From laura at mmb.pcb.ub.es Wed Jul 9 03:59:18 2008 From: laura at mmb.pcb.ub.es (laura) Date: Wed, 09 Jul 2008 09:59:18 +0200 Subject: [emboss-dev] HELP: problems with allversusall tool Message-ID: <0d038ccddac56c3a1c07ed3efd284c4a@mmb.pcb.ub.es> Dear emboss developers, I am using allversus all tool for global sequence alignment. I am writing to you because I am obtaining perfect aligments between sequences that have a very different length.. for example if I have a 100 residues protein sequence and a 2 residues protein sequence I obtain a 100% identity when I perform the alignment, in which I would expect a very poor sequence identity. Is there any way to prevent it or it is a posible bug in the program?? I would thank you to answer me as soon as possible, Regards, Laura. From gbottu at vub.ac.be Thu Jul 10 09:44:08 2008 From: gbottu at vub.ac.be (Guy Bottu) Date: Thu, 10 Jul 2008 15:44:08 +0200 Subject: [emboss-dev] The location of the HTML manuals Message-ID: <48761228.40309@vub.ac.be> Dear Peter and Alan, We are currently working on a new version of wEMBOSS+wrappers4EMBOSS and on this occasion we were again disturbed by the location of the manuals in HTML format. Indeed, they once were all in one directory, but now they are partly in .../share/EMBOSS/doc/html/emboss/apps and partly in .../share/EMBOSS/doc/html/embassy/xxx. I actually wonder what problem you tried to solve by doing that. It certainly creates a problem for developers of Web interfaces, because popping up a manual by generating a hyperlink is not easy ; when all the manuals are in the same directory the interface program must just generate an hyperlink yyyyyy/xxx.html, where yyyyy is always the same thing and xxx is the name of the program. At the BEN site it works because I manually copied all the manuals to one location. This however does not make life easy for those who download+install wEMBOSS(+wrappers4EMBOSS). Regards, Guy Bottu, BEN From gbottu at vub.ac.be Wed Jul 16 13:24:46 2008 From: gbottu at vub.ac.be (Guy Bottu) Date: Wed, 16 Jul 2008 19:24:46 +0200 Subject: [emboss-dev] on-line manual blues Message-ID: <487E2EDE.5070302@vub.ac.be> Dear Peter and Alan, We are on the verge of releasing a new version of wEMBOSS. The recent release of EMBOSS 6 forced us to perform a last minute change to make it work. Good news is that Marc Colet found a way to let wEMBOSS find the on-line manuals in HTML format, no matter where they are. So, you can ignore the mail I send last week. At this occasion I spent a lot of work on getting at the BEN site the manuals (and all the internal hyperlinks) right and I discovered that my old complaint about the manual for extractalign not being there was due to the fact that it is in the distribution but was not installed because not mentioned in the Makefile. This is corrected in EMBOSS version 6. Idem for edit_group.html. But there are some troubles that persist in the Embassy packages : - In the PHYLIPNEW package the manuals for fdnamove, fdolmove and frestdist are there but are not installed - In the package TOPO the file topo.gif is lacking and hence topo.html has a "dead" hyperlink. I managed to rescue the file topo.gif from .../EMBOSS-3.0.0/doc/programs/html/ Regards, Guy Bottu, BEN From breedaditi at yahoo.com Fri Jul 18 15:50:58 2008 From: breedaditi at yahoo.com (Aditi Breed) Date: Fri, 18 Jul 2008 12:50:58 -0700 (PDT) Subject: [emboss-dev] Installation (make ) error Message-ID: <954760.98297.qm@web35906.mail.mud.yahoo.com> Hello , I get the following error when i try to make EMBOSS. Can some one guide me as to what i need to do , to get rid of this error . xwin.c:3378: error: 'XwDisplay' has no member named 'display' xwin.c:3378: error: 'XwDev' has no member named 'window' xwin.c:3378: error: 'XwDev' has no member named 'gc' xwin.c:3379: error: 'XwDev' has no member named 'width' xwin.c:3379: error: 'XwDev' has no member named 'height' xwin.c: In function 'imageops': xwin.c:3394: error: 'XwDev' has no member named 'write_to_window' xwin.c:3398: error: 'XwDev' has no member named 'write_to_window' xwin.c:3402: error: 'XwDev' has no member named 'write_to_pixmap' xwin.c:3406: error: 'XwDisplay' has no member named 'display' xwin.c:3407: error: 'XwDev' has no member named 'write_to_pixmap' make[2]: *** [xwin.lo] Error 1 make[2]: Leaving directory `/home/akhunovlab/DOWNLOADS/EMBOSS/EMBOSS-6.0.1/plplot' make[1]: *** [all-recursive] Error 1 make[1]: Leaving directory `/home/akhunovlab/DOWNLOADS/EMBOSS/EMBOSS-6.0.1/plplot' make: *** [all-recursive] Error 1 I shall be grateful if someone could please help .. Regards, Aditi "Great spirits often meet violent opposition with mediocre minds" - Albert Einstein From jbdundas at gmail.com Wed Jul 30 08:31:46 2008 From: jbdundas at gmail.com (jitesh dundas) Date: Wed, 30 Jul 2008 18:01:46 +0530 Subject: [emboss-dev] Request For Work In-Reply-To: <326ea8620807300515n521c4f1ekf9042983fbc136f5@mail.gmail.com> References: <326ea8620807300515n521c4f1ekf9042983fbc136f5@mail.gmail.com> Message-ID: <326ea8620807300531o43c7d25emad126ac26f0c376a@mail.gmail.com> Dear All, Greetings! I am interested in contributing to this wonderful project. Can somebody please suggest where to start? *About MySelf* I want to persue a doctoral program in Bio-Informatics next year, for which I am preparing right now. However, I am still looking for some guidance and work in this field to help me get the experience needed. I have an inclination towards the fields of Finance,Medicine and Computers and constanlty look out for ways to use my knowledge and capabilities to innovate and discover in them. I have a passion for research-work, working on complex and ambiguous problems. I relentlessly work towards resolving them until they are solved permanently with the best possible solution. I am always ready to learn new things and teach others too. I can work independently as well as in teams with minimum supervision. I continuously try to improvize in my work by focussing on innovation and scientific reasoning. I am a hard-working, sincere and research-oriented professional with a scientific bend of mind and a never give-up attitude. I hope you will give me an opportunity to explore the world of research under you. Yours sincerely, Jitesh Dundas http://jiteshbdundas.blogspot.com Mobile- +91-9860925706 From laura at mmb.pcb.ub.es Wed Jul 9 07:59:18 2008 From: laura at mmb.pcb.ub.es (laura) Date: Wed, 09 Jul 2008 09:59:18 +0200 Subject: [emboss-dev] HELP: problems with allversusall tool Message-ID: <0d038ccddac56c3a1c07ed3efd284c4a@mmb.pcb.ub.es> Dear emboss developers, I am using allversus all tool for global sequence alignment. I am writing to you because I am obtaining perfect aligments between sequences that have a very different length.. for example if I have a 100 residues protein sequence and a 2 residues protein sequence I obtain a 100% identity when I perform the alignment, in which I would expect a very poor sequence identity. Is there any way to prevent it or it is a posible bug in the program?? I would thank you to answer me as soon as possible, Regards, Laura. From gbottu at vub.ac.be Thu Jul 10 13:44:08 2008 From: gbottu at vub.ac.be (Guy Bottu) Date: Thu, 10 Jul 2008 15:44:08 +0200 Subject: [emboss-dev] The location of the HTML manuals Message-ID: <48761228.40309@vub.ac.be> Dear Peter and Alan, We are currently working on a new version of wEMBOSS+wrappers4EMBOSS and on this occasion we were again disturbed by the location of the manuals in HTML format. Indeed, they once were all in one directory, but now they are partly in .../share/EMBOSS/doc/html/emboss/apps and partly in .../share/EMBOSS/doc/html/embassy/xxx. I actually wonder what problem you tried to solve by doing that. It certainly creates a problem for developers of Web interfaces, because popping up a manual by generating a hyperlink is not easy ; when all the manuals are in the same directory the interface program must just generate an hyperlink yyyyyy/xxx.html, where yyyyy is always the same thing and xxx is the name of the program. At the BEN site it works because I manually copied all the manuals to one location. This however does not make life easy for those who download+install wEMBOSS(+wrappers4EMBOSS). Regards, Guy Bottu, BEN From gbottu at vub.ac.be Wed Jul 16 17:24:46 2008 From: gbottu at vub.ac.be (Guy Bottu) Date: Wed, 16 Jul 2008 19:24:46 +0200 Subject: [emboss-dev] on-line manual blues