From shrish at ccmb.res.in Tue Jan 9 05:36:17 2007 From: shrish at ccmb.res.in (Shrish Tiwari) Date: Tue, 9 Jan 2007 16:06:17 +0530 (IST) Subject: [EMBOSS] (no subject) Message-ID: <18119340.1168338977168.JavaMail.root@mailserver> An embedded and charset-unspecified text was scrubbed... Name: not available Url: http://lists.open-bio.org/pipermail/emboss/attachments/20070109/d1681de2/attachment.pl From Squig at web.de Mon Jan 15 06:19:13 2007 From: Squig at web.de (Squig at web.de) Date: Mon, 15 Jan 2007 12:19:13 +0100 Subject: [EMBOSS] EMBOSS 4.0 and libnucleus.so.4 Message-ID: <1056759432@web.de> Hello, I just installed EMBOSS 4.0 on my system and wanted to run a few tests if everything is working right. Every tool I tried ends up with following message: splitter: error while loading shared libraries: libnucleus.so.4: cannot open shared object file: No such file or directory The binaries are loacted in "/usr/local/bin" and the libaries in "/usr/local/lib". There are also these "libnucleus" files and symlinks: libnucleus.a libnucleus.la libnucleus.so -> libnucleus.so.4.0.0 libnucleus.so.4 -> libnucleus.so.4.0.0 libnucleus.so.4.0.0 Do I oversee some more symlinks to add? Some hint or help would be really appreciated. With kind regards Stefan Kesberg _______________________________________________________________________ Viren-Scan f?r Ihren PC! Jetzt f?r jeden. Sofort, online und kostenlos. Gleich testen! http://www.pc-sicherheit.web.de/freescan/?mc=022222 From Squig at web.de Mon Jan 15 08:21:23 2007 From: Squig at web.de (Squig at web.de) Date: Mon, 15 Jan 2007 14:21:23 +0100 Subject: [EMBOSS] EMBOSS 4.0 and libnucleus.so.4 Message-ID: <1057011473@web.de> Hello, Using "ldd" shows that there were some dynamic libaries unknow. I added their path to "ld.so.conf" and restarted the system. Now everything works fine :) Thank you. With kind regards Stefan Kesberg _______________________________________________________________________ Viren-Scan f?r Ihren PC! Jetzt f?r jeden. Sofort, online und kostenlos. Gleich testen! http://www.pc-sicherheit.web.de/freescan/?mc=022222 From pmr at ebi.ac.uk Mon Jan 15 15:52:03 2007 From: pmr at ebi.ac.uk (pmr at ebi.ac.uk) Date: Mon, 15 Jan 2007 20:52:03 -0000 (GMT) Subject: [EMBOSS] emboss-bug list and Debian 2.0 on IBM T22 In-Reply-To: <20070115192119.907C087049@webmail223.herald.ox.ac.uk> References: <20070115192119.907C087049@webmail223.herald.ox.ac.uk> Message-ID: <3884.86.133.34.142.1168894323.squirrel@webmail.ebi.ac.uk> Dear Robert, > NB. My email to: emboss_bug at emboss.open-bio.org did not get transmitted, > isn't > there anyone there anymore? Anyway, I hope I can get help at this address Yes we are here. The list address is emboss-bug (dash, not underscore). But we have had very few messages on the emboss-bug list in the past month. Has anyone else had error messages (or not had a reply from us) from an emboss-bug message? > I got a rather disagreeable rejection message when I sent this to > emboss at emboss.open-bio.org Hmm .... this one did get through to the emboss list. > Dear Emboss_support > > I have tried and failed to install Emboss (on an IBM T22 laptop running > under > Debian 2.0). > > The config* files and the error messages from 'make' are attached. The files seem to be corrupted ... only the config.log file looked right, so I cannot see the error message(s). > PS. I will also attempt to compile under cygwin on another machine. Wish > me > luck! good luck! regards, Peter Rice From shrish at ccmb.res.in Tue Jan 16 06:56:55 2007 From: shrish at ccmb.res.in (Shrish Tiwari) Date: Tue, 16 Jan 2007 17:26:55 +0530 (IST) Subject: [EMBOSS] extracting 3' UTRs Message-ID: <12502499.1168948615113.JavaMail.root@mailserver> An embedded and charset-unspecified text was scrubbed... Name: not available Url: http://lists.open-bio.org/pipermail/emboss/attachments/20070116/734a50ae/attachment.pl From jison at ebi.ac.uk Tue Jan 16 09:49:53 2007 From: jison at ebi.ac.uk (Jon Ison) Date: Tue, 16 Jan 2007 14:49:53 -0000 (GMT) Subject: [EMBOSS] extracting 3' UTRs In-Reply-To: <12502499.1168948615113.JavaMail.root@mailserver> References: <12502499.1168948615113.JavaMail.root@mailserver> Message-ID: <49980.84.92.187.247.1168958993.squirrel@webmail.ebi.ac.uk> Hi Shrish So far as I know, not directly, but it's easily done using a combination of e.g. coderet, getorf, plotorf and seqret. Should be obvious from the documentation, e.g. http://emboss.sourceforge.net/apps/cvs/index.html http://emboss.sourceforge.net/docs/emboss_tutorial/node4.html If you envisage a single tool for your task, please let us know to emboss-bug at emboss.open-bio.org please) Cheers Jon > Hi! > Is there a way to extract 3' UTRs using EMBOSS programs? > Shrish > Dr. Shrish Tiwari > E503, Centre for Cellular and Molecular Biology > Uppal Road, Hyderabad - 500 007, INDIA > Phone: 91-40-27192777 > Alternate email: shrish.geo at yahoo.com > _______________________________________________ > EMBOSS mailing list > EMBOSS at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/emboss > From David.Bauer at SCHERING.DE Tue Jan 16 10:44:23 2007 From: David.Bauer at SCHERING.DE (David.Bauer at SCHERING.DE) Date: Tue, 16 Jan 2007 16:44:23 +0100 Subject: [EMBOSS] extracting 3' UTRs In-Reply-To: <49980.84.92.187.247.1168958993.squirrel@webmail.ebi.ac.uk> Message-ID: Hi Shrish, in principle this would be an easy task for 'extractfeat' because the EMBL feature table definition contains also the feature key "3' UTR". But nearly nobody uses this feature key in praxi. So I would use coderet to look for the end of a CDS and then extract the remaining part with seqret. or extractseq. It will be straightforward for single mRNA entries with one CDS. If you want to do this on a genome level, you should take a look at Ensembl (www.ensembl.org) and the Mart interface. There you can extract 3'UTR. But from my experience the annotation of UTRs is very incomplete so don't expect to get something comprehensive with these methods. HTH, David. emboss-bounces at lists.open-bio.org schrieb am 16/01/2007 15:49:53: > Hi Shrish > > So far as I know, not directly, but it's easily done using a combination > of e.g. coderet, getorf, plotorf and seqret. > > Should be obvious from the documentation, e.g. > http://emboss.sourceforge.net/apps/cvs/index.html > http://emboss.sourceforge.net/docs/emboss_tutorial/node4.html > > If you envisage a single tool for your task, please let us know to > emboss-bug at emboss.open-bio.org please) > > Cheers > > Jon > > > > > > Hi! > > Is there a way to extract 3' UTRs using EMBOSS programs? > > Shrish > > Dr. Shrish Tiwari > > E503, Centre for Cellular and Molecular Biology > > Uppal Road, Hyderabad - 500 007, INDIA > > Phone: 91-40-27192777 > > Alternate email: shrish.geo at yahoo.com > > _______________________________________________ > > EMBOSS mailing list > > EMBOSS at lists.open-bio.org > > http://lists.open-bio.org/mailman/listinfo/emboss > > > > > _______________________________________________ > EMBOSS mailing list > EMBOSS at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/emboss From maoj at helix.nih.gov Tue Jan 16 13:14:15 2007 From: maoj at helix.nih.gov (Jean Mao) Date: Tue, 16 Jan 2007 13:14:15 -0500 Subject: [EMBOSS] bug in restrict? Message-ID: <000001c7399a$222f71f0$be4de780@CIT.NIH.GOV> I used est:af436075 and run 'restrict' program in EMBOSS. One of the enzyme which cut this sequence is called 'Tth111II' . When using 'redata' program to search for this enzyme, result shows this is from unpublished observations. Since the default of 'restrict' is to search enzymes that is only commercially available, I think the appearance of 'Tth111II' is a bug. Please advise. Thanks. Jean Mao From maoj at helix.nih.gov Tue Jan 16 13:41:43 2007 From: maoj at helix.nih.gov (Jean Mao) Date: Tue, 16 Jan 2007 13:41:43 -0500 Subject: [EMBOSS] Bug in 'remap' program? Message-ID: <000501c7399d$f7da5c40$be4de780@CIT.NIH.GOV> Hi, I used genbank:A00006 sequence to run 'remap' program in emboss. Among the Enzymes that cut, BmgT120I , FmuI , PabI , TspRI , UnbI does not show any Isoschizomers. However, they all have Isoschizomers based on the 'redata' program'. One thing they have in common is that they don't exist in the embossre.equ file. All of them exist in withrefm file. All of them except 'TspRI' exist in proto file. How can I make the rebaseextract program work the way that they will show their Isoschizomers if exist? Thank you. Jean Mao From gbottu at ben.vub.ac.be Wed Jan 17 03:59:24 2007 From: gbottu at ben.vub.ac.be (Guy Bottu) Date: Wed, 17 Jan 2007 09:59:24 +0100 Subject: [EMBOSS] Bug in 'remap' program? - Checked by AntiVir DEMO version In-Reply-To: <000501c7399d$f7da5c40$be4de780@CIT.NIH.GOV> References: <000501c7399d$f7da5c40$be4de780@CIT.NIH.GOV> Message-ID: <20070117085924.GA2027@bigben.ulb.ac.be> Dear Jean, The program remap by default only outputs one representative member (the prototype) of a series of isoschizomers and it only considers enzymes that have a commercial provider. If you want to see all enzymes you must run remap with parameters -nolimit -nocommercial. Regards, Guy Bottu, Belgian EMBnet Node From maoj at helix.nih.gov Wed Jan 17 08:30:45 2007 From: maoj at helix.nih.gov (Jean Mao) Date: Wed, 17 Jan 2007 08:30:45 -0500 Subject: [EMBOSS] Bug in 'remap' program? - Checked by AntiVir DEMO version In-Reply-To: <20070117085924.GA2027@bigben.ulb.ac.be> References: <000501c7399d$f7da5c40$be4de780@CIT.NIH.GOV> <20070117085924.GA2027@bigben.ulb.ac.be> Message-ID: <000a01c73a3b$b15dbb60$be4de780@CIT.NIH.GOV> Hi Guy, There has inconsistency in the result I get. You may want to run remap with the sequence I provide below to see the problem. on the commend line, I run : % remap -opt accept all the default using the file provided below, part of the output file look like this (which I don't see when not using -opt flag, why?) : =============================================================== # Enzymes that cut Frequency Isoschizomers AluI 1 MltI ApaI 1 PpeI AsuI 2 AspS9I,AvcI,Bac36I,Bal228I,BavAII,BavBII,Bce22I,BshKI,BsiZI,Bsp1894I,BspBII, BspF4I,Bsu54I,CcuI,Cfr13I,MaeK81 II,Nsp7121I,NspIV,Pde12I,PspPI,Sau96I BfiI 1 BmrI,BmuI BmgT120I 2 BseSI 1 Bme1580I BsiYI 1 BflI,Bsc107I,Bsc4I,BseLI,AfiI,BslI,Bst22I Bsp120I 1 PspOMI BsrI 1 BseNI,Bse1I,BsrSI,Bst11I,Tsp1I Csp6I 1 CviQI,CviRII CviJI 2 CviKI,CviKI-1 CviRI 1 HpyCH4V,HpyF44III DraII 1 EcoO109I FmuI 2 HaeIII 1 BecAII,Bim19II,Bme361I,BseQI,BshFI,BshI,BsnI,Bsp211I,BspANI,BspBRI,BspKI,Bsp RI,BsuRI,BteI,CltI,DsaII,EsaBC4I ,FnuDI,BanAI,MchAII,MfoAI,NgoPII,NspLKI,PalI,Pde133I,PflKI,PhoI,PlaI,Pru2I,S bvI,SfaI,SuaI HgiJII 1 BpuI,Bsp519I,Bsu1854I,BvuI,Eco24I,Eco75KI,EcoT38I,FriOI,BanII,KoxII,PaeHI,Sa cNI Hpy8I 1 HpyBII Kaz48kI 1 PssI NlaIV 1 BmiI,BscBI,BspLI,AspNI,PspN4I PabI 1 RsaI 1 HpyBI,PlaAII,AfaI SduI 1 BmyI,BsoCI,Bsp1286I,BspLS2I,MhlI,NspII,AocII TspRI 1 UnbI 2 ========================================================================== As you can see, 6 enzymes show NO isoschizomers. I assume all of them have commercial supplier(s) since I accept the default setting. However, using 'redata' program in EMBOSS on these 6 enzymers, some of them DO have isoschizomers but the field was left blank. In addition, some of them has NO suppliers listed which is not suppose to appear when I use the default settings, isn't it? Thank you in advance. ================= Sequence I Used ============================================= !!NA_SEQUENCE 1.0 LOCUS A00006 26 bp DNA linear PAT 10-FEB-1993 DEFINITION Artificial oligonucleotide sequence (Fra 3), sequence 5 from patent application EP0238993. ACCESSION A00006 VERSION A00006.1 GI:57973 KEYWORDS . SOURCE synthetic construct ORGANISM synthetic construct other sequences; artificial sequences. REFERENCE 1 (bases 1 to 26) AUTHORS Auerswald,E.A., Schroeder,W., Schnabel,E., Bruns,W., Reinhardt,G. and Kotick,M. TITLE Aprotinin homologues produced by genetic engineering JOURNAL Patent: EP 0238993-A 5 30-SEP-1987; BAYER AG FEATURES Location/Qualifiers source 1. .26 /organism="synthetic construct" /mol_type="unassigned DNA" /db_xref="taxon:32630" ORIGIN A00006 Length: 26 January 11, 2007 09:44 Type: N Check: 4746 .. 1 CGCCGTACAC TGGGCCCTGC AAAGCT -----Original Message----- From: Guy Bottu [mailto:gbottu at ben.vub.ac.be] Sent: 2007?1?17? 3:59 To: Jean Mao Cc: emboss at lists.open-bio.org Subject: Re: [EMBOSS] Bug in 'remap' program? - Checked by AntiVir DEMO version Dear Jean, The program remap by default only outputs one representative member (the prototype) of a series of isoschizomers and it only considers enzymes that have a commercial provider. If you want to see all enzymes you must run remap with parameters -nolimit -nocommercial. Regards, Guy Bottu, Belgian EMBnet Node From gbottu at ben.vub.ac.be Thu Jan 18 04:05:27 2007 From: gbottu at ben.vub.ac.be (Guy Bottu) Date: Thu, 18 Jan 2007 10:05:27 +0100 Subject: [EMBOSS] Bug in 'remap' program? - Checked by AntiVir DEMO version In-Reply-To: <416B9A34D7CA1C4C9ED58354E75101BB021CB2EC@NIHCESMLBX3.nih.gov> References: <000501c7399d$f7da5c40$be4de780@CIT.NIH.GOV> <20070117085924.GA2027@bigben.ulb.ac.be> <000a01c73a3b$b15dbb60$be4de780@CIT.NIH.GOV> <20070117164311.GA8769@bigben.ulb.ac.be> <416B9A34D7CA1C4C9ED58354E75101BB021CB2EC@NIHCESMLBX3.nih.gov> Message-ID: <20070118090527.GA22252@bigben.ulb.ac.be> On Wed, Jan 17, 2007 at 12:07:31PM -0500, Mao, Jean (NIH/CIT) [E] wrote: > How about BmgT120I, based on the 'redata' program, it has isoschizomers, but non was listed in my output. > UnbI has isoschizomers also and has NO commercial provider listed. You have indeed pinpointed a bug or misfeature. The problem might be that the prototype enzyme is AsuI. But AsuI has no commercial providers. It is more easy to see this in our MRS server than using redata : http://bendisk.ulb.ac.be/mrs/cgi-bin/mrs.cgi?db=rebase&query=BmgT120I So, several isoschizomers of AsuI are displayed in the output instead of just one enzyme. Could Alan Bleasby comment about this ? Guy