From n.celik at pgrad.unimelb.edu.au Tue Feb 3 22:24:34 2009 From: n.celik at pgrad.unimelb.edu.au (Nermin Celik) Date: Wed, 04 Feb 2009 14:24:34 +1100 (EST) Subject: [EMBOSS] How to find protein sequences in a given genome using CDS information Message-ID: <28718.128.250.91.230.1233717874.squirrel@webmail.student.unimelb.edu.au> Hi, I have the CDS section of a feature table and a genome of an organism. Which EMBOSS program will allow me to extract the coding regions defined in the CDS file from the genome and then translate them to protein sequences? Example of CDS file: FT CDS 166..231 FT /systematic_id="ROD00001" FT CDS 313..2775 FT /systematic_id="ROD00011" FT CDS 2778..3707 Thank you. Nermin From gbottu at vub.ac.be Wed Feb 4 03:49:01 2009 From: gbottu at vub.ac.be (Guy Bottu) Date: Wed, 04 Feb 2009 09:49:01 +0100 Subject: [EMBOSS] How to find protein sequences in a given genome using CDS information In-Reply-To: <28718.128.250.91.230.1233717874.squirrel@webmail.student.unimelb.edu.au> References: <28718.128.250.91.230.1233717874.squirrel@webmail.student.unimelb.edu.au> Message-ID: <4989567D.7030402@vub.ac.be> Dear Nermin, You can do that with coderet. At the command line you can do : coderet AAA -cdsoutseq=XXX -translationoutseq=YYY -outfile=/dev/null -mrnaoutseq=/dev/null -restoutseq=/dev/null where AAA contains one or more sequences in EMBL or GenBank format. You will get the coding sequences in XXX and the protein sequences in YYY. How to do it in a GUI or dataflow system should be obvious to figure out. Regards, Guy Bottu, Belgian EMBnet Node From pmr at ebi.ac.uk Wed Feb 4 04:21:37 2009 From: pmr at ebi.ac.uk (Peter Rice) Date: Wed, 04 Feb 2009 09:21:37 +0000 Subject: [EMBOSS] How to find protein sequences in a given genome using CDS information In-Reply-To: <28718.128.250.91.230.1233717874.squirrel@webmail.student.unimelb.edu.au> References: <28718.128.250.91.230.1233717874.squirrel@webmail.student.unimelb.edu.au> Message-ID: <49895E21.1070303@ebi.ac.uk> Nermin Celik wrote: > Hi, > > I have the CDS section of a feature table and a genome of an organism. > Which EMBOSS program will allow me to extract the coding regions defined > in the CDS file from the genome and then translate them to protein > sequences? > > Example of CDS file: > FT CDS 166..231 > FT /systematic_id="ROD00001" > FT CDS 313..2775 > FT /systematic_id="ROD00011" > FT CDS 2778..3707 Ah, that highlights something we meant to fix. We have the application coderet that, in theory, will read the sequence and the feature table and do exactly what you want. Unfortunately the original author of coderet used a shortcut - it reads a sequence database entry and parses the feature table. Not good. However, what you can do is convert your genomic sequence and feature table into an EMBL entry: seqret -feature genomic.fasta -ufo embl::feature.table embl.entry coderet embl.entry GenBank entries also work in coderet. We will be working on coderet to fix this and read feature data normally. Any other suggestions for improvements are welcome. regards, Peter Rice From rls at ebi.ac.uk Wed Feb 4 04:32:15 2009 From: rls at ebi.ac.uk (Rodrigo Lopez) Date: Wed, 04 Feb 2009 09:32:15 +0000 Subject: [EMBOSS] How to find protein sequences in a given genome using CDS information In-Reply-To: <28718.128.250.91.230.1233717874.squirrel@webmail.student.unimelb.edu.au> References: <28718.128.250.91.230.1233717874.squirrel@webmail.student.unimelb.edu.au> Message-ID: <4989609F.7000606@ebi.ac.uk> Hi Nermin, To complement Guy's reply: You could also use the EMBLCDS database. This one contains all CDSs in EMBL-Bank (soon to be called ENA = European Nucleotide Archive). This one is available via the EBI's ftp server at pub/databases/embl/cds. The identifiers in this database correspond to the protein_id feature in the EMBL-Bank Feature Table which maps each CDS to corresponding protein translation. These in turn can be identified in UniProtKB. Please see the README.txt file at: ftp.ebi.ac.uk/pub/databases/embl/cds/README.txt for further details. Further to the above, and depending on the proteome in question, you could have a look at the integr8 directory on the ftp server as well: ftp.ebi.ac.uk/pub/databases/integr8 In here you will find the proteomes of more than 1600 organisms, mainly bacteria and archea, but also human, rat, mouse, etc. R:) Nermin Celik wrote: > Hi, > > I have the CDS section of a feature table and a genome of an organism. > Which EMBOSS program will allow me to extract the coding regions defined > in the CDS file from the genome and then translate them to protein > sequences? > > Example of CDS file: > FT CDS 166..231 > FT /systematic_id="ROD00001" > FT CDS 313..2775 > FT /systematic_id="ROD00011" > FT CDS 2778..3707 > > Thank you. > Nermin > > _______________________________________________ > EMBOSS mailing list > EMBOSS at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/emboss From malabady at gmail.com Wed Feb 4 07:27:24 2009 From: malabady at gmail.com (Magdy Alabady) Date: Wed, 4 Feb 2009 06:27:24 -0600 Subject: [EMBOSS] How to find protein sequences in a given genome using CDS information In-Reply-To: <4989609F.7000606@ebi.ac.uk> References: <28718.128.250.91.230.1233717874.squirrel@webmail.student.unimelb.edu.au> <4989609F.7000606@ebi.ac.uk> Message-ID: <6967ac4e0902040427q26671bc0h1e3fd3e8140fcdd1@mail.gmail.com> Hi, How about using fastacmd. If you have your genome sequence formatted with formatdb (in blast algorithm), you can easily use fastacmd to retrieve any sequence you want : fastacmd -d (your formatted genome db) -s (sequence name) (location) On Wed, Feb 4, 2009 at 3:32 AM, Rodrigo Lopez wrote: > Hi Nermin, > > To complement Guy's reply: You could also use the EMBLCDS database. This > one contains all CDSs in EMBL-Bank (soon to be called ENA = European > Nucleotide Archive). This one is available via the EBI's ftp server at > pub/databases/embl/cds. The identifiers in this database correspond to the > protein_id feature in the EMBL-Bank Feature Table which maps each CDS to > corresponding protein translation. These in turn can be identified in > UniProtKB. Please see the README.txt file at: > > ftp.ebi.ac.uk/pub/databases/embl/cds/README.txt > > for further details. > > Further to the above, and depending on the proteome in question, you could > have a look at the integr8 directory on the ftp server as well: > > ftp.ebi.ac.uk/pub/databases/integr8 > > In here you will find the proteomes of more than 1600 organisms, mainly > bacteria and archea, but also human, rat, mouse, etc. > > R:) > > > > Nermin Celik wrote: > >> Hi, >> >> I have the CDS section of a feature table and a genome of an organism. >> Which EMBOSS program will allow me to extract the coding regions defined >> in the CDS file from the genome and then translate