EMBOSS programs are just "wrappers", you need in the first place the fastA programs themselves properly installed and configured with a collection of databanks in fastA format. Guy Bottu From ruediger at sanbi.ac.za Wed Oct 22 14:41:20 2003 From: ruediger at sanbi.ac.za (Ruediger Braeuning) Date: Wed, 22 Oct 2003 16:41:20 +0200 (SAST) Subject: [EMBOSS] "fasta" program In-Reply-To: <200310221417.h9MEHflw1266502@black.vub.ac.be> References: <200310221417.h9MEHflw1266502@black.vub.ac.be> Message-ID: <20031022163856.G2720@fling.sanbi.ac.za> Dear Guy, > I think it would be a good idea to distribute our BLAST and fastA wrappers as an > "Embassadir". I will start a conversation with the EMBOSS developement team > about what is necessary to make it work. Great, that would be a valuable addition. Thanks for sharing. > If you are in a hurry, I can send you the files in their present state. > To make it work you mainly need to edit the files and replace the paths > of the programs and the names of the databanks by what you have at your > site. Note that, since the EMBOSS programs are just "wrappers", you need > in the first place the fastA programs themselves properly installed and > configured with a collection of databanks in fastA format. If possible, I would like to have these wrappers as well. Thanks and best regards, Ruediger ------------------------------------------------------------------------- Ruediger Braeuning / South African National Bioinformatics Institute (=) University of the Western Cape Ph. +27 21 959 3645 / Private Bag X17 Fax +27 21 959 2512 (=) Bellville, 7535 www.sanbi.ac.za / South Africa From idrummon at receptor.mgh.harvard.edu Wed Oct 22 18:03:49 2003 From: idrummon at receptor.mgh.harvard.edu (Iain Drummond) Date: Wed, 22 Oct 2003 14:03:49 -0400 Subject: [EMBOSS] maximum number of sequences for eprimer3 In-Reply-To: Message-ID: Hi Sebastian, Interesting that you see the same problem with eprimer3 but the cutoff number varies; I wonder what the key variable is. I have used primer3 (primer3_core) and that has no cutoff; all the sequences are processed. I was hoping to use eprimer3 because the input and output files are easier to manage; I have limited perl scripting skills and I was trying to avoid converting the input to Boulder io format which for me would be laborious. Thanks, Iain Hello, I've been looking at the files you sent to me. Now I realize that I always used primer3, not eprimer3 and the input file is in different format. Anyway I made the test (with eprimer3) and the cut off value seems to be 10 sequences (more than that end into a sleep process). A workaround would be to send the job to eprimer3 in batch with the size it can handle. This will not correct the problem but at least you could get te results. Have you tried with the primer3 instead of eprimer3? Sebastian Bassi. Advanta Seeds. Balcarce Research Station. -------------- next part -------------- An HTML attachment was scrubbed... URL: From maojn at hotmail.com Wed Oct 22 18:08:06 2003 From: maojn at hotmail.com (Jean Mao) Date: Wed, 22 Oct 2003 14:08:06 -0400 Subject: [EMBOSS] question about refseq database Message-ID: Hi, I would like to include the RefSeq database from NCBI into our databases collection. Is there any specific format of the database prefered (flat or fasta) or work better? is there any know bugs that I should be aware of? Any suggestion is appreciated. Thanks. ------------------------------------------------------------------- Jean Mao, Ph.D. Helix Systems Bldg 12B, Rm 2N207 National Institutes of Health Bethesda, MD 20895 Email:maoj at helix.nih.gov ------------------------------------------------------------------ From maojn at hotmail.com Wed Oct 22 18:08:06 2003 From: maojn at hotmail.com (Jean Mao) Date: Wed, 22 Oct 2003 14:08:06 -0400 Subject: [EMBOSS] question about refseq database Message-ID: Hi, I would like to include the RefSeq database from NCBI into our databases collection. Is there any