From ebs15242 at gmail.com Thu Mar 1 14:18:50 2012 From: ebs15242 at gmail.com (Ed Siefker) Date: Thu, 1 Mar 2012 13:18:50 -0600 Subject: [EMBOSS] sixpack -orfminsize Message-ID: Why do I get protein sequences that are shorter than orfminsize/3 when I use that option with sixpack? Do I misunderstand what an ORF is? ebs15242 at biox:~/Data/EMBOSS$ sixpack -orfminsize 500 kras.gb Display a DNA sequence with 6-frame translation and ORFs Output file [nm_004985.sixpack]: protein output sequence(s) [nm_004985.fasta]: ebs15242 at biox:~/Data/EMBOSS$ head nm_004985.fasta >NM_004985_1_ORF1 Translation of NM_004985 in frame 1, ORF 1, threshold 500, 62aa GRGGGGSSGGGSGGGEGGGGSASTPGPRHFGLGASAAQALKAAAGPEAQRLPGAGERPAE ND >NM_004985_1_ORF2 Translation of NM_004985 in frame 1, ORF 2, threshold 500, 31aa SKICNIFVMNCTTPNYCNVIKIVTVTKKKKX 62aa and 31aa lead to sizes of 186bp and 93bp. What's happening to the other 300-400 base pairs in the ORF? Why are they not getting translated? From pmr at ebi.ac.uk Fri Mar 2 04:02:12 2012 From: pmr at ebi.ac.uk (Peter Rice) Date: Fri, 02 Mar 2012 09:02:12 +0000 Subject: [EMBOSS] sixpack -orfminsize In-Reply-To: References: Message-ID: <4F508C94.8030000@ebi.ac.uk> On 03/01/12 19:18, Ed Siefker wrote: > Why do I get protein sequences that are shorter than orfminsize/3 when > I use that option with sixpack? Do I misunderstand what an ORF is? orfminsize is in protein units, so your threshold is higher than the longest ORF. We will update the help and documentation to make this clearer. > ebs15242 at biox:~/Data/EMBOSS$ sixpack -orfminsize 500 kras.gb > Display a DNA sequence with 6-frame translation and ORFs > Output file [nm_004985.sixpack]: > protein output sequence(s) [nm_004985.fasta]: > ebs15242 at biox:~/Data/EMBOSS$ head nm_004985.fasta >> NM_004985_1_ORF1 Translation of NM_004985 in frame 1, ORF 1, threshold 500, 62aa > GRGGGGSSGGGSGGGEGGGGSASTPGPRHFGLGASAAQALKAAAGPEAQRLPGAGERPAE > ND >> NM_004985_1_ORF2 Translation of NM_004985 in frame 1, ORF 2, threshold 500, 31aa > SKICNIFVMNCTTPNYCNVIKIVTVTKKKKX > > 62aa and 31aa lead to sizes of 186bp and 93bp. What's happening to > the other 300-400 base pairs in the ORF? Why are they not getting > translated? With those options you will see only 12 ORFs, all less than your 500aa threshold. Sixpack also reports (by default) the ORFs at the beginning and end of the sequence in case they are part of a longer translation. These are the ORFs that you see in th eoutput. You can turn them off with the options -nofirst and -nolast. The longest ORF in your sequence is 208aa. The -orfminsize value is the length of the protein translation so 208 is the largest threshold that will find a complete ORF. Hope this helps, Peter Rice EMBOSS Team From wolfgang.brosch at gmx.at Sat Mar 3 04:02:00 2012 From: wolfgang.brosch at gmx.at (Wolfgang Brosch) Date: Sat, 03 Mar 2012 10:02:00 +0100 Subject: [EMBOSS] In silico cloning Message-ID: <20120303090200.64770@gmx.net> Hello, in our faculty we want to set up a bioinformatics homepage where we offer the solutions for different needs. In most cases we can refer to our EMBOSS Server and are very happy with this solution. Only for "in silico cloning" we have no solution we are happy with. There is so little missing in EMBOSS and people most time don't believe me that they have to use another software for this. What I think of, when I am talking about in silico cloning is already perfectly described in this list: http://lists.open-bio.org/pipermail/emboss/2011-December/004234.html Now I would be happy to know something concrete: - Are there any plans to implement this functionality into EMBOSS? - If yes: When can we expect to get this functionality? Thank you very much for information Wolfgang -- NEU: FreePhone 3-fach-Flat mit kostenlosem Smartphone! Jetzt informieren: http://mobile.1und1.de/?ac=OM.PW.PW003K20328T7073a From stefanielager at gmail.com Sun Mar 4 23:49:12 2012 From: stefanielager at gmail.com (Stefanie Lager) Date: Mon, 5 Mar 2012 06:49:12 +0200 Subject: [EMBOSS] In silico cloning In-Reply-To: <20120303090200.64770@gmx.net> References: <20120303090200.64770@gmx.net> Message-ID: Hi, I do