them to protein >> sequences? >> >> Example of CDS file: >> FT CDS 166..231 >> FT /systematic_id="ROD00001" >> FT CDS 313..2775 >> FT /systematic_id="ROD00011" >> FT CDS 2778..3707 >> >> Thank you. >> Nermin >> >> _______________________________________________ >> EMBOSS mailing list >> EMBOSS at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/emboss >> > _______________________________________________ > EMBOSS mailing list > EMBOSS at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/emboss > -- -------------------------------------------------------- Magdy S. Alabady, PhD Energy Bioscience Institute (EBI) Institute for Genome Biology (IGB) University of Illinois At Urbana-Champaign, Illinois ------------------------------------------------------ Imagination is more important than knowledge. For knowledge is limited, whereas imagination embraces the entire world, stimulating progress, giving birth to evolution.. .....Albert Einstein ------------------------------------------------------------- From karinlag at ifi.uio.no Wed Feb 4 10:29:21 2009 From: karinlag at ifi.uio.no (Karin Lagesen) Date: Wed, 04 Feb 2009 16:29:21 +0100 Subject: [EMBOSS] fdnadist output not accepted by fneighbor Message-ID: I am trying to use the phylipnew package. I have the following sequences in phylip format: 4 15 C ATGGCCGGGA GGTT- D ATGGCAGGGA GGTT- A ATGGCCGGAA GGTTA B ATGGCCGGTA GGGTA produced by clustal. I now input it into fdnadist and get this one out: 4 C 0.000000 0.083014 0.074877 0.174794 D 0.083014 0.000000 0.170786 0.310384 A 0.074877 0.170786 0.000000 0.155764 B 0.174794 0.310384 0.155764 0.000000 I next try to input this one into fneighbor: alanine[15:54]:/projects/karin/phyliptest> /site/bioinf/EMBOSS-6.0.1/bin/fneighbor Phylogenies from distance matrix by N-J or UPGMA method Phylip distance matrix file: a.fdnadist Error: Distances file found -1 rows, expected 4 Error: Unable to read distances file 'a.fdnadist' Phylip distance matrix file: alanine[15:54]:/projects/karin/phyliptest> I get the same thing when I try to input the file from the examples on the webpage for fneighbor: alanine[16:02]:/projects/karin/phyliptest> cat embosstest.dat 7 Bovine 0.0000 1.6866 1.7198 1.6606 1.5243 1.6043 1.5905 Mouse 1.6866 0.0000 1.5232 1.4841 1.4465 1.4389 1.4629 Gibbon 1.7198 1.5232 0.0000 0.7115 0.5958 0.6179 0.5583 Orang 1.6606 1.4841 0.7115 0.0000 0.4631 0.5061 0.4710 Gorilla 1.5243 1.4465 0.5958 0.4631 0.0000 0.3484 0.3083 Chimp 1.6043 1.4389 0.6179 0.5061 0.3484 0.0000 0.2692 Human 1.5905 1.4629 0.5583 0.4710 0.3083 0.2692 0.0000 alanine[16:02]:/projects/karin/phyliptest> /site/bioinf/EMBOSS-6.0.1/bin/fneighbor Phylogenies from distance matrix by N-J or UPGMA method Phylip distance matrix file: embosstest.dat Error: Distances file found -1 rows, expected 7 Error: Unable to read distances file 'embosstest.dat' Phylip distance matrix file: Error: Distances file is required Died: fneighbor terminated: Bad value for '-datafile' and no more retries alanine[16:02]:/projects/karin/phyliptest> What am I doing wrong here? Have I misunderstood things completely? Thanks! Karin -- Karin Lagesen, Ph.D. karin.lagesen at medisin.uio.no http://folk.uio.no/karinlag From jeedward at yahoo.com Wed Feb 4 16:36:59 2009 From: jeedward at yahoo.com (John Edward) Date: Wed, 4 Feb 2009 13:36:59 -0800 (PST) Subject: [EMBOSS] Draft paper submission deadline extended: BCBGC-09 Message-ID: <103222.42756.qm@web45913.mail.sp1.yahoo.com> Draft paper submission deadline extended: BCBGC-09 ? The deadline for draft paper submission at the 2009 International Conference on Bioinformatics, Computational Biology, Genomics and Chemoinformatics (BCBGC-09) (website: http://www.PromoteResearch.org ) is extended due to numerous requests from the authors. The conference 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 aengus.stewart at cancer.org.uk Fri Feb 6 11:11:10 2009 From: aengus.stewart at cancer.org.uk (Aengus Stewart) Date: Fri, 06 Feb 2009 16:11:10 +0000 Subject: [EMBOSS] Align 12bp DNA back to genome In-Reply-To: References: Message-ID: <498C611E.7010700@cancer.org.uk> Hi all, This isnt an EMBOSS question per se but I thought it would go to the right audience. After trimming a bunch of illumina reads I have sequences that are 12bp long and "we" want to find their genomic location Before anyone even says "Why do you want to do that?" can I suggest 1) Treat it as a hypothetical case 2) because the scientist who asked me wants it :-) I have both a perl regex and fuzznuc running now for oh about a week.......... I have also attempted to build/configure/run without success maq soap blat So can anyone suggest anything else to try (probably I have missed the obvious) before the regex and fuzznuc finish? This completes the Friday pm puzzler........ Cheers Aengus -- ----------------------------------------------------------------------- Aengus Stewart Head of Bioinformatics and BioStatistics Bioinformatics and BioStatistics Tel: +44 (0)20 7269 3679 Cancer Research UK, Lincoln's Inn Fields, Holborn, London, WC2A 3PX, UK ----------------------------------------------------------------------- This electronic message contains information which may be privileged and confidential. The information is intended to be for the use of the individual(s) or entity named above. Be aware that any third party disclosure, distribution, copying or use of this communication, without prior permission, is strictly prohibited. This communication is from Cancer Research UK. Our website is at www.cancerresearchuk.org. We are a charity registered under number 1089464 and a company limited by guarantee registered in England & Wales under number 4325234. Our registered address is 61 Lincoln's Inn Fields, London WC2A 3PX. Our central telephone number is 020 7242 0200. This communication and any attachments contain information which is confidential and may also be privileged. It is for the exclusive use of the intended recipient(s). If you are not the intended recipient(s) please note that any form of disclosure, distribution, copying or use of this communication or the information in it or in any attachments is strictly prohibited and may be unlawful. If you have received this communication in error, please notify the sender and delete the email and destroy any copies of it. E-mail communications cannot be guaranteed to be secure or error free, as information could be intercepted, corrupted, amended, lost, destroyed, arrive late or incomplete, or contain viruses. We do not accept liability for any such matters or their consequences. Anyone who communicates with us by e-mail is taken to accept the risks in doing so. From pmr at ebi.ac.uk Fri Feb 6 11:42:27 2009 From: pmr at ebi.ac.uk (Peter Rice) Date: Fri, 06 Feb 2009 16:42:27 +0000 Subject: [EMBOSS] Align 12bp DNA back