Bottu, BEN From ajb at ebi.ac.uk Thu Jan 18 04:47:20 2007 From: ajb at ebi.ac.uk (ajb at ebi.ac.uk) Date: Thu, 18 Jan 2007 09:47:20 -0000 (GMT) Subject: [EMBOSS] Bug in 'remap' program? - Checked by AntiVir DEMO version In-Reply-To: <20070118090527.GA22252@bigben.ulb.ac.be> References: <000501c7399d$f7da5c40$be4de780@CIT.NIH.GOV> <20070117085924.GA2027@bigben.ulb.ac.be> <000a01c73a3b$b15dbb60$be4de780@CIT.NIH.GOV> <20070117164311.GA8769@bigben.ulb.ac.be> <416B9A34D7CA1C4C9ED58354E75101BB021CB2EC@NIHCESMLBX3.nih.gov> <20070118090527.GA22252@bigben.ulb.ac.be> Message-ID: <56655.81.98.244.247.1169113640.squirrel@webmail.ebi.ac.uk> Hi Jean, Guy, > Could Alan Bleasby comment about this ? I'm currently looking at that area of the code (for restrict). I suspect that it is just a problem with the positioning of the commercial availability test. Alan From maoj at helix.nih.gov Thu Jan 18 09:14:20 2007 From: maoj at helix.nih.gov (Jean Mao) Date: Thu, 18 Jan 2007 09:14:20 -0500 Subject: [EMBOSS] question using 'matpatmotifs' Message-ID: <000b01c73b0a$f2bd6a40$be4de780@CIT.NIH.GOV> Hi, I used 'swissprot:hair_drome' as input sequence and run 'matpatmotifs' in EMBOSS and got 0 hits. However, when I used the same input sequnce on interproscan, the result (http://www.ebi.ac.uk/cgi-bin/iprscan/iprscan?tool=iprscan&jobid=iprscan-200 70118-14025926) show that it contains basic Helix-loop-helix motif which is ID PS50888 in prosite database. Is this a bug or did I do something wrong? I also run the same sequence against the 'motifs' program in GCG package. Again no hit was found. Thank you. Jean Mao From ajb at ebi.ac.uk Thu Jan 18 09:42:44 2007 From: ajb at ebi.ac.uk (ajb at ebi.ac.uk) Date: Thu, 18 Jan 2007 14:42:44 -0000 (GMT) Subject: [EMBOSS] question using 'matpatmotifs' In-Reply-To: <000b01c73b0a$f2bd6a40$be4de780@CIT.NIH.GOV> References: <000b01c73b0a$f2bd6a40$be4de780@CIT.NIH.GOV> Message-ID: <39856.81.98.244.247.1169131364.squirrel@webmail.ebi.ac.uk> Hi Jean, It is more like a feature. PS50888 is a matrix and patmatmotifs doesn't deal with that type of PROSITE entry - it just compares the pattern string entries. Alan > Hi, > > I used 'swissprot:hair_drome' as input sequence and run 'matpatmotifs' in > EMBOSS and got 0 hits. However, when I used the same input sequnce on > interproscan, the result > (http://www.ebi.ac.uk/cgi-bin/iprscan/iprscan?tool=iprscan&jobid=iprscan-200 > 70118-14025926) show that it contains basic Helix-loop-helix motif which > is > ID PS50888 in prosite database. Is this a bug or did I do something wrong? > I > also run the same sequence against the 'motifs' program in GCG package. > Again no hit was found. > > Thank you. > > Jean Mao > _______________________________________________ > EMBOSS mailing list > EMBOSS at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/emboss > From gbottu at ben.vub.ac.be Thu Jan 18 10:04:31 2007 From: gbottu at ben.vub.ac.be (Guy Bottu) Date: Thu, 18 Jan 2007 16:04:31 +0100 Subject: [EMBOSS] question using 'matpatmotifs' - Checked by AntiVir DEMO ve In-Reply-To: <000b01c73b0a$f2bd6a40$be4de780@CIT.NIH.GOV> References: <000b01c73b0a$f2bd6a40$be4de780@CIT.NIH.GOV> Message-ID: <20070118150431.GA28210@bigben.ulb.ac.be> On Thu, Jan 18, 2007 at 09:14:20AM -0500, Jean Mao wrote: > I used 'swissprot:hair_drome' as input sequence and run 'matpatmotifs' in > EMBOSS and got 0 hits. However, when I used the same input sequnce on > interproscan, the result > (http://www.ebi.ac.uk/cgi-bin/iprscan/iprscan?tool=iprscan&jobid=iprscan-200 > 70118-14025926) show that it contains basic Helix-loop-helix motif which is > ID PS50888 in prosite database. Is this a bug or did I do something wrong? I > also run the same sequence against the 'motifs' program in GCG package. > Again no hit was found. The reason is that GCG motifs and EMBOSS patmatmotif search only the PROSITE entries of type "pattern", while PS50888 is of type "matrix". If you want to search the complete PROSITE (patterns+matrices+rules), you can download the ps_scan script from ftp://ftp.expasy.org/databases/prosite/tools/ps_scan/sources and the pftools package from ftp://ftp.isrec.isb-sib.ch/pub/sib-isrec/pftools/pft2.3 You can run this under EMBOSS with the wrappers4EMBOSS package (http://wemboss.sourceforge.net/). Hope this helps, Guy Bottu, BEN From David.Bauer at SCHERING.DE Thu Jan 18 09:58:09 2007 From: David.Bauer at SCHERING.DE (David.Bauer at SCHERING.DE) Date: Thu, 18 Jan 2007 15:58:09 +0100 Subject: [EMBOSS] Antwort: question using 'matpatmotifs' In-Reply-To: <000b01c73b0a$f2bd6a40$be4de780@CIT.NIH.GOV> Message-ID: Hi Jean, this is an old problem with patmatmotifs. This program makes use only of the traditonal Prosite patterns and unfortunately can not handle the newer type Prosite matrix entries. Cheers, David. emboss-bounces at lists.open-bio.org schrieb am 18/01/2007 15:14:20: > Hi, > > I used 'swissprot:hair_drome' as input sequence and run 'matpatmotifs' in > EMBOSS and got 0 hits. However, when I used the same input sequnce on > interproscan, the result > (http://www.ebi.ac.uk/cgi-bin/iprscan/iprscan?tool=iprscan&jobid=iprscan-200 > 70118-14025926) show that it contains basic Helix-loop-helix motif which is > ID PS50888 in prosite database. Is this a bug or did I do something wrong? I > also run the same sequence against the 'motifs' program in GCG package. > Again no hit was found. > > Thank you. > > Jean Mao > _______________________________________________ > EMBOSS mailing list > EMBOSS at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/emboss From maoj at helix.nih.gov Thu Jan 18 14:05:51 2007 From: maoj at helix.nih.gov (Jean Mao) Date: Thu, 18 Jan 2007 14:05:51 -0500 Subject: [EMBOSS] about 'helixturnhelix'e Message-ID: <001001c73b33$abca20f0$be4de780@CIT.NIH.GOV> Now that I know the reason why patmatmotifs can't find HTH in my hair_drome input sequence, I would like to know what program in EMBOSS package CAN find it in my sequence. I tried helixturnhelix but still it couldn't find it. Does helixturnhelix using matrix or motif? looks like matrix to me in the documentation. Please advise. Thank you very much! Jean From pmr at ebi.ac.uk Thu Jan 18 18:02:15 2007 From: pmr at ebi.ac.uk (pmr at ebi.ac.uk) Date: Thu, 18 Jan 2007 23:02:15 -0000 (GMT) Subject: [EMBOSS] about 'helixturnhelix'e In-Reply-To: <001001c73b33$abca20f0$be4de780@CIT.NIH.GOV> References: <001001c73b33$abca20f0$be4de780@CIT.NIH.GOV> Message-ID: <1771.86.141.183.176.1169161335.squirrel@webmail.ebi.ac.uk> Hi Jean, > Now that I know the reason why patmatmotifs can't find HTH in my > hair_drome > input sequence, I would like to know what program in EMBOSS package CAN > find > it in my sequence. I tried helixturnhelix but still it couldn't find it. > Does helixturnhelix using matrix or motif? looks like matrix to me in the > documentation. Please advise. helixturnhelix uses a matrix, but it is quite an old one from the days when there were only about 20 HTH examples (and 2 of them were wrong). We will look at ways