agree that it would be nice to have these features included in EMBOSS. But there are also non-commercial alternatives available e.g. PlasmaDNA Stefanie On Sat, Mar 3, 2012 at 11:02 AM, Wolfgang Brosch wrote: > Hello, > > in our faculty we want to set up a bioinformatics homepage where we offer the solutions for different needs. In most cases we can refer to our EMBOSS Server and are very happy with this solution. Only for "in silico cloning" we have no solution we are happy with. There is so little missing in EMBOSS and people most time don't believe me that they have to use another software for this. > > What I think of, when I am talking about in silico cloning is already perfectly described in this list: > http://lists.open-bio.org/pipermail/emboss/2011-December/004234.html > > Now I would be happy to know something concrete: > - Are there any plans to implement this functionality into EMBOSS? > - If yes: When can we expect to get this functionality? > > Thank you very much for information > Wolfgang > > > -- > NEU: FreePhone 3-fach-Flat mit kostenlosem Smartphone! > Jetzt informieren: http://mobile.1und1.de/?ac=OM.PW.PW003K20328T7073a > _______________________________________________ > EMBOSS mailing list > EMBOSS at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/emboss From wolfgang.brosch at gmx.at Mon Mar 5 04:24:58 2012 From: wolfgang.brosch at gmx.at (Wolfgang Brosch) Date: Mon, 05 Mar 2012 10:24:58 +0100 Subject: [EMBOSS] In silico cloning In-Reply-To: References: <20120303090200.64770@gmx.net> Message-ID: <20120305092458.209310@gmx.net> 2012/3/5 Stefanie Lager : > I do agree that it would be nice to have these features included in > EMBOSS. But there are also non-commercial alternatives available e.g. > PlasmaDNA This is what we do in the moment: referring to alternatives. But people are not happy with this, because first they learn to work with EMBOSS, learn to love it and then they have to use an other software for such simple bioinformatics stuff. This is why I am asking... It is possible without EMBOSS, but this little addition would be a great improve for usability in praxis. Wolfgang -- NEU: FreePhone 3-fach-Flat mit kostenlosem Smartphone! Jetzt informieren: http://mobile.1und1.de/?ac=OM.PW.PW003K20328T7073a From marvin.stodolsky at gmail.com Mon Mar 5 12:37:19 2012 From: marvin.stodolsky at gmail.com (Marvin Stodolsky) Date: Mon, 5 Mar 2012 11:37:19 -0600 Subject: [EMBOSS] dicodon rankin software, Perl to C translation Message-ID: It is well established that there are species specific biases in codon and dicodon usage which strongly affect the efficiency of mRNAs translation. There are a few companies offering protein production services, based on calculating these biases and "recoding" mRNAs for better expression in new host species. I have worked up dicodon calculation software, which I want to put in the public domain. The problem is that I have no formal IT training the code is a heterogenous hack. It draws on: some EMBOSS binaries PERL scripts donated by my son (an IT professional) and some Linux binaries all called through my hack of a master BASH script It would clearly be best of all of the above could be combined into some EMBOSS functionality. Thus a collaborator(s) are being sought to wok this through. I am 72 and retired, and do not at this time want to start a new career learning C coding. So anyone interested please contact me. Through mid March I am traveling until returning to the Wash DC area. So my responses may be slow until then. Sincerely: Marvin Stodolsky, Ph.D Biophysics retired from the US Dept. of Energy, Office of Science, Office of Biological & Environ. Rsch From jmsallen12 at gmail.com Thu Mar 15 14:07:55 2012 From: jmsallen12 at gmail.com (James Allen) Date: Thu, 15 Mar 2012 14:07:55 -0400 Subject: [EMBOSS] World's biggest fake conference in computer science Message-ID: --- Better not to have a publication than to publish in WORLDCOMP and spoil the resume forever --- If you didn't know already, WORLDCOMP is the World's biggest fake conference in computer science http://sites.google.com/site/worlddump1 The next WORLDCOMP (consists of