From ajhernan at lcg.unam.mx Wed Jan 9 13:00:03 2008 From: ajhernan at lcg.unam.mx (Alfredo Jose Hernandez Alvarez) Date: Wed, 09 Jan 2008 12:00:03 -0600 Subject: [EMBOSS] embl and dbxflat segmentation fault Message-ID: <47850BA3.4010102@lcg.unam.mx> Hello, and happy 2008. When I index the embl database with dbxflat, a segmentation fault occurs: $ dbxflat -dbname embl -dbresource embl -idformat EMBL -filenames "*.dat" -directory . -fields id,acc -release 93.0 -date 08/01/08 Database b+tree indexing for flat file databases Processing file ./rel_ann_env_01_r93.dat ... Processing file ./wgs_aahc_inv.dat Segmentation fault The "embl" database is defined in emboss.default, also the "embl" resource with default values. The embl release is 93, and the segmentation fault seems to happen in the file wgs_aahc_inv.dat. I downloaded it again, it seems ok, but still same error happens. When I index only that file, i.e dbxflat -filenames "wgs_aahc_inv.dat" etc etc, it works ok. What could be the problem? I have emboss 4.1 on linux on IA64 with enough disk space. Thank you very much! -- Hern?ndez Alvarez Alfredo Jos? Unidad de Administraci?n de Tecnolog?as de Informaci?n Licenciatura en Ciencias Gen?micas Centro de Ciencias Gen?micas UNAM Ext. 38221 Red UNAM / Tel. (01) 777 3290821 ajhernan at lcg.unam.mx / ajhernan at ccg.unam.mx From ajb at ebi.ac.uk Wed Jan 9 13:56:51 2008 From: ajb at ebi.ac.uk (ajb at ebi.ac.uk) Date: Wed, 9 Jan 2008 18:56:51 -0000 (GMT) Subject: [EMBOSS] embl and dbxflat segmentation fault In-Reply-To: <47850BA3.4010102@lcg.unam.mx> References: <47850BA3.4010102@lcg.unam.mx> Message-ID: <58517.81.98.241.17.1199905011.squirrel@webmail.ebi.ac.uk> Hi, You should upgrade to EMBOSS 5.0.0. Make sure you apply the patch in the pub/EMBOSS/fixes/patches/ directory before configuring. Both 5.0.0 and the patch contain indexing fixes. HTH Alan > Hello, and happy 2008. > > When I index the embl database with dbxflat, a segmentation fault occurs: > > $ dbxflat -dbname embl -dbresource embl -idformat EMBL -filenames > "*.dat" -directory . -fields id,acc -release 93.0 -date 08/01/08 > Database b+tree indexing for flat file databases > Processing file ./rel_ann_env_01_r93.dat > ... > Processing file ./wgs_aahc_inv.dat > Segmentation fault > > The "embl" database is defined in emboss.default, also the "embl" > resource with default values. The embl release is 93, and the > segmentation fault seems to happen in the file wgs_aahc_inv.dat. I > downloaded it again, it seems ok, but still same error happens. > > When I index only that file, i.e dbxflat -filenames "wgs_aahc_inv.dat" > etc etc, it works ok. > > What could be the problem? > > I have emboss 4.1 on linux on IA64 with enough disk space. > > Thank you very much! > > -- > Hern?ndez Alvarez Alfredo Jos? > Unidad de Administraci?n de Tecnolog?as de Informaci?n > Licenciatura en Ciencias Gen?micas > Centro de Ciencias Gen?micas UNAM > Ext. 38221 Red UNAM / Tel. (01) 777 3290821 > ajhernan at lcg.unam.mx / ajhernan at ccg.unam.mx > _______________________________________________ > EMBOSS mailing list > EMBOSS at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/emboss > From ajb at ebi.ac.uk Tue Jan 15 10:40:17 2008 From: ajb at ebi.ac.uk (ajb at ebi.ac.uk) Date: Tue, 15 Jan 2008 15:40:17 -0000 (GMT) Subject: [EMBOSS] Vienna 1.6.5 Message-ID: <50010.81.98.241.17.1200411617.squirrel@webmail.ebi.ac.uk> Ryan Golhar wrote: > Vienna 1.6.5 has been released. Right now, EMBOSS 5 uses 1.6.4. There > are any plans on upgrading EMBOSS to use 1.6.5? > > Is all the needs to be done is updating the ACD files? Vienna 1.7 is now in the CVS (development) version of EMBOSS. Regard it, for the moment, as alpha. Porting it requires a lot more than just updating ACD