From jeedward at yahoo.com Thu Dec 4 11:14:16 2008 From: jeedward at yahoo.com (John Edward) Date: Thu, 4 Dec 2008 08:14:16 -0800 (PST) Subject: [EMBOSS] BCBGC-09 call for papers Message-ID: <865899.36598.qm@web45906.mail.sp1.yahoo.com> BCBGC-09 call for papers ? The 2009 International Conference on Bioinformatics, Computational Biology, Genomics and Chemoinformatics (BCBGC-09) (website: http://www.PromoteResearch.org ) will be held during July 13-16 2009 in Orlando, FL, USA. We invite draft paper submissions. The conference will take place at the same time and venue where several other international conferences are taking place. The other conferences include: ????????? International Conference on Artificial Intelligence and Pattern Recognition (AIPR-09) ????????? International Conference on Automation, Robotics and Control Systems (ARCS-09) ????????? International Conference on Enterprise Information Systems and Web Technologies (EISWT-09) ????????? International Conference on High Performance Computing, Networking and Communication Systems (HPCNCS-09) ????????? International Conference on Information Security and Privacy (ISP-09) ????????? International Conference on Recent Advances in Information Technology and Applications (RAITA-09) ????????? International Conference on Software Engineering Theory and Practice (SETP-09) ????????? International Conference on Theory and Applications of Computational Science (TACS-09) ????????? International Conference on Theoretical and Mathematical Foundations of Computer Science (TMFCS-09) ? The website http://www.PromoteResearch.org contains more details. ? Sincerely John Edward Publicity committee ? ? ? From staffa at niehs.nih.gov Tue Dec 9 08:43:54 2008 From: staffa at niehs.nih.gov (Staffa, Nick (NIH/NIEHS)) Date: Tue, 09 Dec 2008 08:43:54 -0500 Subject: [EMBOSS] Archive In-Reply-To: <492D621D.6050104@umdnj.edu> Message-ID: Is there a web archive of these messages? I sure like to use someone else's disk space until I get around to viewing all these. Thanks Nick Staffa Telephone: 919-316-4569 (NIEHS: 6-4569) Scientific Computing Support Group NIEHS Enterprise-Wide Information Technology Support Contract National Institute of Environmental Health Sciences National Institutes of Health Research Triangle Park, North Carolina From uludag at ebi.ac.uk Tue Dec 9 09:22:54 2008 From: uludag at ebi.ac.uk (Mahmut Uludag) Date: Tue, 09 Dec 2008 14:22:54 +0000 Subject: [EMBOSS] Archive In-Reply-To: References: Message-ID: <1228832574.8069.43.camel@emboss2.ebi.ac.uk> > Is there a web archive of these messages? Did you mean this? http://lists.open-bio.org/pipermail/emboss/ Regards, Mahmut From staffa at niehs.nih.gov Tue Dec 9 09:24:58 2008 From: staffa at niehs.nih.gov (Staffa, Nick (NIH/NIEHS) [C]) Date: Tue, 9 Dec 2008 09:24:58 -0500 Subject: [EMBOSS] Archive In-Reply-To: <1228832574.8069.43.camel@emboss2.ebi.ac.uk> References: <1228832574.8069.43.camel@emboss2.ebi.ac.uk> Message-ID: <7930EE6CD7CA354D93B444D0433C061106848CBC@NIHCESMLBX6.nih.gov> Thanks Nickolas G. Staffa, Jr. Ph.D. Telephone: 919-316-4569 (NIEHS: 6-4569) Scientific Computing Support Group NIEHS E-WITS Contract National Institute of Environmental Health Sciences National Institutes of Health Research Triangle Park, North Carolina > -----Original Message----- > From: Mahmut Uludag [mailto:uludag at ebi.ac.uk] > Sent: Tuesday, December 09, 2008 9:23 AM > To: Staffa, Nick (NIH/NIEHS) [C] > Cc: emboss at lists.open-bio.org > Subject: Re: [EMBOSS] Archive > > > > Is there a web archive of these messages? > > Did you mean this? > > http://lists.open-bio.org/pipermail/emboss/ > > Regards, > Mahmut > From sufei at mail.sdu.edu.cn Wed Dec 10 08:30:31 2008 From: sufei at mail.sdu.edu.cn (sufei) Date: Wed, 10 Dec 2008 21:30:31 +0800 Subject: [EMBOSS] how to merge two sequence file Message-ID: <428915968.10036@mail.sdu.edu.cn> hi, I am new for emboss. When I use merger to merge two sequence file, I find that it only can input s single sequence. How can I merge the two sequence file? sufei From ztu at msi.umn.edu Wed Dec 10 08:59:52 2008 From: ztu at msi.umn.edu (Zheng Jin Tu) Date: Wed, 10 Dec 2008 07:59:52 -0600 (CST) Subject: [EMBOSS] how to merge two sequence file In-Reply-To: <428915968.10036@mail.sdu.edu.cn> References: <428915968.10036@mail.sdu.edu.cn> Message-ID: On UNIX/Linux computer, use simple UNIX cat command: cat seqfile1 seqfile2 .... seqfilex > new_merged_seqfile Thanks, Tu ================================================ On Wed, 10 Dec 2008, sufei wrote: > hi, > I am new for emboss. When I use merger to merge two sequence file, I find that it only can input s single sequence. How can I merge the two sequence file? > > sufei > From malabady at gmail.com Wed Dec 10 10:00:54 2008 From: malabady at gmail.com (Magdy Alabady) Date: Wed, 10 Dec 2008 09:00:54 -0600 Subject: [EMBOSS] EMBOSS proplem Message-ID: <6967ac4e0812100700s3708c00br7dbc606e79a6529c@mail.gmail.com> Hi I am new user of EMBOSS. I followed the instruction to install EMBOSS on my Mac OS X. I am running into the following problem. Every time I run any program I get the following message: Error: File /usr/local/biotools/share/EMBOSS/acd/plotcon.acd line 0: ACD file not opened I tried to run the 'wossname' test, I also get this message: Error: File /usr/local/biotools/share/EMBOSS/acd/wossname.acd line 0: ACD file not opened Any help to resolve this problem please? Thanks Magdy On Wed, Dec 10, 2008 at 7:59 AM, Zheng Jin Tu wrote: > > On UNIX/Linux computer, use simple UNIX cat command: > > cat seqfile1 seqfile2 .... seqfilex > new_merged_seqfile > > Thanks, Tu > > ================================================ > > On Wed, 10 Dec 2008, sufei wrote: > > > hi, > > I am new for emboss. When I use merger to merge two sequence file, I find > that it only can input s single sequence. How can I merge the two sequence > file? > > > > sufei > > > _______________________________________________ > EMBOSS mailing list > EMBOSS at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/emboss > -- Magdy S. Alabady, PhD ------------------------------------------------------ If A is a success in life, then A equals x plus y plus z. Work is x; y is play; and z is keeping your mouth shut. .....Albert Einstein ------------------------------------------------------------- From gbottu at vub.ac.be Fri Dec 12 10:59:28 2008 From: gbottu at vub.ac.be (Guy Bottu) Date: Fri, 12 Dec 2008 16:59:28 +0100 Subject: [EMBOSS] Is someone still using EMBOSS version 3 or 4 ? Message-ID: <49428A60.8010107@vub.ac.be> Dear all, The current version of the wrappers4EMBOSS suite uses EMBOSS version 3.0.0 subroutine names and is therefore compatible with all EMBOSS versions from 3.0.0 up to 6.0.1. I am however considering upgrading the names to those of version 5.0.0, if not for other reasons then certainly to get rid of annoying long lists of compiler warning messages. Therefore my question : is still someone using EMBOSS version 3 or 4 and has some reason for not willing to upgrade between now and the first months of 2009 ? Regards, Guy Bottu, Belgian EMBnet Node - wEMBOSS development team From gbottu at vub.ac.be Fri Dec 12 10:58:53 2008 From: gbottu at vub.ac.be (Guy Bottu) Date: Fri, 12 Dec 2008 16:58:53 +0100 Subject: [EMBOSS] wrappers4EMBOSS 2.2.0 released Message-ID: <49428A3D.6010509@vub.ac.be> Dear users of wrappers4EMBOSS, This message only concerns you if you are using wrappers4EMBOSS with one of the following : EMBOSS version 6, a local installation of MRS version 3, fastA, ps_scan.pl for searching PROSITE, InterProScan version 4.4, a Web Service access to WU-BLAST and fastA at the EBI. You might have to upgrade for the following reasons : - The MYEMBOSS-6.0.0 package does not contain test programs. As a