more than twenty different conferences) will be during July 16-19, 2012, USA. Hamid Arabnia (a professor in computer science from University of Georgia, USA) has been running this fake (bogus or junk or scam) conference business to collect registration fee for over a decade. He accepts almost all submitted papers but cheating that there is a review by "two experts". He accumulated millions of dollars by this business. If the above link didn't work, you may try http://copy-shake-paste.blogspot.com/2012/02/fake-conference-worldcomp.html If none of these links work, search internet using worldcomp bogus If you have a paper in WORLDCOMP 2011 or earlier, you may file a lawsuit against Hamid Arabnia because he cheated you about reviews, reviewers, acceptance policies and acceptance rates. Sincerely, James Allen LATEST NEWS (as of March 11, 2012): Hamid Arabnia removed his name and address (ie, University of Georgia, where he is working as a professor) from WORLDCOMP website. If the conference is not fake, why he removed them suddenly? Who is the chair/coordinator of this bogus conference now? There are no committee members, keynote speeches and sponsors. The draft paper submission date is quietly extended. Why is Hamid Arabnia still running the fake conference anonymously and for whose benefit? We ask him to answer all these questions. This is the first time (in the entire world) a conference is running without the chair/coordinator name listed. Hamid Arabnia may soon bring another person (just for name sake) as the chair of WORLDCOMP and still Hamdid Arabnia run it from behind the scenes forever. From cjfields at illinois.edu Thu Mar 15 14:20:43 2012 From: cjfields at illinois.edu (Fields, Christopher J) Date: Thu, 15 Mar 2012 18:20:43 +0000 Subject: [EMBOSS] World's biggest fake conference in computer science In-Reply-To: References: Message-ID: <093F525B-C5AE-4B46-B130-91742E7092C0@illinois.edu> Interesting, but what exactly does this have to do with EMBOSS? chris On Mar 15, 2012, at 1:07 PM, James Allen wrote: > --- Better not to have a publication than to publish in WORLDCOMP and > spoil the resume forever --- > > If you didn't know already, WORLDCOMP is the World's biggest fake > conference in computer science > http://sites.google.com/site/worlddump1 The next WORLDCOMP (consists > of more than twenty different conferences) will be during July 16-19, > 2012, USA. > > Hamid Arabnia (a professor in computer science from University of > Georgia, USA) has been running this fake (bogus or junk or scam) > conference business to collect registration fee for over a decade. He > accepts almost all submitted papers but cheating that there is a > review by "two experts". He accumulated millions of dollars by this > business. > > > If the above link didn't work, you may try > http://copy-shake-paste.blogspot.com/2012/02/fake-conference-worldcomp.html > > If none of these links work, search internet using worldcomp bogus > > > If you have a paper in WORLDCOMP 2011 or earlier, you may file a > lawsuit against Hamid Arabnia because he cheated you about reviews, > reviewers, acceptance policies and acceptance rates. > > Sincerely, > James Allen > > > > LATEST NEWS (as of March 11, 2012): Hamid Arabnia removed his name and > address (ie, University of Georgia, where he is working as a > professor) from WORLDCOMP website. If the conference is not fake, why > he removed them suddenly? Who is the chair/coordinator of this bogus > conference now? There are no committee members, keynote speeches and > sponsors. The draft paper submission date is quietly extended. Why is > Hamid Arabnia still running the fake conference anonymously and for > whose benefit? We ask him to answer all these questions. This is the > first time (in the entire world) a conference is running without the > chair/coordinator name listed. Hamid Arabnia may soon bring another > person (just for name sake) as the chair of WORLDCOMP and still Hamdid > Arabnia run it from behind the scenes forever. > _______________________________________________ > EMBOSS mailing list > EMBOSS at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/emboss