files: the data input part of the code has to be modified extensively (the applications cannot be wrapped and still conform to EMBOSS input conventions). Alan From jeedward at gmail.com Wed Jan 16 10:56:38 2008 From: jeedward at gmail.com (John E. Edward) Date: Wed, 16 Jan 2008 10:56:38 -0500 Subject: [EMBOSS] BCBGC-08 Final call for papers Message-ID: BCBGC-08 Final call for papers The 2008 International Conference on Bioinformatics, Computational Biology, Genomics and Chemoinformatics (BCBGC-08) (website: www.PromoteResearch.org) will be held during July 7-10 2008 in Orlando, FL, USA. We invite draft paper submissions. The conference will be held at the same time and place where several other major events are taking place. The website contains more details. Sincerely John Edward From ajhernan at lcg.unam.mx Wed Jan 16 11:31:58 2008 From: ajhernan at lcg.unam.mx (Alfredo Jose Hernandez Alvarez) Date: Wed, 16 Jan 2008 10:31:58 -0600 Subject: [EMBOSS] embl and dbxflat segmentation fault In-Reply-To: <58517.81.98.241.17.1199905011.squirrel@webmail.ebi.ac.uk> References: <47850BA3.4010102@lcg.unam.mx> <58517.81.98.241.17.1199905011.squirrel@webmail.ebi.ac.uk> Message-ID: <478E317E.6050405@lcg.unam.mx> ajb at ebi.ac.uk wrote: > You should upgrade to EMBOSS 5.0.0. Make sure you apply the > patch in the pub/EMBOSS/fixes/patches/ directory before > configuring. Both 5.0.0 and the patch contain indexing Thanks, that solved it. I had the opportunity/time to upgrade until 4 days ago. EMBOSS 5.0.0 had the same "segmentation fault" error when doing dbxflat of embl. EMBOSS 5.0.0 + patch-1-2 solved it. Thanks again. -- Hern?ndez Alvarez Alfredo Jos? Unidad de Administraci?n de Tecnolog?as de Informaci?n Licenciatura en Ciencias Gen?micas Centro de Ciencias Gen?micas UNAM Ext. 38221 Red UNAM / Tel. (01) 777 3290821 ajhernan at lcg.unam.mx / ajhernan at ccg.unam.mx From hnlin at yahoo.com Tue Jan 22 15:42:08 2008 From: hnlin at yahoo.com (Haining Lin) Date: Tue, 22 Jan 2008 12:42:08 -0800 (PST) Subject: [EMBOSS] fretree Message-ID: <22171.29643.qm@web36114.mail.mud.yahoo.com> Hello, I?d like to use the fretree program from EMBOSS. There is a web interface for it (http://pro.genomics.purdue.edu/cgi-bin/emboss/). However, I need to run it on local unix machine and I couldn?t find it in the stable release EMBOSS-5.0.0.tar.gz I downloaded from http://emboss.sourceforge.net/download/#Stable. Can anyone help me out? Thank you very much for your assistance! Helen ____________________________________________________________________________________ Looking for last minute shopping deals? Find them fast with Yahoo! Search. http://tools.search.yahoo.com/newsearch/category.php?category=shopping From uludag at ebi.ac.uk Tue Jan 22 18:13:09 2008 From: uludag at ebi.ac.uk (uludag at ebi.ac.uk) Date: Tue, 22 Jan 2008 23:13:09 -0000 (GMT) Subject: [EMBOSS] fretree In-Reply-To: <22171.29643.qm@web36114.mail.mud.yahoo.com> References: <22171.29643.qm@web36114.mail.mud.yahoo.com> Message-ID: <55680.86.137.132.98.1201043589.squirrel@webmail.ebi.ac.uk> > I?d like to use the fretree program from EMBOSS. There is a web interface > for it (http://pro.genomics.purdue.edu/cgi-bin/emboss/). However, I need > to run it on local unix machine and I > couldn?t find it in the stable release EMBOSS-5.0.0.tar.gz I downloaded > from http://emboss.sourceforge.net/download/#Stable. Can anyone help me > out? You probably need to install the following EMBASSY package. ftp://emboss.open-bio.org/pub/EMBOSS/PHYLIP-3.6b.tar.gz Regards, Mahmut From shrish at ccmb.res.in Fri Jan 25 07:21:57 2008 From: shrish at ccmb.res.in (Shrish Tiwari) Date: Fri, 25 Jan 2008 17:51:57 +0530 (IST) Subject: [EMBOSS] extracting "promoter" regions Message-ID: <3216322.1201263717914.JavaMail.root@127.0.0.1> An embedded and charset-unspecified text was scrubbed... Name: not available URL: From gbottu at vub.ac.be Fri Jan 25 10:54:36 2008 From: gbottu at vub.ac.be (Guy Bottu) Date: Fri, 25 Jan 2008 16:54:36 +0100 Subject: [EMBOSS] extracting "promoter" regions In-Reply-To: <3216322.1201263717914.JavaMail.root@127.0.0.1> References: <3216322.1201263717914.JavaMail.root@127.0.0.1> Message-ID: <479A063C.5020603@vub.ac.be> Shrish Tiwari wrote: > Is there a way using EMBOSS programs to extract 2kb region around the transcription start site. When I use > extractfeat -type mrna -before 1000 -after 1000 > I get 2kb regions around every splice site apart from what I need. Any suggestions? Try adding the parameter -join Regards, Guy Bottu, Belgian From fernan at iib.unsam.edu.ar Thu Jan 31 08:29:49 2008 From: fernan at iib.unsam.edu.ar (Fernan Aguero) Date: Thu, 31 Jan 2008 10:29:49 -0300 Subject: [EMBOSS] pepstats: (im)probability of expression in inclusion bodies? Message-ID: <20080131132949.GH813@iib.unsam.edu.ar> Hi, I was just looking at the output of pepstats for the probability of expression in inclusion bodies in E. coli, and noticed that in some cases the values reported are not for the probability but for the 'Improbability' of expression. Why is that? I have just run one small genome (805 genes) through pepstats and I've found 625 cases of 'Improbability' vs 180 for 'Probability'. Suspiciously, in both cases the values ranged from ~ 0.49 to ~ 0.97. Am I safe to assume that pepstats is reporting low probability values of expression in inclusion bodies as high Improbability values instead? (i.e. 1 - probabiliy )? If this is the case, why? Why not standardize the output for all cases, reporting just the probability values? This is on EMBOSS-5.0.0 BTW, the fine manual does not say anything about this behaviour :) Fernan From ajhernan at lcg.unam.mx Wed Jan 9 18:00:03 2008 From: ajhernan at lcg.unam.mx (Alfredo Jose Hernandez Alvarez) Date: Wed, 09 Jan 2008 12:00:03 -0600 Subject: [EMBOSS] embl and dbxflat segmentation fault Message-ID: <47850BA3.4010102@lcg.unam.mx> Hello, and happy 2008. When I index the embl database with dbxflat, a segmentation fault occurs: $ dbxflat -dbname embl -dbresource embl -idformat EMBL -filenames "*.dat" -directory . -fields id,acc -release 93.0 -date 08/01/08 Database b+tree indexing for flat file databases Processing file ./rel_ann_env_01_r93.dat ... Processing file ./wgs_aahc_inv.dat Segmentation fault The "embl" database is defined in emboss.default, also the "embl" resource with default values. The embl release is 93, and the segmentation fault seems to happen in the file wgs_aahc_inv.dat. I downloaded it again, it seems ok, but still same error happens. When I index only that file, i.e dbxflat -filenames "wgs_aahc_inv.dat" etc etc, it works ok. What could be the problem? I have emboss 4.1 on linux on IA64 with enough disk space. Thank you very much! -- Hern?ndez Alvarez Alfredo Jos? Unidad de Administraci?n de Tecnolog?as de Informaci?n Licenciatura en Ciencias Gen?micas Centro de Ciencias Gen?micas UNAM Ext. 38221 Red UNAM / Tel. (01) 777 3290821 ajhernan at lcg.unam.mx / ajhernan at ccg.unam.mx From ajb at ebi.ac.uk Wed Jan 9 18:56:51 2008 From: ajb at ebi.ac.uk (ajb at ebi.ac.uk) Date: Wed, 9 Jan 2008 18:56:51 -0000 (GMT) Subject: [EMBOSS] embl and dbxflat segmentation fault In-Reply-To: <47850BA3.4010102@lcg.unam.mx> References: <47850BA3.4010102@lcg.unam.mx> Message-ID: <58517.81.98.241.17.1199905011.squirrel@webmail.ebi.ac.uk> Hi, You should upgrade to EMBOSS 5.0.0. Make sure you apply the patch in the pub/EMBOSS/fixes/patches/ directory before configuring. Both 5.0.0 and the patch contain indexing fixes. HTH Alan > Hello, and