consequence the installation script of wrappers4EMBOSS failed on a "fresh" installation and had to be re-run. This bug has been fixed. - The script mrsget.pl (used to query a local MRS 3 installation) sometimes gave erroneous results. This bug has been fixed (with help of MRS developer Maarten Hekkelman). - The programs fastasearch and fastapid from the fastA module have been modified so that the entire description line is now included in the output (truncated description lines can be terribly uninformative...). Bug fixes in both the "wrapper" and in the fastA suite itself (by "Bill" Pearson after submission of a bug report) make that it is (again) possible to switch off statistics and obtain just a list of n best "hits" (in case you might need that). We have also made the installation of the old fastA version 2 suite for the purpose of pairwise comparison optional. - A novelty is that PROSITE pattern matches can be validated using a second search against a mini-profile. The "wrapper" for ps_scan has been adapted to run with the latest version of ps_scan.pl and the evaluator.dat file that is distributed with PROSITE. This validation is performed by default but can be switched off. This new way of handling PROSITE has also been introduced in InterProScan version 4.4 and the "wrapper" has been modified accordingly. - The lists of available databases in the ebi_blast and ebi_fasta programs has been updated. We can mention that the HGVBASE at the EBI is now at last searchable by WU-BLAST. Regards, Guy Bottu, Belgian EMBnet Node - wEMBOSS development team From malabady at gmail.com Thu Dec 18 18:00:30 2008 From: malabady at gmail.com (Magdy Alabady) Date: Thu, 18 Dec 2008 17:00:30 -0600 Subject: [EMBOSS] backtranseq Message-ID: <6967ac4e0812181500m18e5532cg83bbf1be1f6d8c60@mail.gmail.com> Hello all, Can backtranseq run input file contains several 100's of protein sequences in Fasta format? can it make bulk back translation? please tell me how to do so if it is possible Thanks -- Magdy S. Alabady, PhD ------------------------------------------------------ If A is a success in life, then A equals x plus y plus z. Work is x; y is play; and z is keeping your mouth shut. .....Albert Einstein ------------------------------------------------------------- From pmr at ebi.ac.uk Thu Dec 18 18:20:21 2008 From: pmr at ebi.ac.uk (Peter Rice) Date: Thu, 18 Dec 2008 23:20:21 +0000 Subject: [EMBOSS] backtranseq In-Reply-To: <6967ac4e0812181500m18e5532cg83bbf1be1f6d8c60@mail.gmail.com> References: <6967ac4e0812181500m18e5532cg83bbf1be1f6d8c60@mail.gmail.com> Message-ID: <494ADAB5.8030606@ebi.ac.uk> Magdy Alabady wrote: > Hello all, > > Can backtranseq run input file contains several 100's of protein sequences > in Fasta format? can it make bulk back translation? please tell me how to do > so if it is possible Backtranseq only processes a single sequence. You have several choices: 1. make a new version of backtranseq that can process multiple sequences (easy to do ... but you need to learn a little EMBOSS programming first :-) 2. put your sequence file in a directory and name it with anything other than a .fasta extension. use seqret -ossingle to convert your file into 100s of single sequence files run backtranseq on each of the individual files. I wonder ... do you really want 100s of backtranslations in a single file? regards, Peter Rice From andrespinzon at gmail.com Fri Dec 19 11:56:51 2008 From: andrespinzon at gmail.com (Andres Pinzon) Date: Fri, 19 Dec 2008 11:56:51 -0500 Subject: [EMBOSS] backtranseq In-Reply-To: <494ADAB5.8030606@ebi.ac.uk> References: <6967ac4e0812181500m18e5532cg83bbf1be1f6d8c60@mail.gmail.com> <494ADAB5.8030606@ebi.ac.uk> Message-ID: <8968fc7e0812190856g777f9b3du78db85473a1f0679@mail.gmail.com> This is a not too elegant solution to your problem: paste the following code in a file called "script.sh": ====================================== #!/bin/bash seqret -ossingle -sequence $1 -outseq 1.fasta for i in $( ls ); do if [ "$i" != "script.sh" ]; then echo Processing: $i backtranseq -sequence $i -outfile $i.bt fi done cat *.bt > $1.backtranslated.fasta ================================================= and run the script as this: ================================================== ./script.sh ../yourMultipleFastaFile ================================================== This script will take your multiple fasta file, will create single files from it. will run backtranslate on each of them and will create an output file with your results called: yourMultipleFastaFile_backtranslated.fasta Hope it helps. regards, On Thu, Dec 18, 2008 at 6:20 PM, Peter Rice wrote: > Magdy Alabady wrote: >> >> Hello all, >> >> Can backtranseq run input file contains several 100's of protein sequences >> in Fasta format? can it make bulk back translation? please tell me how to >> do >> so if it is possible > > Backtranseq only processes a single sequence. You have several choices: > > 1. make a new version of backtranseq that can process multiple sequences > (easy to do ... but you need to learn a little EMBOSS programming first :-) > > 2. put your sequence file in a directory and name it with anything other > than a .fasta extension. > > use seqret -ossingle to convert your file into 100s of single sequence files > > run backtranseq on each of the individual files. > > > I wonder ... do you really want 100s of backtranslations in a single file? > > regards, > > Peter Rice > _______________________________________________ > EMBOSS mailing list > EMBOSS at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/emboss > -- Andr?s Pinz?n http://bioinf.ibun.unal.edu.co/~apinzon/ Bioinformatics Center, Colombia EMBnet node http://bioinf.ibun.unal.edu.co Tel +57 3165000 ext 16961 Fax +571 3165415 Micology and Phytopathology Laboratory - Los Andes University. http://bioinf.uniandes.edu.co Tel +571 3394949 ext. 2768 From malabady at gmail.com Fri Dec 19 15:58:31 2008 From: malabady at gmail.com (Magdy Alabady) Date: Fri, 19 Dec 2008 14:58:31 -0600 Subject: [EMBOSS] backtranseq In-Reply-To: <8968fc7e0812190856g777f9b3du78db85473a1f0679@mail.gmail.com> References: <6967ac4e0812181500m18e5532cg83bbf1be1f6d8c60@mail.gmail.com> <494ADAB5.8030606@ebi.ac.uk> <8968fc7e0812190856g777f9b3du78db85473a1f0679@mail.gmail.com> Message-ID: <6967ac4e0812191258p40e082e4gaed25170042c0eb8@mail.gmail.com> Thanks Peter, it works well except it produces so many files. the number of files is 4 or 5 times more than the number of sequences x2. for example, if I have 10 sequences, I would expected 21 files produced: 10 protein sequences, 10 backtranslation files, and one concatenated file. Is this correct: one other thing, forgive me if it bad question, in the first line of the script isn't the "-outseq 1.fasta" should be "-outseq $1.fasta" thanks On Fri, Dec 19, 2008 at 10:56 AM, Andres Pinzon wrote: > This is a not too elegant solution to your problem: > paste the following code in a file called "script.sh": > ====================================== > > > #!