From ebs15242 at gmail.com Thu Mar 1 19:18:50 2012 From: ebs15242 at gmail.com (Ed Siefker) Date: Thu, 1 Mar 2012 13:18:50 -0600 Subject: [EMBOSS] sixpack -orfminsize Message-ID: Why do I get protein sequences that are shorter than orfminsize/3 when I use that option with sixpack? Do I misunderstand what an ORF is? ebs15242 at biox:~/Data/EMBOSS$ sixpack -orfminsize 500 kras.gb Display a DNA sequence with 6-frame translation and ORFs Output file [nm_004985.sixpack]: protein output sequence(s) [nm_004985.fasta]: ebs15242 at biox:~/Data/EMBOSS$ head nm_004985.fasta >NM_004985_1_ORF1 Translation of NM_004985 in frame 1, ORF 1, threshold 500, 62aa GRGGGGSSGGGSGGGEGGGGSASTPGPRHFGLGASAAQALKAAAGPEAQRLPGAGERPAE ND >NM_004985_1_ORF2 Translation of NM_004985 in frame 1, ORF 2, threshold 500, 31aa SKICNIFVMNCTTPNYCNVIKIVTVTKKKKX 62aa and 31aa lead to sizes of 186bp and 93bp. What's happening to the other 300-400 base pairs in the ORF? Why are they not getting translated? From pmr at ebi.ac.uk Fri Mar 2 09:02:12 2012 From: pmr at ebi.ac.uk (Peter Rice) Date: Fri, 02 Mar 2012 09:02:12 +0000 Subject: [EMBOSS] sixpack -orfminsize In-Reply-To: References: Message-ID: <4F508C94.8030000@ebi.ac.uk> On 03/01/12 19:18, Ed Siefker wrote: > Why do I get protein sequences that are shorter than orfminsize/3 when > I use that option with sixpack? Do I misunderstand what an ORF is? orfminsize is in protein units, so your threshold is higher than the longest ORF. We will update the help and documentation to make this clearer. > ebs15242 at biox:~/Data/EMBOSS$ sixpack -orfminsize 500 kras.gb > Display a DNA sequence with 6-frame translation and ORFs > Output file [nm_004985.sixpack]: > protein output sequence(s) [nm_004985.fasta]: > ebs15242 at biox:~/Data/EMBOSS$ head nm_004985.fasta >> NM_004985_1_ORF1 Translation of NM_004985 in frame 1, ORF 1, threshold 500, 62aa > GRGGGGSSGGGSGGGEGGGGSASTPGPRHFGLGASAAQALKAAAGPEAQRLPGAGERPAE > ND >> NM_004985_1_ORF2 Translation of NM_004985 in frame 1, ORF 2, threshold 500, 31aa > SKICNIFVMNCTTPNYCNVIKIVTVTKKKKX > > 62aa and 31aa lead to sizes of 186bp and 93bp. What's happening to > the other 300-400 base pairs in the ORF? Why are they not getting > translated? With those options you will see only 12 ORFs, all less than your 500aa threshold. Sixpack also reports (by default) the ORFs at the beginning and end of the sequence in case they are part of a longer translation. These are the ORFs that you see in th eoutput. You can turn them off with the options -nofirst and -nolast. The longest ORF in your sequence is 208aa. The -orfminsize value is the length of the protein translation so 208 is the largest threshold that will find a complete ORF. Hope this helps, Peter Rice EMBOSS Team From wolfgang.brosch at gmx.at Sat Mar 3 09:02:00 2012 From: wolfgang.brosch at gmx.at (Wolfgang Brosch) Date: Sat, 03 Mar 2012 10:02:00 +0100 Subject: [EMBOSS] In silico cloning Message-ID: <20120303090200.64770@gmx.net> Hello, in our faculty we want to set up a bioinformatics homepage where we offer the solutions for different needs. In most cases we can refer to our EMBOSS Server and are very happy with this solution. Only for "in silico cloning" we have no solution we are happy with. There is so little missing in EMBOSS and people most time don't believe me that they have to use another software for this. What I think of, when I am talking about in silico cloning is already perfectly described in this list: http://lists.open-bio.org/pipermail/emboss/2011-December/004234.html Now I would be happy to know something concrete: - Are there any plans to implement this functionality into EMBOSS? - If yes: When can we expect to get this functionality? Thank you very much for information Wolfgang -- NEU: FreePhone 3-fach-Flat mit kostenlosem Smartphone! Jetzt informieren: http://mobile.1und1.de/?ac=OM.PW.PW003K20328T7073a From stefanielager at gmail.com Mon Mar 5 04:49:12 2012 From: stefanielager at gmail.com (Stefanie Lager) Date: Mon, 5 Mar 2012 06:49:12 +0200 Subject: [EMBOSS] In silico cloning In-Reply-To: <20120303090200.64770@gmx.net> References: <20120303090200.64770@gmx.net> Message-ID: Hi, I do