to genome In-Reply-To: <498C611E.7010700@cancer.org.uk> References: <498C611E.7010700@cancer.org.uk> Message-ID: <498C6873.6040304@ebi.ac.uk> Aengus Stewart wrote: > After trimming a bunch of illumina reads I have sequences that are 12bp > long and "we" want to find their genomic location Can you say that they should match exactly (depending on the size of genome, and the accuracy of the reads)? A word matching algorithm should work well. How many reads do you have? This is actually a problem we are very interested in writing EMBOSS applications for. regards, Peter From malabady at gmail.com Fri Feb 6 11:49:41 2009 From: malabady at gmail.com (Magdy Alabady) Date: Fri, 6 Feb 2009 10:49:41 -0600 Subject: [EMBOSS] Align 12bp DNA back to genome In-Reply-To: <498C6873.6040304@ebi.ac.uk> References: <498C611E.7010700@cancer.org.uk> <498C6873.6040304@ebi.ac.uk> Message-ID: <6967ac4e0902060849w33ccb487x2ab9c6643166869@mail.gmail.com> Hi, I have used GMap to exactly what you are asking for but with little longer reads (sRNA). It worked well. You might want to try GMap. magdy On Fri, Feb 6, 2009 at 10:42 AM, Peter Rice wrote: > Aengus Stewart wrote: > >> After trimming a bunch of illumina reads I have sequences that are 12bp >> long and "we" want to find their genomic location >> > > Can you say that they should match exactly (depending on the size of > genome, and the accuracy of the reads)? > > A word matching algorithm should work well. > > How many reads do you have? > > This is actually a problem we are very interested in writing EMBOSS > applications for. > > regards, > > Peter > > _______________________________________________ > EMBOSS mailing list > EMBOSS at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/emboss > -- -------------------------------------------------------- Magdy S. Alabady, PhD Energy Bioscience Institute (EBI) Institute for Genome Biology (IGB) University of Illinois At Urbana-Champaign, Illinois ------------------------------------------------------ Imagination is more important than knowledge. For knowledge is limited, whereas imagination embraces the entire world, stimulating progress, giving birth to evolution.. .....Albert Einstein ------------------------------------------------------------- From aengus.stewart at cancer.org.uk Fri Feb 6 12:12:10 2009 From: aengus.stewart at cancer.org.uk (Aengus Stewart) Date: Fri, 06 Feb 2009 17:12:10 +0000 Subject: [EMBOSS] Align 12bp DNA back to genome In-Reply-To: <498C611E.7010700@cancer.org.uk> References: <498C611E.7010700@cancer.org.uk> Message-ID: <498C6F6A.8010205@cancer.org.uk> hmmmmmm bowtie is on the list to build and test, but not for this problem. Can you assure me that both bowtie and GMap will work with 12bp sequences? Regards Aengus -- ----------------------------------------------------------------------- Aengus Stewart Head of Bioinformatics and BioStatistics Bioinformatics and BioStatistics Tel: +44 (0)20 7269 3679 Cancer Research UK, Lincoln's Inn Fields, Holborn, London, WC2A 3PX, UK ----------------------------------------------------------------------- This electronic message contains information which may be privileged and confidential. The information is intended to be for the use of the individual(s) or entity named above. Be aware that any third party disclosure, distribution, copying or use of this communication, without prior permission, is strictly prohibited. This communication is from Cancer Research UK. Our website is at www.cancerresearchuk.org. We are a charity registered under number 1089464 and a company limited by guarantee registered in England & Wales under number 4325234. Our registered address is 61 Lincoln's Inn Fields, London WC2A 3PX. Our central telephone number is 020 7242 0200. This communication and any attachments contain information which is confidential and may also be privileged. It is for the exclusive use of the intended recipient(s). If you are not the intended recipient(s) please note that any form of disclosure, distribution, copying or use of this communication or the information in it or in any attachments is strictly prohibited and may be unlawful. If you have received this communication in error, please notify the sender and delete the email and destroy any copies of it. E-mail communications cannot be guaranteed to be secure or error free, as information could be intercepted, corrupted, amended, lost, destroyed, arrive late or incomplete, or contain viruses. We do not accept liability for any such matters or their consequences. Anyone who communicates with us by e-mail is taken to accept the risks in doing so. From David.Lapointe at umassmed.edu Fri Feb 6 11:47:53 2009 From: David.Lapointe at umassmed.edu (Lapointe, David) Date: Fri, 6 Feb 2009 11:47:53 -0500 Subject: [EMBOSS] Align 12bp DNA back to genome In-Reply-To: <498C611E.7010700@cancer.org.uk> References: <498C611E.7010700@cancer.org.uk> Message-ID: <5ECA525B88314B48870E4AC72E3B9AF20246A225@EDUNIVMAIL05.ad.umassmed.edu> Aengus, You might try looking here for other software. Maq, soap, rmap, etc are relatively fast but still time-consuming. http://seqanswers.com/forums/showthread.php?t=43 David -----Original Message----- From: emboss-bounces at lists.open-bio.org [mailto:emboss-bounces at lists.open-bio.org] On Behalf Of Aengus Stewart Sent: Friday, February 06, 2009 11:11 AM To: emboss at lists.open-bio.org Subject: [EMBOSS] Align 12bp DNA back to genome Hi all, This isnt an EMBOSS question per se but I thought it would go to the right audience. After trimming a bunch of illumina reads I have sequences that are 12bp long and "we" want to find their genomic location Before anyone even says "Why do you want to do that?" can I suggest 1) Treat it as a hypothetical case 2) because the scientist who asked me wants it :-) I have both a perl regex and fuzznuc running now for oh about a week.......... I have also attempted to build/configure/run without success maq soap blat So can anyone suggest anything else to try (probably I have missed the obvious) before the regex and fuzznuc finish? This completes the Friday pm puzzler........ Cheers Aengus -- ----------------------------------------------------------------------- Aengus Stewart Head of Bioinformatics and BioStatistics Bioinformatics and BioStatistics Tel: +44 (0)20 7269 3679 Cancer Research UK, Lincoln's Inn Fields, Holborn, London, WC2A 3PX, UK ----------------------------------------------------------------------- This electronic message contains information which may be privileged and confidential. The information is intended to be for the use of the individual(s) or entity named above. Be aware that any third party disclosure, distribution, copying or use of this communication, without prior permission, is strictly prohibited. This communication is from Cancer Research UK. Our website is at www.cancerresearchuk.org. We are a charity registered under number 1089464 and a company limited by guarantee registered in England & Wales under number 4325234. Our registered address is 61 Lincoln's Inn Fields, London WC2A 3PX. Our central telephone number is 020 7242 0200. This communication and any attachments contain information which is confidential and may also be privileged. It is for the exclusive use of the intended recipient(s). If you are not the intended recipient(s) please note that any form of disclosure, distribution, copying or use of this communication or the information in it or in any attachments is strictly prohibited and may be unlawful. If you have received this communication in error, please notify the sender and delete the email and destroy any copies of it. E-mail communications cannot be guaranteed to be secure or error free, as information could be intercepted, corrupted, amended, lost, destroyed, arrive late or incomplete, or contain viruses. We do not accept liability for any such matters or their consequences. Anyone who communicates with us by e-mail is taken to accept the risks in doing so. _______________________________________________ EMBOSS mailing list EMBOSS at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/emboss From malabady at gmail.com Fri Feb 6 12:56:18 2009 From: malabady at gmail.com (Magdy Alabady) Date: Fri, 6 Feb 2009 11:56:18 -0600 Subject: [EMBOSS] Align 12bp DNA back to genome In-Reply-To: <498C6F6A.8010205@cancer.org.uk> References: <498C611E.7010700@cancer.org.uk> <498C6F6A.8010205@cancer.org.uk> Message-ID: <6967ac4e0902060956w268ea749pe1af52b0576823a@mail.gmail.com> I haven't use bowite before, sorry. I used GMap extensivly to map sRNA to genomes like rice, and it works fine. bear in mind that sRNA is around 20 bp. I don't a problem in your case, but a trial is needed to judge it On Fri, Feb 6, 2009 at 11:12 AM, Aengus Stewart < aengus.stewart at cancer.org.uk> wrote: > > hmmmmmm > > bowtie is on the list to build and test, but not for this problem. > > Can you assure me that both bowtie and GMap will work with 12bp sequences? > > > Regards > > Aengus > > -- > ----------------------------------------------------------------------- > Aengus Stewart > Head of Bioinformatics and BioStatistics > Bioinformatics and BioStatistics Tel: +44 (0)20 7269 3679 > Cancer Research UK, Lincoln's Inn Fields, Holborn, London, WC2A 3PX, UK > ----------------------------------------------------------------------- > > This electronic message contains information which may be privileged and > confidential. The information is intended to be for the use of the > individual(s) or entity named above. Be aware that any third party > disclosure, distribution, copying or use of this communication, without > prior permission, is strictly prohibited. > > This communication is from Cancer Research UK. Our website is at > www.cancerresearchuk.org. We are a charity registered under number 1089464 > and a company limited by guarantee registered in England & Wales under > number 4325234. Our registered address is 61 Lincoln's Inn Fields, London > WC2A 3PX. Our central telephone number is 020 7242 0200. > > This communication and any attachments contain information which is > confidential and may also be privileged. It is for the exclusive use of > the intended recipient(s). If you are not the intended recipient(s) please > note that any form of disclosure, distribution, copying or use of this > communication or the information in it or in any attachments is strictly > prohibited and may be unlawful. If you have received this communication in > error, please notify the sender and delete the email and destroy any copies > of it. > > E-mail communications cannot be guaranteed to be secure or error free, as > information could be intercepted, corrupted, amended, lost, destroyed, > arrive late or incomplete, or contain viruses. We do not accept liability > for any such matters or their consequences. Anyone who communicates with us > by e-mail is taken to accept the risks in doing so. > _______________________________________________ > EMBOSS mailing list > EMBOSS at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/emboss > -- -------------------------------------------------------- Magdy S. Alabady, PhD Energy Bioscience Institute (EBI) Institute for Genome Biology (IGB) University of Illinois At Urbana-Champaign, Illinois ------------------------------------------------------ Imagination is more important than knowledge. For knowledge is limited, whereas imagination embraces the entire world, stimulating progress, giving birth to evolution.. .....Albert Einstein ------------------------------------------------------------- From mathog at caltech.edu Fri Feb 6 14:56:45 2009 From: mathog at caltech.edu (David Mathog) Date: Fri, 06 Feb 2009 11:56:45 -0800 Subject: [EMBOSS] Align 12bp DNA back to genome Message-ID: > After trimming a bunch of illumina reads I have sequences that are 12bp long and "we" want to find > their genomic location location(S!) > > I have both a perl regex and fuzznuc running now for oh about a week.......... It shouldn't take that long. Assuming the words are perfectly known (so identity match only), and you have more than one of these words to do, the fastest way would be to break the genome(s) down into words, sort that form, and then just pull out matching word positions from the resulting table(s). If on the other hand, you are allowing mismatches, well, ugh. 12 is pretty small to start with... > > I have also attempted to build/configure/run without success > maq > soap > blat Here is a tool which is very simple to get you started: http://saf.bio.caltech.edu/pub/software/molbio/fastatuples.c Do fastatuples -h to see the options. Run it like (for instance) fastatuples -n -w 12 -d -p -s References: <498C611E.7010700@cancer.org.uk> <5ECA525B88314B48870E4AC72E3B9AF20246A225@EDUNIVMAIL05.ad.umassmed.edu> Message-ID: <5aa3b3570902070657h4238c57fwf349ce000915df7c@mail.gmail.com> On 2/6/09, Lapointe, David wrote: > Aengus, > > You might try looking here for other software. Maq, soap, rmap, etc are > relatively fast but still time-consuming. > > http://seqanswers.com/forums/showthread.php?t=43 > > David > > -----Original Message----- > From: emboss-bounces at lists.open-bio.org > [mailto:emboss-bounces at lists.open-bio.org] On Behalf Of Aengus Stewart > Sent: Friday, February 06, 2009 11:11 AM > To: emboss at lists.open-bio.org > Subject: [EMBOSS] Align 12bp DNA back to genome > > > Hi all, > > This isnt an EMBOSS question per se but I thought it would go to the > right audience. > > After trimming a bunch of illumina reads I have sequences that are 12bp > long and "we" want to find > their genomic location I think 12 bp is too short to obtain good results. How much big is the genome that you want to search? Have you calculated the probability that your 12 bp sequences match to a random location in the genome? Or to two distinct positions? The human genome is not homogenously sequenced: there are still regions full of errors and of 'N's. What if one of your sequences falls in such a zone? Moreover, the genomic sequence that you are working with could not be the same as the one from which you have extracted your seqs. > > Before anyone even says "Why do you want to do that?" can I suggest > > 1) Treat it as a hypothetical case > 2) because the scientist who asked me wants it > > :-) > > I have both a perl regex and fuzznuc running now for oh about a > week.......... > > I have also attempted to build/configure/run without success > > maq > soap > blat > > So can anyone suggest anything else to try (probably I have missed the > obvious) before the regex and > fuzznuc finish? > > This completes the Friday pm puzzler........ > > > > Cheers > Aengus > > -- > ----------------------------------------------------------------------- > Aengus Stewart > Head of Bioinformatics and BioStatistics > Bioinformatics and BioStatistics Tel: +44 (0)20 7269 3679 > Cancer Research UK, Lincoln's Inn Fields, Holborn, London, WC2A 3PX, UK > ----------------------------------------------------------------------- > > This electronic message contains information which may be privileged and > confidential. The information is intended to be for the use of the > individual(s) or entity named above. Be aware that any third party > disclosure, distribution, copying or use of this communication, without > prior permission, is strictly prohibited. > > This communication is from Cancer Research UK. Our website is at > www.cancerresearchuk.org. We are a charity registered under number > 1089464 and a company limited by guarantee registered in England & Wales > under number 4325234. Our registered address is 61 Lincoln's Inn Fields, > London WC2A 3PX. Our central telephone number is 020 7242 0200. > > This communication and any attachments contain information which is > confidential and may also be privileged. It is for the exclusive use > of the intended recipient(s). If you are not the intended recipient(s) > please note that any form of disclosure, distribution, copying or use of > this communication or the information in it or in any attachments is > strictly prohibited and may be unlawful. If you have received this > communication in error, please notify the sender and delete the email > and destroy any copies of it. > > E-mail communications cannot be guaranteed to be secure or error free, > as information could be intercepted, corrupted, amended, lost, > destroyed, arrive late or incomplete, or contain viruses. We do not > accept liability for any such matters or their consequences. Anyone who > communicates with us by e-mail is taken to accept the risks in doing so. > _______________________________________________ > EMBOSS mailing list > EMBOSS at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/emboss > > > > _______________________________________________ > EMBOSS mailing list > EMBOSS at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/emboss > -- My blog on bioinformatics (now in English): http://bioinfoblog.it From charles-listes-emboss at plessy.org Fri Feb 13 21:04:39 2009 From: charles-listes-emboss at plessy.org (Charles Plessy) Date: Sat, 14 Feb 2009 11:04:39 +0900 Subject: [EMBOSS] www.emboss.org or emboss.sourceforge.org ? Message-ID: <20090214020439.GA24788@kunpuu.plessy.org> Dear EMBOSS developers, I was just wondering what is the canonical URL for the EMBOSS homepage. Is it emboss.sourceforge.net, emboss.org, or www.emboss.org ? There seems to be a problem with at least www.emboss.org, as the IP address 66.150.161.133 does not answer. Have a nice day, -- Charles Plessy http://charles.plessy.org Tsurumi, Kanagawa, Japan From ajb at ebi.ac.uk Sat Feb 14 04:53:28 2009 From: ajb at ebi.ac.uk (ajb at ebi.ac.uk) Date: Sat, 14 Feb 2009 09:53:28 -0000 (GMT) Subject: [EMBOSS] www.emboss.org or emboss.sourceforge.org ? In-Reply-To: <20090214020439.GA24788@kunpuu.plessy.org> References: <20090214020439.GA24788@kunpuu.plessy.org> Message-ID: <36342.86.9.126.186.1234605208.squirrel@webmail.ebi.ac.uk> Dear Charles, At the moment it is officially emboss.sourceforge.net. However, just to confuse things further, in the near future it is likely to change to emboss.open-bio.org (but we'll redirect sourceforge when that is done). Alan > Dear EMBOSS developers, > > I was just wondering what is the canonical URL for the EMBOSS homepage. Is > it > emboss.sourceforge.net, emboss.org, or www.emboss.org ? > > There seems to be a problem with at least www.emboss.org, as the IP > address > 66.150.161.133 does not answer. > > Have a nice day, > > -- > Charles Plessy > http://charles.plessy.org > Tsurumi, Kanagawa, Japan > _______________________________________________ > EMBOSS mailing list > EMBOSS at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/emboss > From stephen.taylor at imm.ox.ac.uk Mon Feb 16 08:45:07 2009 From: stephen.taylor at imm.ox.ac.uk (Steve Taylor) Date: Mon, 16 Feb 2009 13:45:07 +0000 Subject: [EMBOSS] Diversity / p-distance Message-ID: <49996DE3.7060807@imm.ox.ac.uk> Hi, Is there an EMBOSS tool that that can calculate p-distance as defined in http://evolgen.biol.metro-u.ac.jp/MEGA/manual/Distance.html? I can probably code something to do it but I thought I would ask first.:-) Kind regards and thanks, Steve ------------------------------------------------------------------ Medical Sciences Division Weatherall Institute of Molecular Medicine/Sir William Dunn School Oxford University From jerome.laroche at bioinfo.ulaval.ca Mon Feb 16 11:54:35 2009 From: jerome.laroche at bioinfo.ulaval.ca (=?ISO-8859-1?Q?J=E9r=F4me_Laroche?