Message-ID: <487E2EDE.5070302@vub.ac.be> Dear Peter and Alan, We are on the verge of releasing a new version of wEMBOSS. The recent release of EMBOSS 6 forced us to perform a last minute change to make it work. Good news is that Marc Colet found a way to let wEMBOSS find the on-line manuals in HTML format, no matter where they are. So, you can ignore the mail I send last week. At this occasion I spent a lot of work on getting at the BEN site the manuals (and all the internal hyperlinks) right and I discovered that my old complaint about the manual for extractalign not being there was due to the fact that it is in the distribution but was not installed because not mentioned in the Makefile. This is corrected in EMBOSS version 6. Idem for edit_group.html. But there are some troubles that persist in the Embassy packages : - In the PHYLIPNEW package the manuals for fdnamove, fdolmove and frestdist are there but are not installed - In the package TOPO the file topo.gif is lacking and hence topo.html has a "dead" hyperlink. I managed to rescue the file topo.gif from .../EMBOSS-3.0.0/doc/programs/html/ Regards, Guy Bottu, BEN From breedaditi at yahoo.com Fri Jul 18 19:50:58 2008 From: breedaditi at yahoo.com (Aditi Breed) Date: Fri, 18 Jul 2008 12:50:58 -0700 (PDT) Subject: [emboss-dev] Installation (make ) error Message-ID: <954760.98297.qm@web35906.mail.mud.yahoo.com> Hello , I get the following error when i try to make EMBOSS. Can some one guide me as to what i need to do , to get rid of this error . xwin.c:3378: error: 'XwDisplay' has no member named 'display' xwin.c:3378: error: 'XwDev' has no member named 'window' xwin.c:3378: error: 'XwDev' has no member named 'gc' xwin.c:3379: error: 'XwDev' has no member named 'width' xwin.c:3379: error: 'XwDev' has no member named 'height' xwin.c: In function 'imageops': xwin.c:3394: error: 'XwDev' has no member named 'write_to_window' xwin.c:3398: error: 'XwDev' has no member named 'write_to_window' xwin.c:3402: error: 'XwDev' has no member named 'write_to_pixmap' xwin.c:3406: error: 'XwDisplay' has no member named 'display' xwin.c:3407: error: 'XwDev' has no member named 'write_to_pixmap' make[2]: *** [xwin.lo] Error 1 make[2]: Leaving directory `/home/akhunovlab/DOWNLOADS/EMBOSS/EMBOSS-6.0.1/plplot' make[1]: *** [all-recursive] Error 1 make[1]: Leaving directory `/home/akhunovlab/DOWNLOADS/EMBOSS/EMBOSS-6.0.1/plplot' make: *** [all-recursive] Error 1 I shall be grateful if someone could please help .. Regards, Aditi "Great spirits often meet violent opposition with mediocre minds" - Albert Einstein From jbdundas at gmail.com Wed Jul 30 12:31:46 2008 From: jbdundas at gmail.com (jitesh dundas) Date: Wed, 30 Jul 2008 18:01:46 +0530 Subject: [emboss-dev] Request For Work In-Reply-To: <326ea8620807300515n521c4f1ekf9042983fbc136f5@mail.gmail.com> References: <326ea8620807300515n521c4f1ekf9042983fbc136f5@mail.gmail.com> Message-ID: <326ea8620807300531o43c7d25emad126ac26f0c376a@mail.gmail.com> Dear All, Greetings! I am interested in contributing to this wonderful project. Can somebody please suggest where to start? *About MySelf* I want to persue a doctoral program in Bio-Informatics next year, for which I am preparing right now. However, I am still looking for some guidance and work in this field to help me get the experience needed. I have an inclination towards the fields of Finance,Medicine and Computers and constanlty look out for ways to use my knowledge and capabilities to innovate and discover in them. I have a passion for research-work, working on complex and ambiguous problems. I relentlessly work towards resolving them until they are solved permanently with the best possible solution. I am always ready to learn new things and teach others too. I can work independently as well as in teams with minimum supervision. I continuously try to improvize in my work by focussing on innovation and scientific reasoning. I am a hard-working, sincere and research-oriented professional with a scientific bend of mind and a never give-up attitude. I hope you will give me an opportunity to explore the world of research under you. Yours sincerely, Jitesh Dundas http://jiteshbdundas.blogspot.com Mobile- +91-9860925706