/bin/bash > > seqret -ossingle -sequence $1 -outseq 1.fasta > > > for i in $( ls ); do > if [ "$i" != "script.sh" ]; then > echo Processing: $i > backtranseq -sequence $i -outfile $i.bt > fi > done > > cat *.bt > $1.backtranslated.fasta > > ================================================= > > and run the script as this: > ================================================== > ./script.sh ../yourMultipleFastaFile > ================================================== > > > This script will take your multiple fasta file, will create single > files from it. will run backtranslate on each of them and will create > an output file with your results called: > yourMultipleFastaFile_backtranslated.fasta > > > Hope it helps. > > regards, > > > > On Thu, Dec 18, 2008 at 6:20 PM, Peter Rice wrote: > > Magdy Alabady wrote: > >> > >> Hello all, > >> > >> Can backtranseq run input file contains several 100's of protein > sequences > >> in Fasta format? can it make bulk back translation? please tell me how > to > >> do > >> so if it is possible > > > > Backtranseq only processes a single sequence. You have several choices: > > > > 1. make a new version of backtranseq that can process multiple sequences > > (easy to do ... but you need to learn a little EMBOSS programming first > :-) > > > > 2. put your sequence file in a directory and name it with anything other > > than a .fasta extension. > > > > use seqret -ossingle to convert your file into 100s of single sequence > files > > > > run backtranseq on each of the individual files. > > > > > > I wonder ... do you really want 100s of backtranslations in a single > file? > > > > regards, > > > > Peter Rice > > _______________________________________________ > > EMBOSS mailing list > > EMBOSS at lists.open-bio.org > > http://lists.open-bio.org/mailman/listinfo/emboss > > > > > > -- > Andr?s Pinz?n > http://bioinf.ibun.unal.edu.co/~apinzon/ > Bioinformatics Center, Colombia EMBnet node > http://bioinf.ibun.unal.edu.co > Tel +57 3165000 ext 16961 Fax +571 3165415 > Micology and Phytopathology Laboratory - Los Andes University. > http://bioinf.uniandes.edu.co > Tel +571 3394949 ext. 2768 > -- Magdy S. Alabady, PhD ------------------------------------------------------ If A is a success in life, then A equals x plus y plus z. Work is x; y is play; and z is keeping your mouth shut. .....Albert Einstein ------------------------------------------------------------- From andrespinzon at gmail.com Fri Dec 19 16:45:56 2008 From: andrespinzon at gmail.com (Andres Pinzon) Date: Fri, 19 Dec 2008 16:45:56 -0500 Subject: [EMBOSS] backtranseq In-Reply-To: <6967ac4e0812191258p40e082e4gaed25170042c0eb8@mail.gmail.com> References: <6967ac4e0812181500m18e5532cg83bbf1be1f6d8c60@mail.gmail.com> <494ADAB5.8030606@ebi.ac.uk> <8968fc7e0812190856g777f9b3du78db85473a1f0679@mail.gmail.com> <6967ac4e0812191258p40e082e4gaed25170042c0eb8@mail.gmail.com> Message-ID: <8968fc7e0812191345m13cf5f5awd8743c999d1afebc@mail.gmail.com> Hi Magdy, This is Andres, please dont blame peter!!! for the script I wrote it :-) On Fri, Dec 19, 2008 at 3:58 PM, Magdy Alabady wrote: > Thanks Peter, it works well except it produces so many files. the number of > files is 4 or 5 times more than the number of sequences x2. for example, if > I have 10 sequences, I would expected 21 files produced: 10 protein > sequences, 10 backtranslation files, and one concatenated file. Is this > correct: lets say you have 1 multiple fasta file whith 3 entries. It will create 7 files. 3 single fasta files (one for every multiple fasta enty). 3 ".bt", one for each single fasta file and 1 file which concatenates this ".bt" files. (thjis is the way it works in my machine). Please take into account that if you run it several times on the same place it will multiply your files. > one other thing, forgive me if it bad question, in the first line of the > script isn't the "-outseq 1.fasta" should be "-outseq $1.fasta" nop, this option says seqret how to name the output files. So the first entry in the multiple fasta file will correspond to the 1.fasta file, the second one will correspond to 2.fasta and so on. I hope this helps, Please don hesitate to contact me. Best, > thanks > > On Fri, Dec 19, 2008 at 10:56 AM, Andres Pinzon > wrote: >> >> This is a not too elegant solution to your problem: >> paste the following code in a file called "script.sh": >> ====================================== >> >> >> #!/bin/bash >> >> seqret -ossingle -sequence $1 -outseq 1.fasta >> >> >> for i in $( ls ); do >> if [ "$i" != "script.sh" ]; then >> echo Processing: $i >> backtranseq -sequence $i -outfile $i.bt >> fi >> done >> >> cat *.bt > $1.backtranslated.fasta >> >> ================================================= >> >> and run the script as this: >> ================================================== >> ./script.sh ../yourMultipleFastaFile >> ================================================== >> >> >> This script will take your multiple fasta file, will create single >> files from it. will run backtranslate on each of them and will create >> an output file with your results called: >> yourMultipleFastaFile_backtranslated.fasta >> >> >> Hope it helps. >> >> regards, >> >> >> >> On Thu, Dec 18, 2008 at 6:20 PM, Peter Rice wrote: >> > Magdy Alabady wrote: >> >> >> >> Hello all, >> >> >> >> Can backtranseq run input file contains several 100's of protein >> >> sequences >> >> in Fasta format? can it make bulk back translation? please tell me how >> >> to >> >> do >> >> so if it is possible >> > >> > Backtranseq only processes a single sequence. You have several choices: >> > >> > 1. make a new version of backtranseq that can process multiple sequences >> > (easy to do ... but you need to learn a little EMBOSS programming first >> > :-) >> > >> > 2. put your sequence file in a directory and name it with anything other >> > than a .fasta extension. >> > >> > use seqret -ossingle to convert your file into 100s of single sequence >> > files >> > >> > run backtranseq on each of the individual files. >> > >> > >> > I wonder ... do you really want 100s of backtranslations in a single >> > file? >> > >> > regards, >> > >> > Peter Rice >> > _______________________________________________ >> > EMBOSS mailing list >> > EMBOSS at lists.open-bio.org >> > http://lists.open-bio.org/mailman/listinfo/emboss >> > >> >> >> >> -- >> Andr?s Pinz?n >> http://bioinf.ibun.unal.edu.co/~apinzon/ >> Bioinformatics Center, Colombia EMBnet node >> http://bioinf.ibun.unal.edu.co >> Tel +57 3165000 ext 16961 Fax +571 3165415 >> Micology and Phytopathology Laboratory - Los Andes University. >> http://bioinf.uniandes.edu.co >> Tel +571 3394949 ext. 2768 > > > > -- > Magdy S. Alabady, PhD > ------------------------------------------------------ > If A is a success in life, then A equals x plus y plus z. Work is x; y is > play; and z is keeping your mouth shut. .....Albert Einstein > ------------------------------------------------------------- > > -- Andr?s Pinz?n http://bioinf.ibun.unal.edu.co/~apinzon/ Bioinformatics Center, Colombia EMBnet node http://bioinf.ibun.unal.edu.co Tel +57 3165000 ext 16961 Fax +571 3165415 Micology and Phytopathology Laboratory - Los Andes University. http://bioinf.uniandes.edu.co Tel +571 3394949 ext. 2768 From malabady at gmail.com Fri Dec 19 18:01:17 2008 From: malabady at gmail.com (Magdy Alabady) Date: Fri, 19 Dec 2008 17:01:17 -0600 Subject: [EMBOSS] backtranseq In-Reply-To: <8968fc7e0812191345m13cf5f5awd8743c999d1afebc@mail.gmail.com> References: <6967ac4e0812181500m18e5532cg83bbf1be1f6d8c60@mail.gmail.com> <494ADAB5.8030606@ebi.ac.uk> <8968fc7e0812190856g777f9b3du78db85473a1f0679@mail.gmail.com> <6967ac4e0812191258p40e082e4gaed25170042c0eb8@mail.gmail.com> <8968fc7e0812191345m13cf5f5awd8743c999d1afebc@mail.gmail.com> Message-ID: <6967ac4e0812191501vafe0e43qa2890d820cfdc740@mail.gmail.com> Thanks Andres. On Fri, Dec 19, 2008 at 3:45 PM, Andres Pinzon wrote: > Hi Magdy, > This is Andres, please dont blame peter!!! for the script I wrote it :-) > > On Fri, Dec 19, 2008 at 3:58 PM, Magdy Alabady wrote: > > Thanks Peter, it works well except it produces so many files. the number > of > > files is 4 or 5 times more than the number of sequences x2. for example, > if > > I have 10 sequences, I would expected 21 files produced: 10 protein > > sequences, 10 backtranslation files, and one concatenated file. Is this > > correct: > > lets say you have 1 multiple fasta file whith 3 entries. > It will create 7 files. 3 single fasta files (one for every multiple > fasta enty). 