specific format of the database prefered (flat or fasta) or work better? is there any know bugs that I should be aware of? Any suggestion is appreciated. Thanks. ------------------------------------------------------------------- Jean Mao, Ph.D. Helix Systems Bldg 12B, Rm 2N207 National Institutes of Health Bethesda, MD 20895 Email:maoj at helix.nih.gov ------------------------------------------------------------------ From idrummon at receptor.mgh.harvard.edu Wed Oct 22 18:03:49 2003 From: idrummon at receptor.mgh.harvard.edu (Iain Drummond) Date: Wed, 22 Oct 2003 14:03:49 -0400 Subject: [EMBOSS] maximum number of sequences for eprimer3 In-Reply-To: Message-ID: Hi Sebastian, Interesting that you see the same problem with eprimer3 but the cutoff number varies; I wonder what the key variable is. I have used primer3 (primer3_core) and that has no cutoff; all the sequences are processed. I was hoping to use eprimer3 because the input and output files are easier to manage; I have limited perl scripting skills and I was trying to avoid converting the input to Boulder io format which for me would be laborious. Thanks, Iain Hello, I've been looking at the files you sent to me. Now I realize that I always used primer3, not eprimer3 and the input file is in different format. Anyway I made the test (with eprimer3) and the cut off value seems to be 10 sequences (more than that end into a sleep process). A workaround would be to send the job to eprimer3 in batch with the size it can handle. This will not correct the problem but at least you could get te results. Have you tried with the primer3 instead of eprimer3? Sebastian Bassi. Advanta Seeds. Balcarce Research Station. -------------- next part -------------- An HTML attachment was scrubbed... URL: From ableasby at hgmp.mrc.ac.uk Wed Oct 22 19:06:03 2003 From: ableasby at hgmp.mrc.ac.uk (Alan Bleasby) Date: Wed, 22 Oct 2003 20:06:03 +0100 (BST) Subject: [EMBOSS] maximum number of sequences for eprimer3 Message-ID: <200310221906.h9MJ635K012628@bromine.hgmp.mrc.ac.uk> Having had a quick look at the code I suspect that it is not a variable involved (EMBOSS programs are designed not to be limited in that way, usually only by system resource available). The code uses pipes to redirect stdin and stdout to/from primer3_core. A possible cause is therefore blocking from a full buffer. I'll let the author of the eprimer3 program know about it. HTH Alan From maoj at mail.nih.gov Thu Oct 23 20:44:23 2003 From: maoj at mail.nih.gov (Jean Mao) Date: Thu, 23 Oct 2003 16:44:23 -0400 Subject: [EMBOSS] question about index refseq database Message-ID: <069201c399a6$7169dd10$494de780@CIT.NIH.GOV> Hi, I have the following 2 files for refseq nucleotide and protein databases from NCBI: ---------------------------------------------- rscu.gbff.Z GenBank flatfile view (nucleotide sequence with annotations) rscu.gnp.Z GenPept flatfile view (protein sequence with annotations) ----------------------------------------- When I run dbiflat, should I enter GB or REFSEQ when prompt 'Entry format'? Also, in the .embossrc file, is the following entry correct (method=emblcd and format=genbank)? ---------------------------------------- DB refseqnt [ type: N method: emblcd format: genbank dir: $emboss_db_dir/refseqnt indexdir: $emboss_db_dir/refseqnt file: "*.gbff" release: "1.0" comment: "update 23/Oct/03" ] Any suggestion is appreciated. Jean From henrikki.almusa at helsinki.fi Fri Oct 24 06:38:48 2003 From: henrikki.almusa at helsinki.fi (Henrikki Almusa) Date: Fri, 24 Oct 2003 09:38:48 +0300 Subject: [EMBOSS] question about index refseq database In-Reply-To: <069201c399a6$7169dd10$494de780@CIT.NIH.GOV> References: <069201c399a6$7169dd10$494de780@CIT.NIH.GOV> Message-ID: <200310240938.48134.henrikki.almusa@helsinki.fi> On Thursday 23 October 2003 23:44, Jean Mao wrote: > I have the following 2 files for refseq nucleotide and protein databases > from NCBI: > ---------------------------------------------- > rscu.gbff.Z