agree that it would be nice to have these features included in EMBOSS. But there are also non-commercial alternatives available e.g. PlasmaDNA Stefanie On Sat, Mar 3, 2012 at 11:02 AM, Wolfgang Brosch wrote: > Hello, > > in our faculty we want to set up a bioinformatics homepage where we offer the solutions for different needs. In most cases we can refer to our EMBOSS Server and are very happy with this solution. Only for "in silico cloning" we have no solution we are happy with. There is so little missing in EMBOSS and people most time don't believe me that they have to use another software for this. > > What I think of, when I am talking about in silico cloning is already perfectly described in this list: > http://lists.open-bio.org/pipermail/emboss/2011-December/004234.html > > Now I would be happy to know something concrete: > - Are there any plans to implement this functionality into EMBOSS? > - If yes: When can we expect to get this functionality? > > Thank you very much for information > Wolfgang > > > -- > NEU: FreePhone 3-fach-Flat mit kostenlosem Smartphone! > Jetzt informieren: http://mobile.1und1.de/?ac=OM.PW.PW003K20328T7073a > _______________________________________________ > EMBOSS mailing list > EMBOSS at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/emboss From wolfgang.brosch at gmx.at Mon Mar 5 09:24:58 2012 From: wolfgang.brosch at gmx.at (Wolfgang Brosch) Date: Mon, 05 Mar 2012 10:24:58 +0100 Subject: [EMBOSS] In silico cloning In-Reply-To: References: <20120303090200.64770@gmx.net> Message-ID: <20120305092458.209310@gmx.net> 2012/3/5 Stefanie Lager : > I do agree that it would be nice to have these features included in > EMBOSS. But there are also non-commercial alternatives available e.g. > PlasmaDNA This is what we do in the moment: referring to alternatives. But people are not happy with this, because first they learn to work with EMBOSS, learn to love it and then they have to use an other software for such simple bioinformatics stuff. This is why I am asking... It is possible without EMBOSS, but this little addition would be a great improve for usability in praxis. Wolfgang -- NEU: FreePhone 3-fach-Flat mit kostenlosem Smartphone! Jetzt informieren: http://mobile.1und1.de/?ac=OM.PW.PW003K20328T7073a From marvin.stodolsky at gmail.com Mon Mar 5 17:37:19 2012 From: marvin.stodolsky at gmail.com (Marvin Stodolsky) Date: Mon, 5 Mar 2012 11:37:19 -0600 Subject: [EMBOSS] dicodon rankin software, Perl to C translation Message-ID: It is well established that there are species specific biases in codon and dicodon usage which strongly affect the efficiency of mRNAs translation. There are a few companies offering protein production services, based on calculating these biases and "recoding" mRNAs for better expression in new host species. I have worked up dicodon calculation software, which I want to put in the public domain. The problem is that I have no formal IT training the code is a heterogenous hack. It draws on: some EMBOSS binaries PERL scripts donated by my son (an IT professional) and some Linux binaries all called through my hack of a master BASH script It would clearly be best of all of the above could be combined into some EMBOSS functionality. Thus a collaborator(s) are being sought to wok this through. I am 72 and retired, and do not at this time want to start a new career learning C coding. So anyone interested please contact me. Through mid March I am traveling until returning to the Wash DC area. So my responses may be slow until then. Sincerely: Marvin Stodolsky, Ph.D Biophysics retired from the US Dept. of Energy, Office of Science, Office of Biological & Environ. Rsch From jmsallen12 at gmail.com Thu Mar 15 18:07:55 2012 From: jmsallen12 at gmail.com (James Allen) Date: Thu, 15 Mar 2012 14:07:55 -0400 Subject: [EMBOSS] World's biggest fake conference in computer science Message-ID: --- Better not to have a publication than to publish in WORLDCOMP and spoil the resume forever --- If you didn't know already, WORLDCOMP is the World's biggest fake conference in computer science http://sites.google.com/site/worlddump1 The next WORLDCOMP (consists of