3 ".bt", > one for each single fasta file and 1 file which concatenates this > ".bt" files. (thjis is the way it works in my machine). Please take > into account that if you run it several times on the same place it > will multiply your files. > > > > one other thing, forgive me if it bad question, in the first line of the > > script isn't the "-outseq 1.fasta" should be "-outseq $1.fasta" > > nop, this option says seqret how to name the output files. So the > first entry in the multiple fasta file will correspond to the 1.fasta > file, the second one will correspond to 2.fasta and so on. > I hope this helps, > > Please don hesitate to contact me. > > Best, > > thanks > > > > On Fri, Dec 19, 2008 at 10:56 AM, Andres Pinzon > > wrote: > >> > >> This is a not too elegant solution to your problem: > >> paste the following code in a file called "script.sh": > >> ====================================== > >> > >> > >> #!/bin/bash > >> > >> seqret -ossingle -sequence $1 -outseq 1.fasta > >> > >> > >> for i in $( ls ); do > >> if [ "$i" != "script.sh" ]; then > >> echo Processing: $i > >> backtranseq -sequence $i -outfile $i.bt > >> fi > >> done > >> > >> cat *.bt > $1.backtranslated.fasta > >> > >> ================================================= > >> > >> and run the script as this: > >> ================================================== > >> ./script.sh ../yourMultipleFastaFile > >> ================================================== > >> > >> > >> This script will take your multiple fasta file, will create single > >> files from it. will run backtranslate on each of them and will create > >> an output file with your results called: > >> yourMultipleFastaFile_backtranslated.fasta > >> > >> > >> Hope it helps. > >> > >> regards, > >> > >> > >> > >> On Thu, Dec 18, 2008 at 6:20 PM, Peter Rice wrote: > >> > Magdy Alabady wrote: > >> >> > >> >> Hello all, > >> >> > >> >> Can backtranseq run input file contains several 100's of protein > >> >> sequences > >> >> in Fasta format? can it make bulk back translation? please tell me > how > >> >> to > >> >> do > >> >> so if it is possible > >> > > >> > Backtranseq only processes a single sequence. You have several > choices: > >> > > >> > 1. make a new version of backtranseq that can process multiple > sequences > >> > (easy to do ... but you need to learn a little EMBOSS programming > first > >> > :-) > >> > > >> > 2. put your sequence file in a directory and name it with anything > other > >> > than a .fasta extension. > >> > > >> > use seqret -ossingle to convert your file into 100s of single sequence > >> > files > >> > > >> > run backtranseq on each of the individual files. > >> > > >> > > >> > I wonder ... do you really want 100s of backtranslations in a single > >> > file? > >> > > >> > regards, > >> > > >> > Peter Rice > >> > _______________________________________________ > >> > EMBOSS mailing list > >> > EMBOSS at lists.open-bio.org > >> > http://lists.open-bio.org/mailman/listinfo/emboss > >> > > >> > >> > >> > >> -- > >> Andr?s Pinz?n > >> http://bioinf.ibun.unal.edu.co/~apinzon/ > >> Bioinformatics Center, Colombia EMBnet node > >> http://bioinf.ibun.unal.edu.co > >> Tel +57 3165000 ext 16961 Fax +571 3165415 > >> Micology and Phytopathology Laboratory - Los Andes University. > >> http://bioinf.uniandes.edu.co > >> Tel +571 3394949 ext. 2768 > > > > > > > > -- > > Magdy S. Alabady, PhD > > ------------------------------------------------------ > > If A is a success in life, then A equals x plus y plus z. Work is x; y is > > play; and z is keeping your mouth shut. .....Albert Einstein > > ------------------------------------------------------------- > > > > > > > > -- > Andr?s Pinz?n > http://bioinf.ibun.unal.edu.co/~apinzon/ > Bioinformatics Center, Colombia EMBnet node > http://bioinf.ibun.unal.edu.co > Tel +57 3165000 ext 16961 Fax +571 3165415 > Micology and Phytopathology Laboratory - Los Andes University. > http://bioinf.uniandes.edu.co > Tel +571 3394949 ext. 2768 > -- Magdy S. Alabady, PhD ------------------------------------------------------ If A is a success in life, then A equals x plus y plus z. Work is x; y is play; and z is keeping your mouth shut. .....Albert Einstein ------------------------------------------------------------- From henrikki.almusa at helsinki.fi Tue Dec 23 08:35:33 2008 From: henrikki.almusa at helsinki.fi (Henrikki Almusa) Date: Tue, 23 Dec 2008 15:35:33 +0200 Subject: [EMBOSS] Pairwise matching Message-ID: <4950E925.7040709@helsinki.fi> Hi, I'm doing pairwise matching with strecher on nucleotide sequences. From the limited testing it seems that the strecher will only match sequence I give it and not do the same match to other strand. Is this correct or have I mistaken the result? There is an option '-sreverse' of course but that would change all input to other strand. I have a wrapper script around strecher which allows me to run the program for each pair of inputs (eg. from file 1 seq 1 against file 2 seq and file 1 seq 2 against file 2 seq 2 and so on). What would be preferable way to do local pairwise matching so that it would check the other strand as well and return the best match found? I suppose I could do it twice. Once for current strand and once for other and select best of each pair, but that would require more scripting to select the better result from the two files for each alignment. Regards, -- Henrikki Almusa From gbottu at vub.ac.be Wed Dec 24 09:44:29 2008 From: gbottu at vub.ac.be (Guy Bottu) Date: Wed, 24 Dec 2008 15:44:29 +0100 Subject: [EMBOSS] Pairwise matching In-Reply-To: <4950E925.7040709@helsinki.fi> References: <4950E925.7040709@helsinki.fi> Message-ID: <49524ACD.5020806@vub.ac.be> Dear Henrikki, You could use the bl2seq program from the BLAST suite. It does always try both strands of the second sequence. If you need to have it under EMBOSS, you could use the wrappers4EMBOSS suite (http://wemboss.sourceforge.net). Note by the way that stretcher makes a global alignment, for a local alignment you would have to use matcher. Regards, Guy Bottu, Belgian EMBnet Node From jeedward at yahoo.com Sun Dec 28 15:43:50 2008 From: jeedward at yahoo.com (John Edward) Date: Sun, 28 Dec 2008 12:43:50 -0800 (PST) Subject: [EMBOSS] BCBGC-09 call for papers Message-ID: <110261.43139.qm@web45906.mail.sp1.yahoo.com> BCBGC-09 call for papers ? The 2009 International Conference on Bioinformatics, Computational Biology, Genomics and Chemoinformatics (BCBGC-09) (website: http://www.PromoteResearch.org ) will be held during July 13-16 2009 in Orlando, FL, USA. We invite draft paper submissions. The conference will take place at the same time and venue where several other international conferences are taking place. The other conferences include: ????????? International Conference on Artificial Intelligence and Pattern Recognition (AIPR-09) ????????? International Conference on Automation, Robotics and Control Systems (ARCS-09) ????????? International Conference on Enterprise Information Systems and Web Technologies (EISWT-09) ????????? International Conference on High Performance Computing, Networking and Communication Systems (HPCNCS-09) ????????? International Conference on Information Security and Privacy (ISP-09) ????????? International Conference on Recent Advances in Information Technology and Applications (RAITA-09) ????????? International Conference on Software Engineering Theory and Practice (SETP-09) ????????? International Conference on Theory and Applications of Computational Science (TACS-09) ????????? International Conference on Theoretical and Mathematical Foundations of Computer Science (TMFCS-09) ? The website http://www.PromoteResearch.org contains more details. ? Sincerely John Edward Publicity committee ? From jeedward at yahoo.com Thu Dec 4 16:14:16 2008 From: jeedward at yahoo.com (John Edward) Date: Thu, 4 Dec 2008 08:14:16 -0800 (PST) Subject: [EMBOSS] BCBGC-09 call for papers Message-ID: <865899.36598.qm@web45906.mail.sp1.yahoo.com> BCBGC-09 call for papers ? The 2009 International Conference on Bioinformatics, Computational Biology, Genomics and Chemoinformatics (BCBGC-09) (website: http://www.PromoteResearch.org ) will be held during July 13-16 2009 in Orlando, FL, USA. We invite draft paper submissions. The conference will take place at the same time and venue where several other international conferences are taking place. The other conferences include: ????????? International Conference on Artificial Intelligence and Pattern Recognition (AIPR-09) ????????? International Conference on Automation, Robotics and Control Systems (ARCS-09) ????????? International Conference on Enterprise Information Systems and Web Technologies (EISWT-09) ????????? International Conference on High Performance Computing, Networking and Communication Systems (HPCNCS-09) ????????? International Conference on Information Security and Privacy (ISP-09) ????????? International Conference on Recent Advances in Information Technology and Applications (RAITA-09) ????????? International Conference on Software Engineering Theory and Practice (SETP-09) ????????? International Conference on Theory and Applications of Computational Science (TACS-09) ????????? International Conference on Theoretical and Mathematical Foundations of Computer Science (TMFCS-09) ? The website http://www.PromoteResearch.org contains more details. ? Sincerely John Edward Publicity committee ? ? ? From staffa at niehs.nih.gov Tue Dec 9 13:43:54 2008 From: staffa at niehs.nih.gov (Staffa, Nick (NIH/NIEHS)) Date: Tue, 09 Dec 2008 08:43:54 -0500 Subject: [EMBOSS] Archive In-Reply-To: <492D621D.6050104@umdnj.edu> Message-ID: Is there a web archive of these messages? I sure like to use someone else's disk space until I get around to viewing all these. Thanks Nick Staffa Telephone: 919-316-4569 (NIEHS: 6-4569) Scientific Computing Support Group NIEHS Enterprise-Wide Information Technology Support Contract National Institute of Environmental Health Sciences National Institutes of Health Research Triangle Park, North Carolina From uludag at ebi.ac.uk Tue Dec 9 14:22:54 2008 From: uludag at ebi.ac.uk (Mahmut Uludag) Date: Tue, 09 Dec 2008 14:22:54 +0000 Subject: [EMBOSS] Archive In-Reply-To: References: Message-ID: <1228832574.8069.43.camel@emboss2.ebi.ac.uk> > Is there a web archive of these messages? Did you mean this? http://lists.open-bio.org/pipermail/emboss/ Regards, Mahmut From staffa at niehs.nih.gov Tue Dec 9 14:24:58 2008 From: staffa at niehs.nih.gov (Staffa, Nick (NIH/NIEHS) [C]) Date: Tue, 9 Dec 2008 09:24:58 -0500 Subject: [EMBOSS] Archive In-Reply-To: <1228832574.8069.43.camel@emboss2.ebi.ac.uk> References: <1228832574.8069.43.camel@emboss2.ebi.ac.uk> Message-ID: <7930EE6CD7CA354D93B444D0433C061106848CBC@NIHCESMLBX6.nih.gov> Thanks Nickolas G. Staffa, Jr. Ph.D. Telephone: 919-316-4569 (NIEHS: 6-4569) Scientific Computing Support Group NIEHS E-WITS Contract National Institute of Environmental Health Sciences National Institutes of Health Research Triangle Park, North Carolina > -----Original Message----- > From: Mahmut Uludag [mailto:uludag at ebi.ac.uk] > Sent: Tuesday, December 09, 2008 9:23 AM > To: Staffa, Nick (NIH/NIEHS) [C] > Cc: emboss at lists.open-bio.org > Subject: Re: [EMBOSS] Archive > > > > Is there a web archive of these messages? > > Did you mean this? > > http://lists.open-bio.org/pipermail/emboss/ > > Regards, > Mahmut > From sufei at mail.sdu.edu.cn Wed Dec 10 13:30:31 2008 From: sufei at mail.sdu.edu.cn (sufei) Date: Wed, 10 Dec 2008 21:30:31 +0800 Subject: [EMBOSS] how to merge two sequence file Message-ID: <428915968.10036@mail.sdu.edu.cn> hi, I am new for emboss. When I use merger to merge two sequence file, I find that it only can input s single sequence. How can I merge the two sequence file? sufei From ztu at msi.umn.edu Wed Dec 10 13:59:52 2008 From: ztu at msi.umn.edu (Zheng Jin Tu) Date: Wed, 10 Dec 2008 07:59:52 -0600 (CST) Subject: [EMBOSS] how to merge two sequence file In-Reply-To: <428915968.10036@mail.sdu.edu.cn> References: <428915968.10036@mail.sdu.edu.cn> Message-ID: On UNIX/Linux computer, use simple UNIX cat command: cat seqfile1 seqfile2 .... seqfilex > new_merged_seqfile Thanks, Tu ================================================ On Wed, 10 Dec 2008, sufei wrote: > hi, > I am new for emboss. When I use merger to merge two sequence file, I find that it only can input s single sequence. How can I merge the two sequence file? > > sufei > From malabady at gmail.com Wed Dec 10 15:00:54 2008 From: malabady at gmail.com (Magdy Alabady) Date: Wed, 10 Dec 2008 09:00:54 -0600 Subject: [EMBOSS] EMBOSS proplem Message-ID: <6967ac4e0812100700s3708c00br7dbc606e79a6529c@mail.gmail.com> Hi I am new user of EMBOSS. I followed the instruction to install EMBOSS on my Mac OS X. I am running into the following problem. Every time I run any program I get the following message: Error: File /usr/local/biotools/share/EMBOSS/acd/plotcon.acd line 0: ACD file not opened I tried to run the 'wossname' test, I also get this message: Error: File /usr/local/biotools/share/EMBOSS/acd/wossname.acd line 0: ACD file not opened Any help to resolve this problem please? Thanks Magdy On Wed, Dec 10, 2008 at 7:59 AM, Zheng Jin Tu wrote: > > On UNIX/Linux computer, use simple UNIX cat command: > > cat seqfile1 seqfile2 .... seqfilex > new_merged_seqfile > > Thanks, Tu > > ================================================ > > On Wed, 10 Dec 2008, sufei wrote: > > > hi, > > I am new for emboss. When I use merger to merge two sequence file, I find > that it only can input s single sequence. How can I merge the two sequence > file? > > > > sufei > > > _______________________________________________ > EMBOSS mailing list > EMBOSS at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/emboss > -- Magdy S. Alabady, PhD ------------------------------------------------------ If A is a success in life, then A equals x plus y plus z. Work is x; y is play; and z is keeping your mouth shut. .....Albert Einstein ------------------------------------------------------------- From gbottu at vub.ac.be Fri Dec 12 15:59:28 2008 From: gbottu at vub.ac.be (Guy Bottu) Date: Fri, 12 Dec 2008 16:59:28 +0100 Subject: [EMBOSS] Is someone still using EMBOSS version 3 or 4 ? Message-ID: <49428A60.8010107@vub.ac.be> Dear all, The current version of the wrappers4EMBOSS suite uses EMBOSS version 3.0.0 subroutine names and is therefore compatible with all EMBOSS versions from 3.0.0 up to 6.0.1. I am however considering upgrading the names to those of version 5.0.0, if not for other reasons then certainly to get rid of annoying long lists of compiler warning messages. Therefore my question : is still someone using EMBOSS version 3 or 4 and has some reason for not willing to upgrade between now and the first months of 2009 ? Regards, Guy Bottu, Belgian EMBnet Node - wEMBOSS development team From gbottu at vub.ac.be Fri Dec 12 15:58:53 2008 From: gbottu at vub.ac.be (Guy Bottu) Date: Fri, 12 Dec 2008 16:58:53 +0100 Subject: [EMBOSS] wrappers4EMBOSS 2.2.0 released Message-ID: <49428A3D.6010509@vub.ac.be> Dear users of wrappers4EMBOSS, This message only concerns you if you are using wrappers4EMBOSS with one of the following : EMBOSS version 6, a local installation of MRS version 3, fastA, ps_scan.pl for searching PROSITE, InterProScan version 4.4, a Web Service access to WU-BLAST and fastA at the EBI. You might have to upgrade for the following reasons : - The MYEMBOSS-6.0.0 package does not contain test programs. As a