to use the prosite matrix entries. regards, Peter From pmr at ebi.ac.uk Fri Jan 19 10:49:04 2007 From: pmr at ebi.ac.uk (pmr at ebi.ac.uk) Date: Fri, 19 Jan 2007 15:49:04 -0000 Subject: [EMBOSS] Question regarding dbxflat entry number processed In-Reply-To: <000a01c71946$94beb600$be4de780@CIT.NIH.GOV> References: <000a01c71946$94beb600$be4de780@CIT.NIH.GOV> Message-ID: <13132.193.173.109.1.1165419569.squirrel@webmail.ebi.ac.uk> Hi Jean, > Hi, I am using dbxflat to index a database. I would like to find out how > many entries were processed. In the index file database.pxid, there is a > line : > > Count 123456 > > which is very close to the number of entries in the database file but not > exact the same. Is there a way to find out? Thank you very much. The count should be the number of IDs found. Do you perhaps have some duplicate IDs? regards, Peter From rls at ebi.ac.uk Fri Jan 19 10:49:45 2007 From: rls at ebi.ac.uk (Rodrigo Lopez) Date: Fri, 19 Jan 2007 15:49:45 -0000 Subject: [EMBOSS] Output from seqret in fastaformat. In-Reply-To: <934F95E71B6C9347A873C42AE3C196190B84C672@NZT0004E.dknz.nzcorp.net> References: <934F95E71B6C9347A873C42AE3C196190B84C672@NZT0004E.dknz.nzcorp.net> Message-ID: <4576C594.3080609@ebi.ac.uk> Hi, Use -osdbname UNIPROT in the command line. R:) JK (Jesper Agerbo Krogh) wrote: > Hi.. > > I've godt dbxflat to index the swissprot database.. but I'd like to have the output > formatted with the USA as the fasta ID. > > Current..: > > seqret UNIPROT:Q12345 > Reads and writes (returns) sequences > output sequence(s) [ies3_yeast.fasta]: > >> IES3_YEAST Q12345 Ino eighty subunit 3. > MKFEDLLATNKQVQFAHAATQHYKSVKTPDFLEKDPHHKKFHNADGLNQQGSSTPSTATD > ANAASTASTHTNTTTFKRHIVAVDDISKMNYEMIKNSPGNVITNANQDEIDISTLKTRLY > KDNLYAMNDNFLQAVNDQIVTLNAAEQDQETEDPDLSDDEKIDILTKIQENLLEEYQKLS > QKERKWFILKELLLDANVELDLFSNRGRKASHPIAFGAVAIPTNVNANSLAFNRTKRRKI > NKNGLLENIL > > .. but I'd like.. > >> UNIPROT:Q12345 Ino eighty subunit 3. > MKFEDLLATNKQVQFAHAATQHYKSVKTPDFLEKDPHHKKFHNADGLNQQGSSTPSTATD > ANAASTASTHTNTTTFKRHIVAVDDISKMNYEMIKNSPGNVITNANQDEIDISTLKTRLY > KDNLYAMNDNFLQAVNDQIVTLNAAEQDQETEDPDLSDDEKIDILTKIQENLLEEYQKLS > QKERKWFILKELLLDANVELDLFSNRGRKASHPIAFGAVAIPTNVNANSLAFNRTKRRKI > NKNGLLENIL > > Is that possible? > > From pmr at ebi.ac.uk Fri Jan 19 10:54:41 2007 From: pmr at ebi.ac.uk (pmr at ebi.ac.uk) Date: Fri, 19 Jan 2007 15:54:41 -0000 Subject: [EMBOSS] Output from seqret in fastaformat. In-Reply-To: <934F95E71B6C9347A873C42AE3C196190B84C672@NZT0004E.dknz.nzcorp.net> References: <934F95E71B6C9347A873C42AE3C196190B84C672@NZT0004E.dknz.nzcorp.net> Message-ID: <14850.193.173.109.1.1165419775.squirrel@webmail.ebi.ac.uk> Hi Jesper, > I've godt dbxflat to index the swissprot database.. but I'd like to have > the output > formatted with the USA as the fasta ID. > > Current..: > > seqret UNIPROT:Q12345 > Reads and writes (returns) sequences > output sequence(s) [ies3_yeast.fasta]: > >>IES3_YEAST Q12345 Ino eighty subunit 3. > MKFEDLLATNKQVQFAHAATQHYKSVKTPDFLEKDPHHKKFHNADGLNQQGSSTPSTATD > ANAASTASTHTNTTTFKRHIVAVDDISKMNYEMIKNSPGNVITNANQDEIDISTLKTRLY > KDNLYAMNDNFLQAVNDQIVTLNAAEQDQETEDPDLSDDEKIDILTKIQENLLEEYQKLS > QKERKWFILKELLLDANVELDLFSNRGRKASHPIAFGAVAIPTNVNANSLAFNRTKRRKI > NKNGLLENIL > > .. but I'd like.. > >>UNIPROT:Q12345 Ino eighty subunit 3. > MKFEDLLATNKQVQFAHAATQHYKSVKTPDFLEKDPHHKKFHNADGLNQQGSSTPSTATD > ANAASTASTHTNTTTFKRHIVAVDDISKMNYEMIKNSPGNVITNANQDEIDISTLKTRLY > KDNLYAMNDNFLQAVNDQIVTLNAAEQDQETEDPDLSDDEKIDILTKIQENLLEEYQKLS > QKERKWFILKELLLDANVELDLFSNRGRKASHPIAFGAVAIPTNVNANSLAFNRTKRRKI > NKNGLLENIL > > Is that possible? Tricky to do. Q12345 is not the sequence ID, it is only the accession number. There are ways to rewrite UNiProt as a FASTA format file and index with dbxfasta but that loses the rest of the information in the entries. A simple perl script to rearrange the ID lines is your easiest solution. Alternativelyj, you could invent a new EMBOSS output format that uses the DBname and accession to create the ID. But EMBOSS would still want to write to a file called "ies3_yeast.*" because it uses the ID to make up the default filename. If you insist, you can try: seqret UNIPROT:Q12345 -sid Q12345 -osdbname UNIPROT which gives me the result you expect with the current developers code (I am away from the office todaty, and there have been changes to the way database names are propagated to the output so release 4.0.0 may behave slightly differently). Hope that helps Peter From ajb at ebi.ac.uk Fri Jan 19 11:22:07 2007 From: ajb at ebi.ac.uk (ajb at ebi.ac.uk) Date: Fri, 19 Jan 2007 16:22:07 -0000 (GMT) Subject: [EMBOSS] Explanation: time-warped messages Message-ID: <40703.81.98.244.247.1169223727.squirrel@webmail.ebi.ac.uk> Apologies for all the time-warped messages that have been appearing on this list over the last day or two. There has been a long-standing problem (from early December) with the EBI's email setup in that it didn't always respond correctly to the anti-spam mechanisms on the open-bio email lists. This was fixed by the EBI Systems group this week. So, some messages sent by EBI staff are just getting through. Alan From mathog at caltech.edu Fri Jan 19 11:19:44 2007 From: mathog at caltech.edu (David Mathog) Date: Fri, 19 Jan 2007 08:19:44 -0800 Subject: [EMBOSS] Output from seqret in fastaformat Message-ID: Peter Rice wrote: > "JK (Jesper Agerbo Krogh)" I'm with Peter on this one. There are way too many possible formats for fasta comment lines for any software to support all of them. This command line reformatting is exactly the sort of task my 'extract' program was written to handle (having faced the same task myself more times than I can count). Example: % cat >foo.pfa <IES3_YEAST Q12345 Ino eighty subunit 3. MKFEDLLATNKQVQFAHAATQHYKSVKTPDFLEKDPHHKKFHNADGLNQQGSSTPSTATD ANAASTASTHTNTTTFKRHIVAVDDISKMNYEMIKNSPGNVITNANQDEIDISTLKTRLY KDNLYAMNDNFLQAVNDQIVTLNAAEQDQETEDPDLSDDEKIDILTKIQENLLEEYQKLS QKERKWFILKELLLDANVELDLFSNRGRKASHPIAFGAVAIPTNVNANSLAFNRTKRRKI NKNGLLENIL EOD % cat foo.pfa | extract -if '>' -mt -cols 'UNIPROT:[2,]' UNIPROT:Q12345 Ino eighty subunit 3. MKFEDLLATNKQVQFAHAATQHYKSVKTPDFLEKDPHHKKFHNADGLNQQGSSTPSTATD ANAASTASTHTNTTTFKRHIVAVDDISKMNYEMIKNSPGNVITNANQDEIDISTLKTRLY KDNLYAMNDNFLQAVNDQIVTLNAAEQDQETEDPDLSDDEKIDILTKIQENLLEEYQKLS QKERKWFILKELLLDANVELDLFSNRGRKASHPIAFGAVAIPTNVNANSLAFNRTKRRKI NKNGLLENIL So you can process the whole thing in a pipe or in two stages through a temporary file. Your choice. Extract is part of drm_tools (these have nothing to do with "digital rights management", they were my initials long before drm took on its current common meaning) from here: ftp://saf.bio.caltech.edu/pub/software/linux_or_unix_tools/drm_tools.tar.gz The man page is here: http://saf.caltech.edu/saf_manuals/extract.html Regards, David Mathog mathog at caltech.edu Manager, Sequence Analysis Facility, Biology Division, Caltech From uludag at ebi.ac.uk Mon Jan 22 10:42:32 2007 From: uludag at ebi.ac.uk (Mahmut Uludag) Date: Mon, 22 Jan 2007 15:42:32 +0000 Subject: [EMBOSS] workflow