GenBank flatfile view (nucleotide sequence with annotations) > rscu.gnp.Z GenPept flatfile view (protein sequence with annotations) > ----------------------------------------- > > When I run dbiflat, should I enter GB or REFSEQ when prompt 'Entry format'? I haven't used refseq files but. i'd suggest you use refseq (remember to unzip files first). > Also, in the .embossrc file, is the following entry correct (method=emblcd > and format=genbank)? > ---------------------------------------- > DB refseqnt [ type: N method: emblcd format: genbank dir: > $emboss_db_dir/refseqnt indexdir: $emboss_db_dir/refseqnt file: "*.gbff" > release: "1.0" comment: "update 23/Oct/03" ] Method might be refseq as well. Unfortunately this isn't covered by admin manual in emboss web site. I assume that you have two directories so that there is another entry in .embossrc for protein file. Hoope this helps, -- Henrikki Almusa From yann-francois.bizouerne at bayercropscience.com Fri Oct 24 11:10:56 2003 From: yann-francois.bizouerne at bayercropscience.com (yann-francois.bizouerne at bayercropscience.com) Date: Fri, 24 Oct 2003 13:10:56 +0200 Subject: [EMBOSS] question EMBOSS-GUI Message-ID: Hello, I don't know if you could help me with the little problem I have. I have installed your EMBOSS-GUI application on our server a few month ago. And it works great. Since I have installed SRS on our servern. I have mofified the emboss.default in order to use to the SRS indexes. Now it looks like : DB TREMBL [ methodquery: srs format: SWISS type: P comment: "TREMBL (SPTREMBL + TREMBLNEW) using SRS" app: getz dbalias: TREMBL methodall: direct file: "trembl.dat" dir: $emboss_data_dir/swall ] And that works quitr well on command line, when I need to retrieve a sequence with seqret for example. But if I am using the EMBOSS-GUI interface I just obtain the following errror message: EMBOSS An error in ajfile.c at line 145: execvp ('getz -e '[TREMBL-id:Q977L9]'', NULL) failed: 'No such file or directory' Error: Unable to read sequence 'TREMBL-id:Q977L9' Died: seqret terminated: Bad value for '-sequence' with -auto defined seqret exited with status 1... Do you have a clue for the problem ? Thanks in advance Best regards. Yann-Fran?ois BIZOUERNE BioInformatic Team BAYER CropScience 1, rue Pierre Fontaine 91058 Evry Cedex FRANCE Phone: 33-(0) 1-69-47-61-56 FAX: 33-(0) 1-69-47-61-42 E-mail: yann-francois.bizouerne at bayercropscience.com Intranet: http://bioinfo.evry.fr.bayercropscience/ From gbottu at ben.vub.ac.be Fri Oct 24 13:04:02 2003 From: gbottu at ben.vub.ac.be (Guy Bottu) Date: Fri, 24 Oct 2003 15:04:02 +0200 (CEST) Subject: [EMBOSS] question EMBOSS-GUI Message-ID: <200310241304.h9OD42XI1549926@black.vub.ac.be> from : BEN Dear Yann-Fran?ois, I had exactly the same problem when I first installed Jemoss. At the command line it works because getz is in the "path", but the GUI's often only look for programs in .../emboss/bin. The cure is to install in the directory with the EMBOSS programs a logical link pointing to getz. By the way, this applies also for clustalw and primer3_core. Guy Bottu From tcarver at hgmp.mrc.ac.uk Fri Oct 24 13:08:17 2003 From: tcarver at hgmp.mrc.ac.uk (Dr T. Carver) Date: Fri, 24 Oct 2003 14:08:17 +0100 (BST) Subject: [EMBOSS] question EMBOSS-GUI In-Reply-To: <200310241304.h9OD42XI1549926@black.vub.ac.be> Message-ID: The best way round is to alter the value of embossPath in: $EMBOSS_INSTALL/share/emboss/jemboss/resources/jemboss.properties by adding the path to getz, clustalw and primer3_core. For a description of jemboss.properties see: http://www.rfcgr.mrc.ac.uk/Software/EMBOSS/Jemboss/install/properties.html Regards Tim On Fri, 24 Oct 2003, Guy Bottu wrote: > from : BEN > > Dear Yann-Fran?ois, > > I had exactly the same problem when I first installed Jemoss. At the command > line it works because getz is in the "path", but the GUI's often only look for > programs in .../emboss/bin. The cure is to install in the