consequence the installation script of wrappers4EMBOSS failed on a "fresh" installation and had to be re-run. This bug has been fixed. - The script mrsget.pl (used to query a local MRS 3 installation) sometimes gave erroneous results. This bug has been fixed (with help of MRS developer Maarten Hekkelman). - The programs fastasearch and fastapid from the fastA module have been modified so that the entire description line is now included in the output (truncated description lines can be terribly uninformative...). Bug fixes in both the "wrapper" and in the fastA suite itself (by "Bill" Pearson after submission of a bug report) make that it is (again) possible to switch off statistics and obtain just a list of n best "hits" (in case you might need that). We have also made the installation of the old fastA version 2 suite for the purpose of pairwise comparison optional. - A novelty is that PROSITE pattern matches can be validated using a second search against a mini-profile. The "wrapper" for ps_scan has been adapted to run with the latest version of ps_scan.pl and the evaluator.dat file that is distributed with PROSITE. This validation is performed by default but can be switched off. This new way of handling PROSITE has also been introduced in InterProScan version 4.4 and the "wrapper" has been modified accordingly. - The lists of available databases in the ebi_blast and ebi_fasta programs has been updated. We can mention that the HGVBASE at the EBI is now at last searchable by WU-BLAST. Regards, Guy Bottu, Belgian EMBnet Node - wEMBOSS development team From malabady at gmail.com Thu Dec 18 23:00:30 2008 From: malabady at gmail.com (Magdy Alabady) Date: Thu, 18 Dec 2008 17:00:30 -0600 Subject: [EMBOSS] backtranseq Message-ID: <6967ac4e0812181500m18e5532cg83bbf1be1f6d8c60@mail.gmail.com> Hello all, Can backtranseq run input file contains several 100's of protein sequences in Fasta format? can it make bulk back translation? please tell me how to do so if it is possible Thanks -- Magdy S. Alabady, PhD ------------------------------------------------------ If A is a success in life, then A equals x plus y plus z. Work is x; y is play; and z is keeping your mouth shut. .....Albert Einstein ------------------------------------------------------------- From pmr at ebi.ac.uk Thu Dec 18 23:20:21 2008 From: pmr at ebi.ac.uk (Peter Rice) Date: Thu, 18 Dec 2008 23:20:21 +0000 Subject: [EMBOSS] backtranseq In-Reply-To: <6967ac4e0812181500m18e5532cg83bbf1be1f6d8c60@mail.gmail.com> References: <6967ac4e0812181500m18e5532cg83bbf1be1f6d8c60@mail.gmail.com> Message-ID: <494ADAB5.8030606@ebi.ac.uk> Magdy Alabady wrote: > Hello all, > > Can backtranseq run input file contains several 100's of protein sequences > in Fasta format? can it make bulk back translation? please tell me how to do > so if it is possible Backtranseq only processes a single sequence. You have several choices: 1. make a new version of backtranseq that can process multiple sequences (easy to do ... but you need to learn a little EMBOSS programming first :-) 2. put your sequence file in a directory and name it with anything other than a .fasta extension. use seqret -ossingle to convert your file into 100s of single sequence files run backtranseq on each of the individual files. I wonder ... do you really want 100s of backtranslations in a single file? regards, Peter Rice From andrespinzon at gmail.com Fri Dec 19 16:56:51 2008 From: andrespinzon at gmail.com (Andres Pinzon) Date: Fri, 19 Dec 2008 11:56:51 -0500 Subject: [EMBOSS] backtranseq In-Reply-To: <494ADAB5.8030606@ebi.ac.uk> References: <6967ac4e0812181500m18e5532cg83bbf1be1f6d8c60@mail.gmail.com> <494ADAB5.8030606@ebi.ac.uk> Message-ID: <8968fc7e0812190856g777f9b3du78db85473a1f0679@mail.gmail.com> This is a not too elegant solution to your problem: paste the following code in a file called "script.sh": ====================================== #!/bin/bash seqret -ossingle -sequence $1 -outseq 1.fasta for i in $( ls ); do if [ "$i" != "script.sh" ]; then echo Processing: $i backtranseq -sequence $i -outfile $i.bt fi done cat *.bt > $1.backtranslated.fasta ================================================= and run the script as this: ================================================== ./script.sh ../yourMultipleFastaFile ================================================== This script will take your multiple fasta file, will create single files from it. will run backtranslate on each of them and will create an output file with your results called: yourMultipleFastaFile_backtranslated.fasta Hope it helps. regards, On Thu, Dec 18, 2008 at 6:20 PM, Peter Rice wrote: > Magdy Alabady wrote: >> >> Hello all, >> >> Can backtranseq run input file contains several 100's of protein sequences >> in Fasta format? can it make bulk back translation? please tell me how to >> do >> so if it is possible > > Backtranseq only processes a single sequence. You have several choices: > > 1. make a new version of backtranseq that can process multiple sequences > (easy to do ... but you need to learn a little EMBOSS programming first :-) > > 2. put your sequence file in a directory and name it with anything other > than a .fasta extension. > > use seqret -ossingle to convert your file into 100s of single sequence files > > run backtranseq on each of the individual files. > > > I wonder ... do you really want 100s of backtranslations in a single file? > > regards, > > Peter Rice > _______________________________________________ > EMBOSS mailing list > EMBOSS at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/emboss > -- Andr?s Pinz?n http://bioinf.ibun.unal.edu.co/~apinzon/ Bioinformatics Center, Colombia EMBnet node http://bioinf.ibun.unal.edu.co Tel +57 3165000 ext 16961 Fax +571 3165415 Micology and Phytopathology Laboratory - Los Andes University. http://bioinf.uniandes.edu.co Tel +571 3394949 ext. 2768 From malabady at gmail.com Fri Dec 19 20:58:31 2008 From: malabady at gmail.com (Magdy Alabady) Date: Fri, 19 Dec 2008 14:58:31 -0600 Subject: [EMBOSS] backtranseq In-Reply-To: <8968fc7e0812190856g777f9b3du78db85473a1f0679@mail.gmail.com> References: <6967ac4e0812181500m18e5532cg83bbf1be1f6d8c60@mail.gmail.com> <494ADAB5.8030606@ebi.ac.uk> <8968fc7e0812190856g777f9b3du78db85473a1f0679@mail.gmail.com> Message-ID: <6967ac4e0812191258p40e082e4gaed25170042c0eb8@mail.gmail.com> Thanks Peter, it works well except it produces so many files. the number of files is 4 or 5 times more than the number of sequences x2. for example, if I have 10 sequences, I would expected 21 files produced: 10 protein sequences, 10 backtranslation files, and one concatenated file. Is this correct: one other thing, forgive me if it bad question, in the first line of the script isn't the "-outseq 1.fasta" should be "-outseq $1.fasta" thanks On Fri, Dec 19, 2008 at 10:56 AM, Andres Pinzon wrote: > This is a not too elegant solution to your problem: > paste the following code in a file called "script.sh": > ====================================== > > > #!