ideas Message-ID: <1169480552.4118.80.camel@emboss2.ebi.ac.uk> Hi, We have recently extended the EBI Soaplab server by new webservices for EMBOSS 4.0 applications including the EMBASSY applications, and made it publicly available through the following address. http://www.ebi.ac.uk/soaplab/emboss4/index.html We are now in the process of building Taverna workflows to demonstrate use cases for these services. We need ideas for these use cases. If you have any use case ideas for EMBOSS services you or your colleagues would use in the future and would like us to prepare workflow(s) for those use cases please email me with a brief description then I will prepare workflow(s) for your use case(s). These workflows will later be published from a public repository. We are also interested in use cases that would include other webservices together with the EMBOSS services, basically to demonstrate the interoperability of the services. Regards, Mahmut From maoj at helix.nih.gov Mon Jan 22 16:52:33 2007 From: maoj at helix.nih.gov (jean mao) Date: Mon, 22 Jan 2007 16:52:33 -0500 Subject: [EMBOSS] question about seqret Message-ID: Hi, I would like to know is there a way I can search all databases available for one accession number I have which I don't know what database(s) it belongs to? May I do some configuration in the emboss.default file for that? Thank you very much in advance. Jean From ajb at ebi.ac.uk Mon Jan 22 17:54:49 2007 From: ajb at ebi.ac.uk (ajb at ebi.ac.uk) Date: Mon, 22 Jan 2007 22:54:49 -0000 (GMT) Subject: [EMBOSS] question about seqret In-Reply-To: References: Message-ID: <39293.81.98.244.247.1169506489.squirrel@webmail.ebi.ac.uk> Hello Jean, The EMBOSS application 'whichdb' should do that. Alan > Hi, I would like to know is there a way I can search all databases > available for one accession number I have which I don't know what > database(s) it belongs to? May I do some configuration in the > emboss.default file for that? > > Thank you very much in advance. > > Jean > _______________________________________________ > EMBOSS mailing list > EMBOSS at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/emboss > From maoj at helix.nih.gov Mon Jan 22 19:51:09 2007 From: maoj at helix.nih.gov (jean mao) Date: Mon, 22 Jan 2007 19:51:09 -0500 Subject: [EMBOSS] question about seqret Message-ID: Thank you for your reply. I solved it by using app method and the emboss farm script by Simon Andrews. Jean Mao. From jison at ebi.ac.uk Tue Jan 23 04:47:03 2007 From: jison at ebi.ac.uk (Jon Ison) Date: Tue, 23 Jan 2007 09:47:03 -0000 (GMT) Subject: [EMBOSS] question about seqret In-Reply-To: References: Message-ID: <1186.84.92.187.247.1169545623.squirrel@webmail.ebi.ac.uk> > Thank you for your reply. I solved it > by using app method and the emboss farm script by Simon Andrews. FYI see http://emboss.sourceforge.net/docs/themes/emboss_farm.script Jon From fangw at CLEMSON.EDU Tue Jan 23 10:54:09 2007 From: fangw at CLEMSON.EDU (fangw at CLEMSON.EDU) Date: Tue, 23 Jan 2007 10:54:09 -0500 (EST) Subject: [EMBOSS] question! Message-ID: <3195.130.127.150.224.1169567649.squirrel@wm.clemson.edu> Dear EMBOSS people: I am a Ph.D. student in Clemson University in USA, who is using your EMBOSS software to extract 5' upstream of a list of genes. However, I met some problem when I use EMBOSS: I installed EMBOSS 2.10.0 in on windowsXP PC. However, when I use command "extractfeat genbank:*", it does not work. The error message is "Error:uable to read sequence 'genbank:4101655', Died: extractfeat termined:Bad value for '-sequence' and no prompt". But it work fine with "extractfeat embl:AK222810".Do you know the reason? Is there any way to access ENsembl database. Is there any new version of EMBOSS which could support more databases which could installed in windowsXP? Are all the databases which EMBOSS connected are the latest version? since I found some database do not give the same results as what I get from the database directly. Thanks! I am looking forward to your reply. FANG WANG Department of Genetics and Biochemistry Clemson University From jison at ebi.ac.uk Tue Jan 23 12:31:02 2007 From: jison at ebi.ac.uk (Jon Ison) Date: Tue, 23 Jan 2007 17:31:02 -0000 (GMT) Subject: [EMBOSS] question! In-Reply-To: <3195.130.127.150.224.1169567649.squirrel@wm.clemson.edu> References: <3195.130.127.150.224.1169567649.squirrel@wm.clemson.edu> Message-ID: <48163.84.92.187.247.1169573462.squirrel@webmail.ebi.ac.uk> Dear FANG The error message suggests that EMBOSS has not been configured to work with "genbank". Every database you intend to use must be defined in one of the EMBOSS configuration files "emboss.default" or ".embossrc". "emboss.default" lives in the top-level emboss directory (e.g. /home/auser/emboss/emboss.default) and is used for site-wide databases. ".embossrc" lives in your personal home directory and is used for your own databases (or for testing). Please read the documentation which describes how to configure database access in these files: http://emboss.sourceforge.net/docs/themes/Databases.html http://emboss.sourceforge.net/admin/ Or ask your sysadmin to setup access for you (a better route if the database is a shared resource). So far as I know, EMBOSS cannot read ensembl directly. The answer to your last question is "It depends on which databases your installation is configured to use" (see "emboss.default" and ".embossrc"). Good luck ! Cheers Jon > Dear EMBOSS people: > > I am a Ph.D. student in Clemson University in USA, who is using your > EMBOSS software to extract 5' upstream of a list of genes. However, I met > some problem when I use EMBOSS: > > I installed EMBOSS 2.10.0 in on windowsXP PC. However, when I use command > "extractfeat genbank:*", it does not work. The error message is > "Error:uable to read sequence 'genbank:4101655', Died: extractfeat > termined:Bad value for '-sequence' and no prompt". But it work fine > with "extractfeat embl:AK222810".Do you know the reason? > > Is there any way to access ENsembl database. Is there any new version of > EMBOSS which could support more databases which could installed in > windowsXP? > > Are all the databases which EMBOSS connected are the latest version? since > I found some database do not give the same results as what I get from the > database directly. > > Thanks! > > I am looking forward to your reply. > > FANG WANG > Department of Genetics and Biochemistry > Clemson University > > > > _______________________________________________ > EMBOSS mailing list > EMBOSS at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/emboss > From pmr at ebi.ac.uk Tue Jan 23 12:45:22 2007 From: pmr at ebi.ac.uk (Peter Rice) Date: Tue, 23 Jan 2007 17:45:22 +0000 Subject: [EMBOSS] question! In-Reply-To: <3195.130.127.150.224.1169567649.squirrel@wm.clemson.edu> References: <3195.130.127.150.224.1169567649.squirrel@wm.clemson.edu> Message-ID: <45B649B2.3030000@ebi.ac.uk> Dear Fang, > I installed EMBOSS 2.10.0 in on windowsXP PC. However, when I use command > "extractfeat genbank:*", it does not work. The error message is "Error:uable > to read sequence 'genbank:4101655', Died: extractfeat termined:Bad value for > '-sequence' and no prompt". But it work fine with "extractfeat > embl:AK222810".Do you know the reason? If you used the database definitions provided with EMBOSS ... your genbank is possibly pointing to the CBR server in Canada which has now closed. There is also a problem with the way SRS servers define the GI number - there are now servers that index it, but as "gid" not as "gi" which EMBOSS anticipated. We sill change the field name in the next release of EMBOSS. To test whether yuor genbank definition works, you could try the ID We are now at release 4.0.0 which allows "gi" as a search field. Earlier versions only had "sv" (sequence version) ... whether that is indexed depends on the database provider. Indexing GenBank in EMBOSS does allow GI searches. > Is there any way to access ENsembl database. Is there any new version of > EMBOSS which could support more databases which could installed in windowsXP? Ah, you are running EMBOSS under windows? embosswin was provided by Andre Blavier up to EMBOSS 2.10.0. We now provide a beta release of EMBOSS 4.0.0 for windows (nobody did version 3.0.0 for windows). Hmmmm ... we need to make that more obvious on the EMBOSS website. EMBOSSWIN is available by FTP from emboss.open-bio.org/pub/EMBOSS/windows/ ... only a few brave people have tested it so far, but they report that it is working. > Are all the databases which EMBOSS connected are the latest version? since I > found some database do not give the same results as what I get from the > database directly. That depends on where the databases are. There is a list of SRS servers you can check for the number of entries and the date they were indexed: http://downloads.biowisdomsrs.com/publicsrs.html for example: DB genbank [ type: N method: srswww format: genbank url: "http://iubio.bio.indiana.edu/srsbin/cgi-bin/wgetz" dbalias: "genbankrelease" fields: "gi sv des org key" comment: "Genbank IDs" ] You can also try Entrez databases in EMBOSS 4.0.0 ... I wonder how many users have been using entrez as an access method? Hope that helps Peter Rice From fangw at CLEMSON.EDU Tue Jan 23 13:42:25 2007 From: fangw at CLEMSON.EDU (fangw at CLEMSON.EDU) Date: Tue, 23 Jan 2007 13:42:25 -0500 (EST) Subject: [EMBOSS] question Message-ID: <4339.130.127.150.224.1169577745.squirrel@wm.clemson.edu> Dear EMBOSS people: If I have a list of genes that I would like to extract only the 5 upstream 2000bp of each gene. I choose "extractfeat", but it did not give me any answer. Someone have met the same problem before? Looking forward to your reply. Thanks! Nice day, Fang Wang From golharam at umdnj.edu Tue Jan 23 14:23:28 2007 From: golharam at umdnj.edu (Ryan Golhar) Date: Tue, 23 Jan 2007 14:23:28 -0500 Subject: [EMBOSS] transeq changes sequence id Message-ID: I'm using transeq to translate a bunch of sequence for me and noticed that upon translation, it adds a '_1' to the seqid. For example: I give it a file with >myseq ATG...TAG After translation, the resulting file contains: >myseq_1 M... Is there a way to prevent transeq from manipulating the FASTA header and just translate the sequence? Ryan From golharam at umdnj.edu Wed Jan 24 00:22:37 2007 From: golharam at umdnj.edu (Ryan Golhar) Date: Wed, 24 Jan 2007 00:22:37 -0500 Subject: [EMBOSS] need or want to support grid comping? Message-ID: <6328897A6BB8418CAF90745B21F9C738@PICO> Does anyone use (or need) EMBOSS tools to be supported in a web environment with grid support? ie using EMBOSS-Explorer and have the programs execute on a grid instead of the web server? Is anyone currently doing this? Ryan From David.Bauer at SCHERING.DE Wed Jan 24 02:06:17 2007 From: David.Bauer at SCHERING.DE (David.Bauer at SCHERING.DE) Date: Wed, 24 Jan 2007 08:06:17 +0100 Subject: [EMBOSS] Antwort: transeq changes sequence id In-Reply-To: Message-ID: Hi, the _1 is there to indicate the frame which was used for translation. You can use transeq myseq.fa -frame 1,2 and this would give a fasta file with two protein sequences. And that's where the added number makes sense; to prevent the creation of protein sequences which all have the same ID. So far about the philosophy of this number ;-) And now a solution for your problem: transeq test.fa | descseq -filter -name `infoseq -nohead -only -name test.fa` This works only if you have just one sequence in the input file. If you have a multiple sequence fasta file, you can use seqretsplit to create individual sequence files for each sequence. HTH, David. emboss-bounces at lists.open-bio.org schrieb am 23/01/2007 20:23:28: > I'm using transeq to translate a bunch of sequence for me and noticed that > upon translation, it adds a '_1' to the seqid. For example: > > I give it a file with > >myseq > ATG...TAG > > After translation, the resulting file contains: > >myseq_1 > M... > > Is there a way to prevent transeq from manipulating the FASTA header and > just translate the sequence? > > Ryan > > _______________________________________________ > EMBOSS mailing list > EMBOSS at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/emboss From David.Bauer at SCHERING.DE Wed Jan 24 02:45:56 2007 From: David.Bauer at SCHERING.DE (David.Bauer at SCHERING.DE) Date: Wed, 24 Jan 2007 08:45:56 +0100 Subject: [EMBOSS] Antwort: question In-Reply-To: <4339.130.127.150.224.1169577745.squirrel@wm.clemson.edu> Message-ID: Hi Fang, what about this: extractfeat myseq.embl -type mRNA -join -before 2000 | seqret -filter -send 2000 HTH, David. emboss-bounces at lists.open-bio.org schrieb am 23/01/2007 19:42:25: > Dear EMBOSS people: > > If I have a list of genes that I would like to extract only the 5 upstream > 2000bp of each gene. I choose "extractfeat", but it did not give me any > answer. Someone have met the same problem before? Looking forward to your > reply. Thanks! > > Nice day, > Fang Wang > > _______________________________________________ > EMBOSS mailing list > EMBOSS at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/emboss From jrvalverde at cnb.uam.es Wed Jan 24 04:54:21 2007 From: jrvalverde at cnb.uam.es (Jose R. Valverde) Date: Wed, 24 Jan 2007 10:54:21 +0100 Subject: [EMBOSS] need or want to support grid comping? In-Reply-To: <6328897A6BB8418CAF90745B21F9C738@PICO> References: <6328897A6BB8418CAF90745B21F9C738@PICO> Message-ID: <20070124105421.35375d32@veda.cnb.uam.es> On Wed, 24 Jan 2007 00:22:37 -0500 "Ryan Golhar" wrote: > Does anyone use (or need) EMBOSS tools to be supported in a web environment > with grid support? ie using EMBOSS-Explorer and have the programs execute > on a grid instead of the web server? > > Is anyone currently doing this? > > Ryan > > _______________________________________________ > EMBOSS mailing list > EMBOSS at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/emboss There are various people working on this that I can think of right now off the top of my head: - ourselves, we are looking into making the jEMBOSS batch facility use the Grid (EGEE) - the EMBnet node at Mexico is also looking into gridifying EMBOSS using EELA (on top of EGEE) - the Argentina EMBnet node in cooperation with the Belgian EMBnet node may already have solved the problem by porting wEMBOSS over DRMAA. We want to look into their approach to see if it works over the GridWay DRMAA implementation which would mean they had it already solved for EGEE and Globus at least - other initiative may be ongoing within EMBRACE but I believe they are currently more interested in Web Services. To the extent I am aware most of these projects are going slowly for a hoard of fortuitous reasons: - we are now busy organizing courses and conferences which delays our work - MX is heating up their development steam - AR's Martin Sarachu is fighting a leukaemia This said, any new hands are welcome. If you are interested we can provide with all the help and assistance needed and it may turn out to be a trivial task starting from Martin's work. Just let us know. Otherwise, I expect this to be ready along this year in one way or another (or all of them). j -- These opinions are mine and only mine. Hey man, I saw them first! Jos? R. Valverde De nada sirve la Inteligencia Artificial cuando falta la Natural From Tim.Troup at ed.ac.uk Wed Jan 24 12:16:16 2007 From: Tim.Troup at ed.ac.uk (Tim Troup) Date: Wed, 24 Jan 2007 17:16:16 +0000 Subject: [EMBOSS] EMBOSS FTP Site Down? Message-ID: <6B6F31BB-0826-4C1C-B463-4B598B68C513@ed.ac.uk> Hi, Is the EMBOSS FTP site down? It keeps timing out for me. ftp://emboss.open-bio.org/pub/EMBOSS Tim From dag at sonsorol.org Wed Jan 24 13:05:03 2007 From: dag at sonsorol.org (Chris Dagdigian) Date: Wed, 24 Jan 2007 13:05:03 -0500 Subject: [EMBOSS] EMBOSS FTP Site Down? In-Reply-To: <6B6F31BB-0826-4C1C-B463-4B598B68C513@ed.ac.uk> References: <6B6F31BB-0826-4C1C-B463-4B598B68C513@ed.ac.uk> Message-ID: FTP working is ok for me. Server side we look OK (open-bio FTP server). I'm also monitoring the IDS and Firewall alerts in real time due to some other non-OBF related issues -- the only real FTP issue is that the intrusion detection appliance thinks that it has seen a few FTP:EXPLOIT:BOUNCE-ATTACK incursions against the open-bio servers today. I'm 99% certain that this is a false alarm but I have not disabled that particular attack signature yet, if your client is trying odd things and redirections (perhaps to get past a NAT gateway or firewall) then maybe you are getting caught in this trap. Random side note: if anyone tries non-anonymous FTP for longer than 2 minutes with more than 5 failed login attempts then they are candidates for instant inclusion into a "drop all packets from this IP" list maintained within the firewall. Tim - if you send me the IP address of where you are trying to connect from I can see if there are any messages on our end. -Chris open-bio.org On Jan 24, 2007, at 12:16 PM, Tim Troup wrote: > Hi, > > Is the EMBOSS FTP site down? It keeps timing out for me. > > ftp://emboss.open-bio.org/pub/EMBOSS > From arareko at campus.iztacala.unam.mx Wed Jan 24 13:14:08 2007 From: arareko at campus.iztacala.unam.mx (Mauricio Herrera Cuadra) Date: Wed, 24 Jan 2007 12:14:08 -0600 Subject: [EMBOSS] EMBOSS FTP Site Down? In-Reply-To: <6B6F31BB-0826-4C1C-B463-4B598B68C513@ed.ac.uk> References: <6B6F31BB-0826-4C1C-B463-4B598B68C513@ed.ac.uk> Message-ID: <45B7A1F0.1090605@campus.iztacala.unam.mx> It's working ok here. Maybe your DNS can't resolve it. Mauricio. Tim Troup wrote: > Hi, > > Is the EMBOSS FTP site down? It keeps timing out for me. > > ftp://emboss.open-bio.org/pub/EMBOSS > > Tim > _______________________________________________ > EMBOSS mailing list > EMBOSS at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/emboss > -- MAURICIO HERRERA CUADRA arareko at campus.iztacala.unam.mx Laboratorio de Gen?tica Unidad de Morfofisiolog?a y Funci?n Facultad de Estudios Superiores Iztacala, UNAM From fangw at CLEMSON.EDU Wed Jan 24 16:05:47 2007 From: fangw at CLEMSON.EDU (fangw at CLEMSON.EDU) Date: Wed, 24 Jan 2007 16:05:47 -0500 (EST) Subject: [EMBOSS] question! Message-ID: <1100.130.127.150.224.1169672747.squirrel@wm.clemson.edu> Hi, All: Does any one know what kind of database version does EMBOSS version 2.10.0. connect to? Since when I use EMBOSS to extract 5'upstream sequence from some gene, there are a lot of NNNN in the beginning in the output file, which is different from the result which I get manualy from Ensembl BioMart. BioMart give the full sequence which match my request, but must be done manually. Looking forward to your reply! ^_^ Nice day, Fang Wang From maoj at helix.nih.gov Thu Jan 25 08:41:55 2007 From: maoj at helix.nih.gov (Jean Mao) Date: Thu, 25 Jan 2007 08:41:55 -0500 Subject: [EMBOSS] question about display double-stranded DNA Message-ID: <001501c74086$9413a820$be4de780@CIT.NIH.GOV> Hi, When using remap, I prefer to use the '-noreverse' flag so that the translation of my DNA is located closer to my DNA strand. However, using this flag also remove the complementary strand of my DNA in the output which is less convinient when design primers. Is there a way in remap to display double-stranded DNA but turn off the restriction sites of the complementary strand? If not, is there a program in EMBOSS which can retrieve the sequence from database, select start/end points and display both strands? I tried seqret but failed. Thank you in advance. Jean Mao From pmr at ebi.ac.uk Thu Jan 25 09:23:00 2007 From: pmr at ebi.ac.uk (Peter Rice) Date: Thu, 25 Jan 2007 14:23:00 +0000 Subject: [EMBOSS] question about display double-stranded DNA In-Reply-To: <001501c74086$9413a820$be4de780@CIT.NIH.GOV> References: <001501c74086$9413a820$be4de780@CIT.NIH.GOV> Message-ID: <45B8BD44.9050509@ebi.ac.uk> Hi Jean, > When using remap, I prefer to use the '-noreverse' flag so that the > translation of my DNA is located closer to my DNA strand. However, using > this flag also remove the complementary strand of my DNA in the output which > is less convinient when design primers. Is there a way in remap to display > double-stranded DNA but turn off the restriction sites of the complementary > strand? I am looking at remap changes at the moment, I will see what I can do. > If not, is there a program in EMBOSS which can retrieve the sequence from > database, select start/end points and display both strands? I tried seqret > but failed. Showseq does that. It has a bug at present (I noticed it this week - fixed in the next release) that makes it show additional bases up to the end of the last line. regards, Peter From pmr at ebi.ac.uk Thu Jan 25 09:39:12 2007 From: pmr at ebi.ac.uk (Peter Rice) Date: Thu, 25 Jan 2007 14:39:12 +0000 Subject: [EMBOSS] question about display double-stranded DNA In-Reply-To: <416B9A34D7CA1C4C9ED58354E75101BB021CB85A@NIHCESMLBX3.nih.gov> References: <001501c74086$9413a820$be4de780@CIT.NIH.GOV> <45B8BD44.9050509@ebi.ac.uk> <416B9A34D7CA1C4C9ED58354E75101BB021CB85A@NIHCESMLBX3.nih.gov> Message-ID: <45B8C110.6040608@ebi.ac.uk> Hi Jean, > Peter, Thanks for reply. seqret can retrieve entry and select start/end > points. But seqret does NOT display both strands. Does it? Right. Seqret returns a sequence, so it can only rpeort one strand at a time. > Showseq does that. > > It has a bug at present (I noticed it this week - fixed in the next release) > that makes it show additional bases up to the end of the last line. Oops. Spoke too soon. showseq uses the dame display functions as remap and has the same limitations. I will see what we can do for the next release. regards, Peter From gbottu at ben.vub.ac.be Thu Jan 25 10:39:15 2007 From: gbottu at ben.vub.ac.be (Guy Bottu) Date: Thu, 25 Jan 2007 16:39:15 +0100 Subject: [EMBOSS] question about display double-stranded DNA - Checked by An In-Reply-To: <45B8BD44.9050509@ebi.ac.uk> References: <001501c74086$9413a820$be4de780@CIT.NIH.GOV> <45B8BD44.9050509@ebi.ac.uk> Message-ID: <20070125153915.GA30474@bigben.ulb.ac.be> On Thu, Jan 25, 2007 at 02:23:00PM +0000, Peter Rice wrote: > I am looking at remap changes at the moment, I will see what I can do. Could you consider an option to reject restriction enzymes that cut within a certain range (or ranges). This feature existed in GCG and is really something we would like to have (back). Allows e.g. to select enzymes that cut around the gene you want to clone, but not inside. Guy Bottu, BEN From golharam at umdnj.edu Thu Jan 25 12:31:22 2007 From: golharam at umdnj.edu (Ryan Golhar) Date: Thu, 25 Jan 2007 12:31:22 -0500 Subject: [EMBOSS] request for a useful addition Message-ID: <08780548D8B54EF086EAEEB74AE41C2D@PICO> The program dottup (and other dotplot tools) takes the two sequence given and displays a dotplot. It would be useful if you could give it the option to reverse complement one of the sequences then perform a dotplot. I was comparing a mRNA with a genomic sequence and wasn't seeing the similarity between the sequences. Then I releazied I needed to rev-comp the mRNA and it showed up fine. Of course, one can do this using revseq, but to have dottup do it for you would be even better. Ryan From David.Bauer at SCHERING.DE Fri Jan 26 01:46:43 2007 From: David.Bauer at SCHERING.DE (David.Bauer at SCHERING.DE) Date: Fri, 26 Jan 2007 07:46:43 +0100 Subject: [EMBOSS] Antwort: request for a useful addition In-Reply-To: <08780548D8B54EF086EAEEB74AE41C2D@PICO> Message-ID: This can be done with the option -sreverse1 or -sreverse2 to use the reverse complement of the firts or second sequence used as input for e.g. dottup. It is a standard option available to all emboss programs. You can get a list of those options with -help -verbose. David. emboss-bounces at lists.open-bio.org schrieb am 25/01/2007 18:31:22: > The program dottup (and other dotplot tools) takes the two sequence given > and displays a dotplot. It would be useful if you could give it the option > to reverse complement one of the sequences then perform a dotplot. > > I was comparing a mRNA with a genomic sequence and wasn't seeing the > similarity between the sequences. Then I releazied I needed to rev-comp the > mRNA and it showed up fine. Of course, one can do this using revseq, but to > have dottup do it for you would be even better. > > Ryan > > > _______________________________________________ > EMBOSS mailing list > EMBOSS at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/emboss From golharam at umdnj.edu Fri Jan 26 12:19:53 2007 From: golharam at umdnj.edu (Ryan Golhar) Date: Fri, 26 Jan 2007 12:19:53 -0500 Subject: [EMBOSS] Antwort: request for a useful addition In-Reply-To: Message-ID: <92EAFE9D771342E99D302B254E3CC6F3@PICO> Thanks. I didn't see this in the list of options in EMBOSS-Explorer. Luke, perhaps this can be added as an option to the interface? Ryan > > -----Original Message----- > > From: David.Bauer at SCHERING.DE [mailto:David.Bauer at SCHERING.DE] > > Sent: Friday, January 26, 2007 1:47 AM > > To: golharam at umdnj.edu > > Cc: emboss at lists.open-bio.org; emboss-bounces at lists.open-bio.org > > Subject: Antwort: [EMBOSS] request for a useful addition > > > > > > This can be done with the option -sreverse1 or -sreverse2 to > > use the reverse complement of the firts or second sequence > > used as input for e.g. dottup. It is a standard option > > available to all emboss programs. You can get a list of those > > options with -help -verbose. > > > > David. > > > > emboss-bounces at lists.open-bio.org schrieb am 25/01/2007 18:31:22: > > > > > The program dottup (and other dotplot tools) takes the > two sequence > > given > > > and displays a dotplot. It would be useful if you could > give it the > > option > > > to reverse complement one of the sequences then perform a dotplot. > > > > > > I was comparing a mRNA with a genomic sequence and wasn't > > seeing the > > > similarity between the sequences. Then I releazied I needed to > > > rev-comp > > the > > > mRNA and it showed up fine. Of course, one can do this > > using revseq, > > but to > > > have dottup do it for you would be even better. > > > > > > Ryan > > > > > > > > > _______________________________________________ > > > EMBOSS mailing list > > > EMBOSS at lists.open-bio.org > > > http://lists.open-bio.org/mailman/listinfo/emboss > > > > > > From gbottu at ben.vub.ac.be Tue Jan 30 04:31:35 2007 From: gbottu at ben.vub.ac.be (Guy Bottu) Date: Tue, 30 Jan 2007 10:31:35 +0100 Subject: [EMBOSS] [dksamuel@gmail.com: Re: question about display double-strande Message-ID: <20070130093135.GA10496@bigben.ulb.ac.be> ----- Forwarded message from Duleep Samuel ----- DomainKey-Signature: a=rsa-sha1; c=nofws; d=gmail.com; s=beta; h=received:message-id:date:from:to:subject:in-reply-to:mime-version:content-type:content-transfer-encoding:content-disposition:references; b=SAzlXlDHdfFJk9cAn6wcMj/Nn8r9SHt3gK528ZaV2wJy2V2yaFiRkPGz3LX4FUAWMl2/Xl582TcZ4BZE6lTi8wAL21S2mv5V4fiAYjp9LM0RHYGDLW9v/xSR8t3N7dvlzEyH0LGk7ejUlYOJQNo9/PYCJP0BJl5oATVEMq9B0xU= Date: Sat, 27 Jan 2007 10:25:55 +0530 From: "Duleep Samuel" To: "Guy Bottu" Subject: Re: [EMBOSS] question about display double-stranded DNA - Checked by An In-Reply-To: <20070125153915.GA30474 at bigben.ulb.ac.be> X-AntiVirus: checked by AntiVir Milter 1.0.6; AVE 7.3.0.32; VDF 6.37.0.228 will be useful please add if possible, regards Samuel On 1/25/07, Guy Bottu wrote: >On Thu, Jan 25, 2007 at 02:23:00PM +0000, Peter Rice wrote: >> I am looking at remap changes at the moment, I will see what I can do. > >Could you consider an option to reject restriction enzymes that cut within >a certain range (or ranges). This feature existed in GCG and is really >something we would like to have (back). Allows e.g. to select enzymes that >cut around the gene you want to clone, but not inside. > > Guy Bottu, > BEN > >_______________________________________________ >EMBOSS mailing list >EMBOSS at lists.open-bio.org >http://lists.open-bio.org/mailman/listinfo/emboss > ----- End forwarded message -----