=) Date: Mon, 16 Feb 2009 11:54:35 -0500 Subject: [EMBOSS] error message with charge and pepstats Message-ID: <54FE4DF2-DFE2-406F-B03F-18C27F5357B7@bioinfo.ulaval.ca> Hi, I get the following error message when using the programs "charge" and "pepstats": EMBOSS An error in embprop.c at line 114: Incorrect (old?) format amino data file I work with EMBOSS 6.0.1 Files tested are in fasta format. Other programs read these files very well. Thanks. J?r?me Laroche Responsable de travaux pratiques et de recherche Centre de bioinformatique et de biologie computationnelle Universit? Laval From ajb at ebi.ac.uk Mon Feb 16 13:03:42 2009 From: ajb at ebi.ac.uk (ajb at ebi.ac.uk) Date: Mon, 16 Feb 2009 18:03:42 -0000 (GMT) Subject: [EMBOSS] error message with charge and pepstats In-Reply-To: <54FE4DF2-DFE2-406F-B03F-18C27F5357B7@bioinfo.ulaval.ca> References: <54FE4DF2-DFE2-406F-B03F-18C27F5357B7@bioinfo.ulaval.ca> Message-ID: <47313.86.9.126.186.1234807422.squirrel@webmail.ebi.ac.uk> Hi J?r?me, The programs aren't complaining about your FASTA files. The error is because the programs are not picking up the correct EMBOSS data file 'Eamino.dat'. That sort of error can happen if you've installed a new version of EMBOSS but, for whatever reason, have set an environment variable (EMBOSS_DATA) pointing to EMBOSS data files from a previous release. Alternatively, an incorrect Eamino.dat file could be being found in your current directory, your home directory or a '.embossdata' subdirectory of your home or current directory. To find out what Eamino.dat is being used by EMBOSS you can type: embossdata Eamino.dat That should give you some clue where to look for the problem. HTH Alan > Hi, > > I get the following error message when using the programs "charge" and > "pepstats": > > EMBOSS An error in embprop.c at line 114: > Incorrect (old?) format amino data file > > I work with EMBOSS 6.0.1 > > Files tested are in fasta format. Other programs read these files very > well. > > > Thanks. > > > > J?r?me Laroche > > Responsable de travaux pratiques et de recherche > Centre de bioinformatique et de biologie computationnelle > Universit? Laval > > > > > _______________________________________________ > EMBOSS mailing list > EMBOSS at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/emboss > From jison at ebi.ac.uk Tue Feb 17 08:46:07 2009 From: jison at ebi.ac.uk (Jon Ison) Date: Tue, 17 Feb 2009 13:46:07 -0000 (GMT) Subject: [EMBOSS] Diversity / p-distance In-Reply-To: <49996DE3.7060807@imm.ox.ac.uk> References: <49996DE3.7060807@imm.ox.ac.uk> Message-ID: <52021.84.92.187.247.1234878367.squirrel@webmail.ebi.ac.uk> Hi Steve I don't think so. You could have a look at: http://emboss.sourceforge.net/apps/cvs/embassy/phylipnew/ Any maybe: http://emboss.sourceforge.net/apps/cvs/emboss/apps/distmat.html If you do write something new in C, please let's have the code so it can be incorporated. Cheers Jon > Hi, > > Is there an EMBOSS tool that that can calculate p-distance as defined in > http://evolgen.biol.metro-u.ac.jp/MEGA/manual/Distance.html? > > I can probably code something to do it but I thought I would ask first.:-) > > Kind regards and thanks, > > Steve > ------------------------------------------------------------------ > Medical Sciences Division > Weatherall Institute of Molecular Medicine/Sir William Dunn School > Oxford University > _______________________________________________ > EMBOSS mailing list > EMBOSS at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/emboss > From stephen.taylor at imm.ox.ac.uk Tue Feb 17 10:56:26 2009 From: stephen.taylor at imm.ox.ac.uk (Steve Taylor) Date: Tue, 17 Feb 2009 15:56:26 +0000 Subject: [EMBOSS] Diversity / p-distance In-Reply-To: <52021.84.92.187.247.1234878367.squirrel@webmail.ebi.ac.uk> References: <49996DE3.7060807@imm.ox.ac.uk> <52021.84.92.187.247.1234878367.squirrel@webmail.ebi.ac.uk> Message-ID: <499ADE2A.9010007@imm.ox.ac.uk> Hi Jon, > > I don't think so. You could have a look at: > http://emboss.sourceforge.net/apps/cvs/embassy/phylipnew/ > > Any maybe: > http://emboss.sourceforge.net/apps/cvs/emboss/apps/distmat.html > Aha from distmat Looks like D = uncorrected distance = p-distance = 1-S > If you do write something new in C, please let's have the code > so it can be incorporated. > Steve ------------------------------------------------------------------ Medical Sciences Division Weatherall Institute of Molecular Medicine/Sir William Dunn School Oxford University From sea99.wang at gmail.com Thu Feb 19 02:43:29 2009 From: sea99.wang at gmail.com (Sea) Date: Thu, 19 Feb 2009 15:43:29 +0800 Subject: [EMBOSS] How to disable jemboss authorization function? Message-ID: <4f3a50530902182343v150c949cj825f7a11d4b4f331@mail.gmail.com> Hi, I installed jemboss on a unix server few years ago and enable the authorization function. (It's a window to login id and pwd before running the jemboss) Now I want to disable this function and run the jemboss directly, but have no idea how to do this. Does somebody have the same experience and have any good suggestions to disable the authorization function? If it is, give me some hints please, thanks a lot! :-) Sea From uludag at ebi.ac.uk Thu Feb 19 12:43:30 2009 From: uludag at ebi.ac.uk (uludag at ebi.ac.uk) Date: Thu, 19 Feb 2009 17:43:30 -0000 (GMT) Subject: [EMBOSS] How to disable jemboss authorization function? In-Reply-To: <4f3a50530902182343v150c949cj825f7a11d4b4f331@mail.gmail.com> References: <4f3a50530902182343v150c949cj825f7a11d4b4f331@mail.gmail.com> Message-ID: <50988.130.88.47.86.1235065410.squirrel@webmail.ebi.ac.uk> > I installed jemboss on a unix server few years ago and enable the > authorization function. > (It's a window to login id and pwd before running the jemboss) > Now I want to disable this function and run the jemboss directly, > but have no idea how to do this. i tested this with my jemboss installation after i have the following setting on the server side jemboss.properties file user.auth=false and the following settings on the client side jemboss.properties file then jemboss doesn't ask user name/password and able to communicate with the server user.auth=false service.public=JembossServer service.private=JembossServer Regards, Mahmut From charles-listes-emboss at plessy.org Fri Feb 20 09:51:06 2009 From: charles-listes-emboss at plessy.org (Charles Plessy) Date: Fri, 20 Feb 2009 23:51:06 +0900 Subject: [EMBOSS] RootDirectory and BaseDirectory hardcoded at build time ? Message-ID: <20090220145106.GA16170@kunpuu.plessy.org> Dear EMBOSS developers, I realised some time ago that when using the Debian 'emboss' package, embossversion would report wrong RootDirectory and BaseDirectory because the binaries are built in a temporary location before being moved in the package and installed on downstream computers: aqwa?~?