directory with the > EMBOSS programs a logical link pointing to getz. By the way, this applies also > for clustalw and primer3_core. > > Guy Bottu > From stefanielager at fastmail.ca Fri Oct 24 13:24:03 2003 From: stefanielager at fastmail.ca (Stefanie Lager) Date: Fri, 24 Oct 2003 09:24:03 -0400 (EDT) Subject: [EMBOSS] question EMBOSS-GUI Message-ID: <3F9927F3.000085.66964@ns.interchange.ca> SRS is set up for the user that runs EMBOSS on command line, while SRS is NOT set up for the user (nobody) that runs through the web interface. If you have SRS running as web interface you can use method: srswww url: "http://the.adress.to local.SRS.com" Or write a script that calls getz, and sets up SRS and use the script with method: app app: "path/to/the/script " Stefanie > > > > > Hello, > > I don't know if you could help me with the little problem I have. > > I have installed your EMBOSS-GUI application on our server a few > month ago. And it works great. > Since I have installed SRS on our servern. I have mofified the > emboss.default in order to use to the SRS indexes. > Now it looks like : > > DB TREMBL [ > methodquery: srs > format: SWISS > type: P > comment: "TREMBL (SPTREMBL + TREMBLNEW) using SRS" > app: getz > dbalias: TREMBL > methodall: direct > file: "trembl.dat" > dir: $emboss_data_dir/swall > ] > > > > > And that works quitr well on command line, when I need to retrieve > a sequence with seqret for example. But if I am using the > EMBOSS-GUI interface I just obtain the following errror message: > > EMBOSS An error in ajfile.c at line 145: execvp ('getz -e > '[TREMBL-id:Q977L9]'', NULL) failed: 'No such file or directory' > Error: Unable to read sequence 'TREMBL-id:Q977L9' Died: seqret > terminated: Bad value for '-sequence' with -auto defined seqret > exited with status 1... > > Do you have a clue for the problem ? > > Thanks in advance > > Best regards. > > > > > > > > Yann-Fran?ois BIZOUERNE > BioInformatic Team > BAYER CropScience > 1, rue Pierre Fontaine > 91058 Evry Cedex > FRANCE > Phone: 33-(0) 1-69-47-61-56 > FAX: 33-(0) 1-69-47-61-42 > E-mail: yann-francois.bizouerne at bayercropscience.com > Intranet: http://bioinfo.evry.fr.bayercropscience/ _________________________________________________________________ http://fastmail.ca/ - Fast Secure Web Email for Canadians From mccarthy at cs.usask.ca Fri Oct 24 15:48:32 2003 From: mccarthy at cs.usask.ca (Luke McCarthy) Date: 24 Oct 2003 09:48:32 -0600 Subject: [EMBOSS] question EMBOSS-GUI In-Reply-To: References: Message-ID: <1067010512.8481.16.camel@crazyharry.usask.ca> On Fri, 2003-10-24 at 05:10, yann-francois.bizouerne at bayercropscience.com wrote: > EMBOSS An error in ajfile.c at line 145: execvp ('getz -e '[TREMBL-id:Q977L9]'', NULL) failed: 'No such file or directory' Error: > Unable to read sequence 'TREMBL-id:Q977L9' Died: seqret terminated: Bad value for '-sequence' with -auto defined seqret exited with > status 1.. I replied to this messages off-list, but it describes a fairly common problem (that will be dealt with when I bring the GUI up to speed for EMBOSS 2.8.0), so I thought I'd reply here, too. The problem in this case is that the getz application is not in the GUI's PATH. There are two solutions: 1) soft link whatever application you need to the directory containing the rest of the EMBOSS applications; 2) edit the statement on or about line 151 of GUI.pm and add the required directory to the GUI's PATH. The statement in question looks like this: $ENV{'PATH'} = "$EMBOSS_BIN:/bin"; To add another directory, simply append it to the colon-separated list on the right hand side of the assignment. For example, if getz were installed as /usr/bin/getz, you would edit the above statement to look like this: $ENV{'PATH'} = "$EMBOSS_BIN:/bin:/usr/bin"; This solution applies to the SRS problem mentioned by the OP above, as well as to a similar problem where emma fails to work because it can't find clustalw. Cheers, Luke -- Luke McCarthy Research