/bin/bash > > seqret -ossingle -sequence $1 -outseq 1.fasta > > > for i in $( ls ); do > if [ "$i" != "script.sh" ]; then > echo Processing: $i > backtranseq -sequence $i -outfile $i.bt > fi > done > > cat *.bt > $1.backtranslated.fasta > > ================================================= > > and run the script as this: > ================================================== > ./script.sh ../yourMultipleFastaFile > ================================================== > > > This script will take your multiple fasta file, will create single > files from it. will run backtranslate on each of them and will create > an output file with your results called: > yourMultipleFastaFile_backtranslated.fasta > > > Hope it helps. > > regards, > > > > On Thu, Dec 18, 2008 at 6:20 PM, Peter Rice wrote: > > Magdy Alabady wrote: > >> > >> Hello all, > >> > >> Can backtranseq run input file contains several 100's of protein > sequences > >> in Fasta format? can it make bulk back translation? please tell me how > to > >> do > >> so if it is possible > > > > Backtranseq only processes a single sequence. You have several choices: > > > > 1. make a new version of backtranseq that can process multiple sequences > > (easy to do ... but you need to learn a little EMBOSS programming first > :-) > > > > 2. put your sequence file in a directory and name it with anything other > > than a .fasta extension. > > > > use seqret -ossingle to convert your file into 100s of single sequence > files > > > > run backtranseq on each of the individual files. > > > > > > I wonder ... do you really want 100s of backtranslations in a single > file? > > > > regards, > > > > Peter Rice > > _______________________________________________ > > EMBOSS mailing list > > EMBOSS at lists.open-bio.org > > http://lists.open-bio.org/mailman/listinfo/emboss > > > > > > -- > Andr?s Pinz?n > http://bioinf.ibun.unal.edu.co/~apinzon/ > Bioinformatics Center, Colombia EMBnet node > http://bioinf.ibun.unal.edu.co > Tel +57 3165000 ext 16961 Fax +571 3165415 > Micology and Phytopathology Laboratory - Los Andes University. > http://bioinf.uniandes.edu.co > Tel +571 3394949 ext. 2768 > -- Magdy S. Alabady, PhD ------------------------------------------------------ If A is a success in life, then A equals x plus y plus z. Work is x; y is play; and z is keeping your mouth shut. .....Albert Einstein ------------------------------------------------------------- From andrespinzon at gmail.com Fri Dec 19 21:45:56 2008 From: andrespinzon at gmail.com (Andres Pinzon) Date: Fri, 19 Dec 2008 16:45:56 -0500 Subject: [EMBOSS] backtranseq In-Reply-To: <6967ac4e0812191258p40e082e4gaed25170042c0eb8@mail.gmail.com> References: <6967ac4e0812181500m18e5532cg83bbf1be1f6d8c60@mail.gmail.com> <494ADAB5.8030606@ebi.ac.uk> <8968fc7e0812190856g777f9b3du78db85473a1f0679@mail.gmail.com> <6967ac4e0812191258p40e082e4gaed25170042c0eb8@mail.gmail.com> Message-ID: <8968fc7e0812191345m13cf5f5awd8743c999d1afebc@mail.gmail.com> Hi Magdy, This is Andres, please dont blame peter!!! for the script I wrote it :-) On Fri, Dec 19, 2008 at 3:58 PM, Magdy Alabady wrote: > Thanks Peter, it works well except it produces so many files. the number of > files is 4 or 5 times more than the number of sequences x2. for example, if > I have 10 sequences, I would expected 21 files produced: 10 protein > sequences, 10 backtranslation files, and one concatenated file. Is this > correct: lets say you have 1 multiple fasta file whith 3 entries. It will create 7 files. 3 single fasta files (one for every multiple fasta enty). 3 ".bt", one for each single fasta file and 1 file which concatenates this ".bt" files. (thjis is the way it works in my machine). Please take into account that if you run it several times on the same place it will multiply your files. > one other thing, forgive me if it bad question, in the first line of the > script isn't the "-outseq 1.fasta" should be "-outseq $1.fasta" nop, this option says seqret how to name the output files. So the first entry in the multiple fasta file will correspond to the 1.fasta file, the second one will correspond to 2.fasta and so on. I hope this helps, Please don hesitate to contact me. Best, > thanks > > On Fri, Dec 19, 2008 at 10:56 AM, Andres Pinzon > wrote: >> >> This is a not too elegant solution to your problem: >> paste the following code in a file called "script.sh": >> ====================================== >> >> >> #!/bin/bash >> >> seqret -ossingle -sequence $1 -outseq 1.fasta >> >> >> for i in $( ls ); do >> if [ "$i" != "script.sh" ]; then >> echo Processing: $i >> backtranseq -sequence $i -outfile $i.bt >> fi >> done >> >> cat *.bt > $1.backtranslated.fasta >> >> ================================================= >> >> and run the script as this: >> ================================================== >> ./script.sh ../yourMultipleFastaFile >> ================================================== >> >> >> This script will take your multiple fasta file, will create single >> files from it. will run backtranslate on each of them and will create >> an output file with your results called: >> yourMultipleFastaFile_backtranslated.fasta >> >> >> Hope it helps. >> >> regards, >> >> >> >> On Thu, Dec 18, 2008 at 6:20 PM, Peter Rice wrote: >> > Magdy Alabady wrote: >> >> >> >> Hello all, >> >> >> >> Can backtranseq run input file contains several 100's of protein >> >> sequences >> >> in Fasta format? can it make bulk back translation? please tell me how >> >> to >> >> do >> >> so if it is possible >> > >> > Backtranseq only processes a single sequence. You have several choices: >> > >> > 1. make a new version of backtranseq that can process multiple sequences >> > (easy to do ... but you need to learn a little EMBOSS programming first >> > :-) >> > >> > 2. put your sequence file in a directory and name it with anything other >> > than a .fasta extension. >> > >> > use seqret -ossingle to convert your file into 100s of single sequence >> > files >> > >> > run backtranseq on each of the individual files. >> > >> > >> > I wonder ... do you really want 100s of backtranslations in a single >> > file? >> > >> > regards, >> > >> > Peter Rice >> > _______________________________________________ >> > EMBOSS mailing list >> > EMBOSS at lists.open-bio.org >> > http://lists.open-bio.org/mailman/listinfo/emboss >> > >> >> >> >> -- >> Andr?s Pinz?n >> http://bioinf.ibun.unal.edu.co/~apinzon/ >> Bioinformatics Center, Colombia EMBnet node >> http://bioinf.ibun.unal.edu.co >> Tel +57 3165000 ext 16961 Fax +571 3165415 >> Micology and Phytopathology Laboratory - Los Andes University. >> http://bioinf.uniandes.edu.co >> Tel +571 3394949 ext. 2768 > > > > -- > Magdy S. Alabady, PhD > ------------------------------------------------------ > If A is a success in life, then A equals x plus y plus z. Work is x; y is > play; and z is keeping your mouth shut. .....Albert Einstein > ------------------------------------------------------------- > > -- Andr?s Pinz?n http://bioinf.ibun.unal.edu.co/~apinzon/ Bioinformatics Center, Colombia EMBnet node http://bioinf.ibun.unal.edu.co Tel +57 3165000 ext 16961 Fax +571 3165415 Micology and Phytopathology Laboratory - Los Andes University. http://bioinf.uniandes.edu.co Tel +571 3394949 ext. 2768 From malabady at gmail.com Fri Dec 19 23:01:17 2008 From: malabady at gmail.com (Magdy Alabady) Date: Fri, 19 Dec 2008 17:01:17 -0600 Subject: [EMBOSS] backtranseq In-Reply-To: <8968fc7e0812191345m13cf5f5awd8743c999d1afebc@mail.gmail.com> References: <6967ac4e0812181500m18e5532cg83bbf1be1f6d8c60@mail.gmail.com> <494ADAB5.8030606@ebi.ac.uk> <8968fc7e0812190856g777f9b3du78db85473a1f0679@mail.gmail.com> <6967ac4e0812191258p40e082e4gaed25170042c0eb8@mail.gmail.com> <8968fc7e0812191345m13cf5f5awd8743c999d1afebc@mail.gmail.com> Message-ID: <6967ac4e0812191501vafe0e43qa2890d820cfdc740@mail.gmail.com> Thanks Andres. On Fri, Dec 19, 2008 at 3:45 PM, Andres Pinzon wrote: > Hi Magdy, > This is Andres, please dont blame peter!!! for the script I wrote it :-) > > On Fri, Dec 19, 2008 at 3:58 PM, Magdy Alabady wrote: > > Thanks Peter, it works well except it produces so many files. the number > of > > files is 4 or 5 times more than the number of sequences x2. for example, > if > > I have 10 sequences, I would expected 21 files produced: 10 protein > > sequences, 10 backtranslation files, and one concatenated file. Is this > > correct: > > lets say you have 1 multiple fasta file whith 3 entries. > It will create 7 files. 3 single fasta files (one for every multiple > fasta enty). 