happy 2008. > > When I index the embl database with dbxflat, a segmentation fault occurs: > > $ dbxflat -dbname embl -dbresource embl -idformat EMBL -filenames > "*.dat" -directory . -fields id,acc -release 93.0 -date 08/01/08 > Database b+tree indexing for flat file databases > Processing file ./rel_ann_env_01_r93.dat > ... > Processing file ./wgs_aahc_inv.dat > Segmentation fault > > The "embl" database is defined in emboss.default, also the "embl" > resource with default values. The embl release is 93, and the > segmentation fault seems to happen in the file wgs_aahc_inv.dat. I > downloaded it again, it seems ok, but still same error happens. > > When I index only that file, i.e dbxflat -filenames "wgs_aahc_inv.dat" > etc etc, it works ok. > > What could be the problem? > > I have emboss 4.1 on linux on IA64 with enough disk space. > > Thank you very much! > > -- > Hern?ndez Alvarez Alfredo Jos? > Unidad de Administraci?n de Tecnolog?as de Informaci?n > Licenciatura en Ciencias Gen?micas > Centro de Ciencias Gen?micas UNAM > Ext. 38221 Red UNAM / Tel. (01) 777 3290821 > ajhernan at lcg.unam.mx / ajhernan at ccg.unam.mx > _______________________________________________ > EMBOSS mailing list > EMBOSS at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/emboss > From ajb at ebi.ac.uk Tue Jan 15 15:40:17 2008 From: ajb at ebi.ac.uk (ajb at ebi.ac.uk) Date: Tue, 15 Jan 2008 15:40:17 -0000 (GMT) Subject: [EMBOSS] Vienna 1.6.5 Message-ID: <50010.81.98.241.17.1200411617.squirrel@webmail.ebi.ac.uk> Ryan Golhar wrote: > Vienna 1.6.5 has been released. Right now, EMBOSS 5 uses 1.6.4. There > are any plans on upgrading EMBOSS to use 1.6.5? > > Is all the needs to be done is updating the ACD files? Vienna 1.7 is now in the CVS (development) version of EMBOSS. Regard it, for the moment, as alpha. Porting it requires a lot more than just updating ACD files: the data input part of the code has to be modified extensively (the applications cannot be wrapped and still conform to EMBOSS input conventions). Alan From jeedward at gmail.com Wed Jan 16 15:56:38 2008 From: jeedward at gmail.com (John E. Edward) Date: Wed, 16 Jan 2008 10:56:38 -0500 Subject: [EMBOSS] BCBGC-08 Final call for papers Message-ID: BCBGC-08 Final call for papers The 2008 International Conference on Bioinformatics, Computational Biology, Genomics and Chemoinformatics (BCBGC-08) (website: www.PromoteResearch.org) will be held during July 7-10 2008 in Orlando, FL, USA. We invite draft paper submissions. The conference will be held at the same time and place where several other major events are taking place. The website contains more details. Sincerely John Edward From ajhernan at lcg.unam.mx Wed Jan 16 16:31:58 2008 From: ajhernan at lcg.unam.mx (Alfredo Jose Hernandez Alvarez) Date: Wed, 16 Jan 2008 10:31:58 -0600 Subject: [EMBOSS] embl and dbxflat segmentation fault In-Reply-To: <58517.81.98.241.17.1199905011.squirrel@webmail.ebi.ac.uk> References: <47850BA3.4010102@lcg.unam.mx> <58517.81.98.241.17.1199905011.squirrel@webmail.ebi.ac.uk> Message-ID: <478E317E.6050405@lcg.unam.mx> ajb at ebi.ac.uk wrote: > You should upgrade to EMBOSS 5.0.0. Make sure you apply the > patch in the pub/EMBOSS/fixes/patches/ directory before > configuring. Both 5.0.0 and the patch contain indexing Thanks, that solved it. I had the opportunity/time to upgrade until 4 days ago. EMBOSS 5.0.0 had the same "segmentation fault" error when doing dbxflat of embl. EMBOSS 5.0.0 + patch-1-2 solved it. Thanks again. -- Hern?ndez Alvarez Alfredo Jos? Unidad de Administraci?n de Tecnolog?as de Informaci?n Licenciatura en Ciencias Gen?micas Centro de Ciencias Gen?micas UNAM Ext. 38221 Red UNAM / Tel. (01) 777 3290821 ajhernan at lcg.unam.mx / ajhernan at ccg.unam.mx