Officer, Bioinformatics Department of Computer Science University of Saskatchewan mccarthy at cs.usask.ca From stefanielager at fastmail.ca Fri Oct 24 12:36:32 2003 From: stefanielager at fastmail.ca (Stefanie Lager) Date: Fri, 24 Oct 2003 08:36:32 -0400 (EDT) Subject: [EMBOSS] question EMBOSS-GUI Message-ID: <3F991CD0.000035.01708@ns.interchange.ca> SRS is set up for the user that runs EMBOSS on command line, while SRS is NOT set up for the user (nobody) that runs through the web interface. If you have SRS running as web interface you can use method: srswww url: "http://the.adress.to local.SRS.com" Or write a script that calls getz, and sets up SRS and use the script with method: app app: "path/to/the/script " Stefanie > > > > > Hello, > > I don't know if you could help me with the little problem I have. > > I have installed your EMBOSS-GUI application on our server a few > month ago. And it works great. > Since I have installed SRS on our servern. I have mofified the > emboss.default in order to use to the SRS indexes. > Now it looks like : > > DB TREMBL [ > methodquery: srs > format: SWISS > type: P > comment: "TREMBL (SPTREMBL + TREMBLNEW) using SRS" > app: getz > dbalias: TREMBL > methodall: direct > file: "trembl.dat" > dir: $emboss_data_dir/swall > ] > > > > > And that works quitr well on command line, when I need to retrieve > a sequence with seqret for example. But if I am using the > EMBOSS-GUI interface I just obtain the following errror message: > > EMBOSS An error in ajfile.c at line 145: execvp ('getz -e > '[TREMBL-id:Q977L9]'', NULL) failed: 'No such file or directory' > Error: Unable to read sequence 'TREMBL-id:Q977L9' Died: seqret > terminated: Bad value for '-sequence' with -auto defined seqret > exited with status 1... > > Do you have a clue for the problem ? > > Thanks in advance > > Best regards. > > > > > > > > Yann-Fran?ois BIZOUERNE > BioInformatic Team > BAYER CropScience > 1, rue Pierre Fontaine > 91058 Evry Cedex > FRANCE > Phone: 33-(0) 1-69-47-61-56 > FAX: 33-(0) 1-69-47-61-42 > E-mail: yann-francois.bizouerne at bayercropscience.com > Intranet: http://bioinfo.evry.fr.bayercropscience/ _________________________________________________________________ http://fastmail.ca/ - Fast Secure Web Email for Canadians From kmr at sanger.ac.uk Wed Oct 29 13:37:32 2003 From: kmr at sanger.ac.uk (Kim Rutherford) Date: Wed, 29 Oct 2003 13:37:32 +0000 Subject: [EMBOSS] Suggested change to seqretsplit Message-ID: <16287.49820.155450.529600@pcs2e.internal.sanger.ac.uk> Hi. Can I suggest this following change to seqretsplit.acd to allow features to be retained (with the -feature flag) when using seqretsplit: *** seqretsplit.acd 2003/10/06 08:52:50 1.9 --- seqretsplit.acd 2003/10/29 13:19:58 *************** *** 9,16 **** --- 9,22 ---- type: "page" ] + boolean: feature [ + default: "N" + information: "Use feature information" + ] + seqall: sequence [ parameter: "Y" + features: "$(feature)" type: "gapany" ] *************** *** 35,40 **** --- 41,47 ---- seqoutall: outseq [ parameter: "Y" ossingle: "Y" + features: "$(feature)" ] endsection: output It seems to work fine for me. Kim. From pmr at ebi.ac.uk Wed Oct 29 13:48:43 2003 From: pmr at ebi.ac.uk (pmr at ebi.ac.uk) Date: Wed, 29 Oct 2003 13:48:43 -0000 (GMT) Subject: [EMBOSS] Suggested change to seqretsplit In-Reply-To: <16287.49820.155450.529600@pcs2e.internal.sanger.ac.uk> References: <16287.49820.155450.529600@pcs2e.internal.sanger.ac.uk> Message-ID: <1228.217.134.9.58.1067435323.squirrel@webmail.ebi.ac.uk> > Hi. Can I suggest this following change to seqretsplit.acd to allow > features to be retained (with the -feature flag) when using > seqretsplit: Yes indeed!!! And we should look for any other programs that read in and write a sequence in case they could use features too. For some programs there is an issue in how the features get split, so it may not be until 2.9.0 that we have the full set. Seqretsplit is an easy one to do. regards, Peter Rice