3 ".bt", > one for each single fasta file and 1 file which concatenates this > ".bt" files. (thjis is the way it works in my machine). Please take > into account that if you run it several times on the same place it > will multiply your files. > > > > one other thing, forgive me if it bad question, in the first line of the > > script isn't the "-outseq 1.fasta" should be "-outseq $1.fasta" > > nop, this option says seqret how to name the output files. So the > first entry in the multiple fasta file will correspond to the 1.fasta > file, the second one will correspond to 2.fasta and so on. > I hope this helps, > > Please don hesitate to contact me. > > Best, > > thanks > > > > On Fri, Dec 19, 2008 at 10:56 AM, Andres Pinzon > > wrote: > >> > >> This is a not too elegant solution to your problem: > >> paste the following code in a file called "script.sh": > >> ====================================== > >> > >> > >> #!/bin/bash > >> > >> seqret -ossingle -sequence $1 -outseq 1.fasta > >> > >> > >> for i in $( ls ); do > >> if [ "$i" != "script.sh" ]; then > >> echo Processing: $i > >> backtranseq -sequence $i -outfile $i.bt > >> fi > >> done > >> > >> cat *.bt > $1.backtranslated.fasta > >> > >> ================================================= > >> > >> and run the script as this: > >> ================================================== > >> ./script.sh ../yourMultipleFastaFile > >> ================================================== > >> > >> > >> This script will take your multiple fasta file, will create single > >> files from it. will run backtranslate on each of them and will create > >> an output file with your results called: > >> yourMultipleFastaFile_backtranslated.fasta > >> > >> > >> Hope it helps. > >> > >> regards, > >> > >> > >> > >> On Thu, Dec 18, 2008 at 6:20 PM, Peter Rice wrote: > >> > Magdy Alabady wrote: > >> >> > >> >> Hello all, > >> >> > >> >> Can backtranseq run input file contains several 100's of protein > >> >> sequences > >> >> in Fasta format? can it make bulk back translation? please tell me > how > >> >> to > >> >> do > >> >> so if it is possible > >> > > >> > Backtranseq only processes a single sequence. You have several > choices: > >> > > >> > 1. make a new version of backtranseq that can process multiple > sequences > >> > (easy to do ... but you need to learn a little EMBOSS programming > first > >> > :-) > >> > > >> > 2. put your sequence file in a directory and name it with anything > other > >> > than a .fasta extension. > >> > > >> > use seqret -ossingle to convert your file into 100s of single sequence > >> > files > >> > > >> > run backtranseq on each of the individual files. > >> > > >> > > >> > I wonder ... do you really want 100s of backtranslations in a single > >> > file? > >> > > >> > regards, > >> > > >> > Peter Rice > >> > _______________________________________________ > >> > EMBOSS mailing list > >> > EMBOSS at lists.open-bio.org > >> > http://lists.open-bio.org/mailman/listinfo/emboss > >> > > >> > >> > >> > >> -- > >> Andr?s Pinz?n > >> http://bioinf.ibun.unal.edu.co/~apinzon/ > >> Bioinformatics Center, Colombia EMBnet node > >> http://bioinf.ibun.unal.edu.co > >> Tel +57 3165000 ext 16961 Fax +571 3165415 > >> Micology and Phytopathology Laboratory - Los Andes University. > >> http://bioinf.uniandes.edu.co > >> Tel +571 3394949 ext. 2768 > > > > > > > > -- > > Magdy S. Alabady, PhD > > ------------------------------------------------------ > > If A is a success in life, then A equals x plus y plus z. Work is x; y is > > play; and z is keeping your mouth shut. .....Albert Einstein > > ------------------------------------------------------------- > > > > > > > > -- > Andr?s Pinz?n > http://bioinf.ibun.unal.edu.co/~apinzon/ > Bioinformatics Center, Colombia EMBnet node > http://bioinf.ibun.unal.edu.co > Tel +57 3165000 ext 16961 Fax +571 3165415 > Micology and Phytopathology Laboratory - Los Andes University. > http://bioinf.uniandes.edu.co > Tel +571 3394949 ext. 2768 > -- Magdy S. Alabady, PhD ------------------------------------------------------ If A is a success in life, then A equals x plus y plus z. Work is x; y is play; and z is keeping your mouth shut. .....Albert Einstein ------------------------------------------------------------- From henrikki.almusa at helsinki.fi Tue Dec 23 13:35:33 2008 From: henrikki.almusa at helsinki.fi (Henrikki Almusa) Date: Tue, 23 Dec 2008 15:35:33 +0200 Subject: [EMBOSS] Pairwise matching Message-ID: <4950E925.7040709@helsinki.fi> Hi, I'm doing pairwise matching with strecher on nucleotide sequences. From the limited testing it seems that the strecher will only match sequence I give it and not do the same match to other strand. Is this correct or have I mistaken the result? There is an option '-sreverse' of course but that would change all input to other strand. I have a wrapper script around strecher which allows me to run the program for each pair of inputs (eg. from file 1 seq 1 against file 2 seq and file 1 seq 2 against file 2 seq 2 and so on). What would be preferable way to do local pairwise matching so that it would check the other strand as well and return the best match found? I suppose I could do it twice. Once for current strand and once for other and select best of each pair, but that would require more scripting to select the better result from the two files for each alignment. Regards, -- Henrikki Almusa From gbottu at vub.ac.be Wed Dec 24 14:44:29 2008 From: gbottu at vub.ac.be (Guy Bottu) Date: Wed, 24 Dec 2008 15:44:29 +0100 Subject: [EMBOSS] Pairwise matching In-Reply-To: <4950E925.7040709@helsinki.fi> References: <4950E925.7040709@helsinki.fi> Message-ID: <49524ACD.5020806@vub.ac.be> Dear Henrikki, You could use the bl2seq program from the BLAST suite. It does always try both strands of the second sequence. If you need to have it under EMBOSS, you could use the wrappers4EMBOSS suite (http://wemboss.sourceforge.net). Note by the way that stretcher makes a global alignment, for a local alignment you would have to use matcher. Regards, Guy Bottu, Belgian EMBnet Node From jeedward at yahoo.com Sun Dec 28 20:43:50 2008 From: jeedward at yahoo.com (John Edward) Date: Sun, 28 Dec 2008 12:43:50 -0800 (PST) Subject: [EMBOSS] BCBGC-09 call for papers Message-ID: <110261.43139.qm@web45906.mail.sp1.yahoo.com> BCBGC-09 call for papers ? The 2009 International Conference on Bioinformatics, Computational Biology, Genomics and Chemoinformatics (BCBGC-09) (website: http://www.PromoteResearch.org ) will be held during July 13-16 2009 in Orlando, FL, USA. We invite draft paper submissions. The conference will take place at the same time and venue where several other international conferences are taking place. The other conferences include: ????????? International Conference on Artificial Intelligence and Pattern Recognition (AIPR-09) ????????? International Conference on Automation, Robotics and Control Systems (ARCS-09) ????????? International Conference on Enterprise Information Systems and Web Technologies (EISWT-09) ????????? International Conference on High Performance Computing, Networking and Communication Systems (HPCNCS-09) ????????? International Conference on Information Security and Privacy (ISP-09) ????????? International Conference on Recent Advances in Information Technology and Applications (RAITA-09) ????????? International Conference on Software Engineering Theory and Practice (SETP-09) ????????? International Conference on Theory and Applications of Computational Science (TACS-09) ????????? International Conference on Theoretical and Mathematical Foundations of Computer Science (TMFCS-09) ? The website http://www.PromoteResearch.org contains more details. ? Sincerely John Edward Publicity committee ?