From hnlin at yahoo.com Tue Jan 22 20:42:08 2008 From: hnlin at yahoo.com (Haining Lin) Date: Tue, 22 Jan 2008 12:42:08 -0800 (PST) Subject: [EMBOSS] fretree Message-ID: <22171.29643.qm@web36114.mail.mud.yahoo.com> Hello, I?d like to use the fretree program from EMBOSS. There is a web interface for it (http://pro.genomics.purdue.edu/cgi-bin/emboss/). However, I need to run it on local unix machine and I couldn?t find it in the stable release EMBOSS-5.0.0.tar.gz I downloaded from http://emboss.sourceforge.net/download/#Stable. Can anyone help me out? Thank you very much for your assistance! Helen ____________________________________________________________________________________ Looking for last minute shopping deals? Find them fast with Yahoo! Search. http://tools.search.yahoo.com/newsearch/category.php?category=shopping From uludag at ebi.ac.uk Tue Jan 22 23:13:09 2008 From: uludag at ebi.ac.uk (uludag at ebi.ac.uk) Date: Tue, 22 Jan 2008 23:13:09 -0000 (GMT) Subject: [EMBOSS] fretree In-Reply-To: <22171.29643.qm@web36114.mail.mud.yahoo.com> References: <22171.29643.qm@web36114.mail.mud.yahoo.com> Message-ID: <55680.86.137.132.98.1201043589.squirrel@webmail.ebi.ac.uk> > I?d like to use the fretree program from EMBOSS. There is a web interface > for it (http://pro.genomics.purdue.edu/cgi-bin/emboss/). However, I need > to run it on local unix machine and I > couldn?t find it in the stable release EMBOSS-5.0.0.tar.gz I downloaded > from http://emboss.sourceforge.net/download/#Stable. Can anyone help me > out? You probably need to install the following EMBASSY package. ftp://emboss.open-bio.org/pub/EMBOSS/PHYLIP-3.6b.tar.gz Regards, Mahmut From shrish at ccmb.res.in Fri Jan 25 12:21:57 2008 From: shrish at ccmb.res.in (Shrish Tiwari) Date: Fri, 25 Jan 2008 17:51:57 +0530 (IST) Subject: [EMBOSS] extracting "promoter" regions Message-ID: <3216322.1201263717914.JavaMail.root@127.0.0.1> An embedded and charset-unspecified text was scrubbed... Name: not available URL: From gbottu at vub.ac.be Fri Jan 25 15:54:36 2008 From: gbottu at vub.ac.be (Guy Bottu) Date: Fri, 25 Jan 2008 16:54:36 +0100 Subject: [EMBOSS] extracting "promoter" regions In-Reply-To: <3216322.1201263717914.JavaMail.root@127.0.0.1> References: <3216322.1201263717914.JavaMail.root@127.0.0.1> Message-ID: <479A063C.5020603@vub.ac.be> Shrish Tiwari wrote: > Is there a way using EMBOSS programs to extract 2kb region around the transcription start site. When I use > extractfeat -type mrna -before 1000 -after 1000 > I get 2kb regions around every splice site apart from what I need. Any suggestions? Try adding the parameter -join Regards, Guy Bottu, Belgian From fernan at iib.unsam.edu.ar Thu Jan 31 13:29:49 2008 From: fernan at iib.unsam.edu.ar (Fernan Aguero) Date: Thu, 31 Jan 2008 10:29:49 -0300 Subject: [EMBOSS] pepstats: (im)probability of expression in inclusion bodies? Message-ID: <20080131132949.GH813@iib.unsam.edu.ar> Hi, I was just looking at the output of pepstats for the probability of expression in inclusion bodies in E. coli, and noticed that in some cases the values reported are not for the probability but for the 'Improbability' of expression. Why is that? I have just run one small genome (805 genes) through pepstats and I've found 625 cases of 'Improbability' vs 180 for 'Probability'. Suspiciously, in both cases the values ranged from ~ 0.49 to ~ 0.97. Am I safe to assume that pepstats is reporting low probability values of expression in inclusion bodies as high Improbability values instead? (i.e. 1 - probabiliy )? If this is the case, why? Why not standardize the output for all cases, reporting just the probability values? This is on EMBOSS-5.0.0 BTW, the fine manual does not say anything about this behaviour :) Fernan