more than twenty different conferences) will be during July 16-19, 2012, USA. Hamid Arabnia (a professor in computer science from University of Georgia, USA) has been running this fake (bogus or junk or scam) conference business to collect registration fee for over a decade. He accepts almost all submitted papers but cheating that there is a review by "two experts". He accumulated millions of dollars by this business. If the above link didn't work, you may try http://copy-shake-paste.blogspot.com/2012/02/fake-conference-worldcomp.html If none of these links work, search internet using worldcomp bogus If you have a paper in WORLDCOMP 2011 or earlier, you may file a lawsuit against Hamid Arabnia because he cheated you about reviews, reviewers, acceptance policies and acceptance rates. Sincerely, James Allen LATEST NEWS (as of March 11, 2012): Hamid Arabnia removed his name and address (ie, University of Georgia, where he is working as a professor) from WORLDCOMP website. If the conference is not fake, why he removed them suddenly? Who is the chair/coordinator of this bogus conference now? There are no committee members, keynote speeches and sponsors. The draft paper submission date is quietly extended. Why is Hamid Arabnia still running the fake conference anonymously and for whose benefit? We ask him to answer all these questions. This is the first time (in the entire world) a conference is running without the chair/coordinator name listed. Hamid Arabnia may soon bring another person (just for name sake) as the chair of WORLDCOMP and still Hamdid Arabnia run it from behind the scenes forever. From cjfields at illinois.edu Thu Mar 15 18:20:43 2012 From: cjfields at illinois.edu (Fields, Christopher J) Date: Thu, 15 Mar 2012 18:20:43 +0000 Subject: [EMBOSS] World's biggest fake conference in computer science In-Reply-To: References: Message-ID: <093F525B-C5AE-4B46-B130-91742E7092C0@illinois.edu> Interesting, but what exactly does this have to do with EMBOSS? chris On Mar 15, 2012, at 1:07 PM, James Allen wrote: > --- Better not to have a publication than to publish in WORLDCOMP and > spoil the resume forever --- > > If you didn't know already, WORLDCOMP is the World's biggest fake > conference in computer science > http://sites.google.com/site/worlddump1 The next WORLDCOMP (consists > of more than twenty different conferences) will be during July 16-19, > 2012, USA. > > Hamid Arabnia (a professor in computer science from University of > Georgia, USA) has been running this fake (bogus or junk or scam) > conference business to collect registration fee for over a decade. He > accepts almost all submitted papers but cheating that there is a > review by "two experts". He accumulated millions of dollars by this > business. > > > If the above link didn't work, you may try > http://copy-shake-paste.blogspot.com/2012/02/fake-conference-worldcomp.html > > If none of these links work, search internet using worldcomp bogus > > > If you have a paper in WORLDCOMP 2011 or earlier, you may file a > lawsuit against Hamid Arabnia because he cheated you about reviews, > reviewers, acceptance policies and acceptance rates. > > Sincerely, > James Allen > > > > LATEST NEWS (as of March 11, 2012): Hamid Arabnia removed his name and > address (ie, University of Georgia, where he is working as a > professor) from WORLDCOMP website. If the conference is not fake, why > he removed them suddenly? Who is the chair/coordinator of this bogus > conference now? There are no committee members, keynote speeches and > sponsors. The draft paper submission date is quietly extended. Why is > Hamid Arabnia still running the fake conference anonymously and for > whose benefit? We ask him to answer all these questions. This is the > first time (in the entire world) a conference is running without the > chair/coordinator name listed. Hamid Arabnia may soon bring another > person (just for name sake) as the chair of WORLDCOMP and still Hamdid > Arabnia run it from behind the scenes forever. > _______________________________________________ > EMBOSS mailing list > EMBOSS at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/emboss