$ embossversion -full Writes the current EMBOSS version number to a file PackageName: EMBOSS LibraryVersion: 6.0.1 InstallDirectory: /usr RootDirectory: /tmp/buildd/emboss-6.0.1/emboss BaseDirectory: /tmp/buildd/emboss-6.0.1/ Using 'strace' and 'strings', I figured out that this information is hard-coded in libajax. Is there a way to indicate the final location (/usr/share/EMBOSS?) at build time? Have a nice day, -- Charles Plessy http://charles.plessy.org Tsurumi, Kanagawa, Japan From jeedward at yahoo.com Fri Feb 20 10:19:59 2009 From: jeedward at yahoo.com (John Edward) Date: Fri, 20 Feb 2009 07:19:59 -0800 (PST) Subject: [EMBOSS] Draft paper submission deadline extended: BCBGC-09 Message-ID: <988357.6613.qm@web45903.mail.sp1.yahoo.com> Draft paper submission deadline extended: BCBGC-09 ? The deadline for draft paper submission at the 2009 International Conference on Bioinformatics, Computational Biology, Genomics and Chemoinformatics (BCBGC-09) (website: http://www.PromoteResearch.org ) is extended due to numerous requests from the authors. The conference 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 pmr at ebi.ac.uk Fri Feb 20 10:27:37 2009 From: pmr at ebi.ac.uk (Peter Rice) Date: Fri, 20 Feb 2009 15:27:37 +0000 Subject: [EMBOSS] RootDirectory and BaseDirectory hardcoded at build time ? In-Reply-To: <20090220145106.GA16170@kunpuu.plessy.org> References: <20090220145106.GA16170@kunpuu.plessy.org> Message-ID: <499ECBE9.5030409@ebi.ac.uk> Charles Plessy wrote: > Dear EMBOSS developers, > > I realised some time ago that when using the Debian 'emboss' package, > embossversion would report wrong RootDirectory and BaseDirectory because the > binaries are built in a temporary location before being moved in the package > and installed on downstream computers: > > aqwa$ embossversion -full > Writes the current EMBOSS version number to a file > PackageName: EMBOSS > LibraryVersion: 6.0.1 > InstallDirectory: /usr > RootDirectory: /tmp/buildd/emboss-6.0.1/emboss > BaseDirectory: /tmp/buildd/emboss-6.0.1/ > > Using 'strace' and 'strings', I figured out that this information is hard-coded > in libajax. Is there a way to indicate the final location (/usr/share/EMBOSS?) > at build time? The values are defined at build time. You can override them with settings in emboss.defaults (the easiest way) as EMBOSS_ROOT (the base directory is simply one level up). embossversion will report these values. This is the usual way where EMBOSS installations have been moved. The directories are defined from the --prefix setting when you run ./configure and we have not needed to define alternatives as the above method works. Of course, you could try hard coding any value you like in ajnam.c but we wouldn't recommend that! Hope that helps, Peter From georgios at biotek.uio.no Fri Feb 20 10:38:47 2009 From: georgios at biotek.uio.no (George Magklaras) Date: Fri, 20 Feb 2009 16:38:47 +0100 Subject: [EMBOSS] RootDirectory and BaseDirectory hardcoded at build time ? In-Reply-To: <20090220145106.GA16170@kunpuu.plessy.org> References: <20090220145106.GA16170@kunpuu.plessy.org> Message-ID: <499ECE87.7030703@biotek.uio.no> In the Makefile, shouldn't they be a: AJAX_FIXED_ROOT directive? I am not exactly familiar with the Debian package process, but at my (manually built) leftovers from the sources, I did a: georgie at slartibartfast# fgrep -i root config.log ... AJAX_FIXED_ROOT='\"/site/sources/EMBOSS-6.0.1/emboss\"' datadir='${datarootdir}' datarootdir='${prefix}/share' docdir='${datarootdir}/doc/${PACKAGE}' infodir='${datarootdir}/info' localedir='${datarootdir}/locale' mandir='${datarootdir}/man' ...... and the location was passed by configure with the --prefix switch. Does the Debian package dist specify a location that way? -- -- George Magklaras BSc Hons MPhil RHCE:805008309135525 Senior Computer Systems Engineer/UNIX-Linux Systems Administrator EMBnet Technical Management Board The Biotechnology Centre of Oslo, University of Oslo http://folk.uio.no/georgios Charles Plessy wrote: > Dear EMBOSS developers, > > I realised some time ago that when using the Debian 'emboss' package, > embossversion would report wrong RootDirectory and BaseDirectory because the > binaries are built in a temporary location before being moved in the package > and installed on downstream computers: > > aqwa?~?$ embossversion -full > Writes the current EMBOSS version number to a file > PackageName: EMBOSS > LibraryVersion: 6.0.1 > InstallDirectory: /usr > RootDirectory: /tmp/buildd/emboss-6.0.1/emboss > BaseDirectory: /tmp/buildd/emboss-6.0.1/ > > Using 'strace' and 'strings', I figured out that this information is hard-coded > in libajax. Is there a way to indicate the final location (/usr/share/EMBOSS?) > at build time? > > Have a nice day, > From pmr at ebi.ac.uk Fri Feb 20 11:12:30 2009 From: pmr at ebi.ac.uk (Peter Rice) Date: Fri, 20 Feb 2009 16:12:30 +0000 Subject: [EMBOSS] RootDirectory and BaseDirectory hardcoded at build time ? In-Reply-To: <499ECBE9.5030409@ebi.ac.uk> References: <20090220145106.GA16170@kunpuu.plessy.org> <499ECBE9.5030409@ebi.ac.uk> Message-ID: <499ED66E.6070506@ebi.ac.uk> Peter Rice wrote: > Charles Plessy wrote: >> Dear EMBOSS developers, >> >> I realised some time ago that when using the Debian 'emboss' package, >> embossversion would report wrong RootDirectory and BaseDirectory >> because the >> binaries are built in a temporary location before being moved in the >> package >> and installed on downstream computers: >> >> aqwa$ embossversion -full >> Writes the current EMBOSS version number to a file >> PackageName: EMBOSS >> LibraryVersion: 6.0.1 >> InstallDirectory: /usr >> RootDirectory: /tmp/buildd/emboss-6.0.1/emboss >> BaseDirectory: /tmp/buildd/emboss-6.0.1/ >> >> Using 'strace' and 'strings', I figured out that this information is >> hard-coded >> in libajax. Is there a way to indicate the final location >> (/usr/share/EMBOSS?) >> at build time? > > The values are defined at build time. You can override them with > settings in emboss.defaults (the easiest way) as EMBOSS_ROOT (the base > directory is simply one level up). embossversion will report > these values. This is the usual way where EMBOSS installations have been > moved. Oops, wrong answer! It is not possible to define it in emboss.default (the correct name) because the values are set before emboss.default is read (they are needed to find the possible locations of emboss.default). That leaves setenv EMBOSS_ROOT as the way to define the values (in csh syntax) but that is not so easy to implement globally. Does the embossversion output give you any other problems? Or do the values give problems for any other EMBOSS applications? Where does the source get moved to? Or is it removed? Peter From pmr at ebi.ac.uk Fri Feb 20 11:16:51 2009 From: pmr at ebi.ac.uk (Peter Rice) Date: Fri, 20 Feb 2009 16:16:51 +0000 Subject: [EMBOSS] RootDirectory and BaseDirectory hardcoded at build time ? In-Reply-To: <499ECE87.7030703@biotek.uio.no> References: <20090220145106.GA16170@kunpuu.plessy.org> <499ECE87.7030703@biotek.uio.no> Message-ID: <499ED773.1020405@ebi.ac.uk> George Magklaras wrote: > In the Makefile, shouldn't they be a: > > AJAX_FIXED_ROOT directive? > > I am not exactly familiar with the Debian package process, but at my > (manually built) leftovers from the sources, I did a: > georgie at slartibartfast# fgrep -i root config.log > ... > AJAX_FIXED_ROOT='\"/site/sources/EMBOSS-6.0.1/emboss\"' > datadir='${datarootdir}' > datarootdir='${prefix}/share' > docdir='${datarootdir}/doc/${PACKAGE}' > infodir='${datarootdir}/info' > localedir='${datarootdir}/locale' > mandir='${datarootdir}/man' > ...... > > and the location was passed by configure with the --prefix switch. Does > the Debian package dist specify a location that way? AJAX_FIXED_ROOT is originally defined in configure.in in the top level directory. > #dnl Define where the EMBOSS package is located > AC_SUBST(AJAX_FIXED_ROOT) > AJAX_FIXED_ROOT="\\\"`pwd`/emboss\\\"" > AC_SUBST(EMBOSS_TOP) > EMBOSS_TOP=`pwd` The values then are used to build ./configure and get copied to config.log when it runs. Peter P.S. I liked the "georgie at slartibartfast" :-) From gbottu at vub.ac.be Fri Feb 20 12:31:48 2009 From: gbottu at vub.ac.be (Guy Bottu) Date: Fri, 20 Feb 2009 18:31:48 +0100 Subject: [EMBOSS] wEMBOSS multiple login problem fixed Message-ID: <499EE904.9050209@vub.ac.be> Dear all, As those of you who use wEMBOSS will have noticed, with recent versions of Web browsers a problem had appeared : you had to type in your username/password for each frame separately (up to 4 times). This problem has been fixed by a change in the login procedure that makes you must again login just once. We have released a new subversion 1.8.1 with the fix and some further minor changes, see http://sourceforge.net/project/shownotes.php?release_id=662615&group_id=170030 http://sourceforge.net/project/shownotes.php?release_id=662578&group_id=170030 Regards, Guy Bottu, Belgian EMBnet Node - wEMBOSS development team From charles-listes-emboss at plessy.org Sat Feb 21 00:22:24 2009 From: charles-listes-emboss at plessy.org (Charles Plessy) Date: Sat, 21 Feb 2009 14:22:24 +0900 Subject: [EMBOSS] RootDirectory and BaseDirectory hardcoded at build time ? In-Reply-To: <499ED773.1020405@ebi.ac.uk> References: <20090220145106.GA16170@kunpuu.plessy.org> <499ECE87.7030703@biotek.uio.no> <499ED773.1020405@ebi.ac.uk> Message-ID: <20090221052224.GA29289@kunpuu.plessy.org> Le Fri, Feb 20, 2009 at 04:16:51PM +0000, Peter Rice a ?crit : > George Magklaras wrote: >> In the Makefile, shouldn't they be a: >> >> AJAX_FIXED_ROOT directive? >> >> I am not exactly familiar with the Debian package process, but at my >> (manually built) leftovers from the sources, I did a: >> georgie at slartibartfast# fgrep -i root config.log >> ... >> AJAX_FIXED_ROOT='\"/site/sources/EMBOSS-6.0.1/emboss\"' >> datadir='${datarootdir}' >> datarootdir='${prefix}/share' >> docdir='${datarootdir}/doc/${PACKAGE}' >> infodir='${datarootdir}/info' >> localedir='${datarootdir}/locale' >> mandir='${datarootdir}/man' >> ...... >> >> and the location was passed by configure with the --prefix switch. Does >> the Debian package dist specify a location that way? > > AJAX_FIXED_ROOT is originally defined in configure.in in the top level > directory. Thanks for all your anwers, I solved the problem by passing AJAX_FIXED_ROOT=\\\"/usr/share/EMBOSS\\\" to the make command. This hardcodes the root to /usr/share/EMBOSS, where all the data files are installed by the Debian package 'emboss-data'. It was not a big problem that embossversion --full reported the directories where EMBOSS was built, but just in case a user would rely on this, I prefer to correct it. Have a nice day, -- Charles From afikolami at gmail.com Mon Feb 23 20:28:51 2009 From: afikolami at gmail.com (Mohd Afiq Hazlami) Date: Tue, 24 Feb 2009 09:28:51 +0800 Subject: [EMBOSS] Problem with showdb and seqret Message-ID: <4e53edca0902231728o2fb9a389gbde8fd5b40ff9e88@mail.gmail.com> Hello, I'm new to EMBOSS and I have a problem that I can't figure out. I have configured and installed EMBOSS-6.0.1 on my Ubuntu machine and I tried doing the exercises according to the tutorial. There's nothing wrong when I typed 'wossname' and the program works fine, just like in the tutorial. But when it comes to 'showdb' tutorial, the program returns this: afiq at peregrin:~/EMBOSS-6.0.1$ showdb Displays information on configured databases # Name Type ID Qry All Comment # ============ ==== == === === ======= afiq at peregrin:~/EMBOSS-6.0.1$ which is totally different from the tutorial where it shows some database names. Is this normal? Then, when I tried to use seqret as in the tutorial given (using xlrhodop), the program returns this: afiq at peregrin:~/EMBOSS-6.0.1$ seqret Reads and writes (returns) sequences Input (gapped) sequence(s): embl:xlrhodop Error: Failed to open filename 'embl' Error: Unable to read sequence 'embl:xlrhodop' Input (gapped) sequence(s): which is really confusing. Can anybody tell me what's wrong? From emno72 at gmail.com Mon Feb 23 22:26:03 2009 From: emno72 at gmail.com (Mohd Noor Mat Isa) Date: Tue, 24 Feb 2009 11:26:03 +0800 Subject: [EMBOSS] Problem with showdb and seqret In-Reply-To: <4e53edca0902231728o2fb9a389gbde8fd5b40ff9e88@mail.gmail.com> References: <4e53edca0902231728o2fb9a389gbde8fd5b40ff9e88@mail.gmail.com> Message-ID: <2e2159f50902231926x78b43697v13b4fd01e3bffe88@mail.gmail.com> Dear Mohd Afiq, I'm not an expert also on EMBOSS installation but I can give you some clues on your problems: First, showdb does not give you any db list as you need to index all the databases that you requires to show. You can get further info here http://emboss.sourceforge.net/docs/adminguide/node56.html on how to index databases. as for seqret you should tell the seqret you input format as *embl::xlrhodop * not embl*:*xlrhodop. Regards Mohd Noor Malaysia Genome Institute On Tue, Feb 24, 2009 at 9:28 AM, Mohd Afiq Hazlami wrote: > Hello, > I'm new to EMBOSS and I have a problem that I can't figure out. I have > configured and installed EMBOSS-6.0.1 on my Ubuntu machine and I tried > doing > the exercises according to the tutorial. There's nothing wrong when I typed > 'wossname' and the program works fine, just like in the tutorial. But when > it comes to 'showdb' tutorial, the program returns this: > > > afiq at peregrin:~/EMBOSS-6.0.1$ showdb > Displays information on configured databases > # Name Type ID Qry All Comment > # ============ ==== == === === ======= > afiq at peregrin:~/EMBOSS-6.0.1$ > > which is totally different from the tutorial where it shows some database > names. Is this normal? > > Then, when I tried to use seqret as in the tutorial given (using xlrhodop), > the program returns this: > > afiq at peregrin:~/EMBOSS-6.0.1$ seqret > Reads and writes (returns) sequences > Input (gapped) sequence(s): embl:xlrhodop > Error: Failed to open filename 'embl' > Error: Unable to read sequence 'embl:xlrhodop' > Input (gapped) sequence(s): > > which is really confusing. Can anybody tell me what's wrong? > _______________________________________________ > EMBOSS mailing list > EMBOSS at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/emboss > From gbottu at vub.ac.be Tue Feb 24 04:26:27 2009 From: gbottu at vub.ac.be (Guy Bottu) Date: Tue, 24 Feb 2009 10:26:27 +0100 Subject: [EMBOSS] Problem with showdb and seqret In-Reply-To: <4e53edca0902231728o2fb9a389gbde8fd5b40ff9e88@mail.gmail.com> References: <4e53edca0902231728o2fb9a389gbde8fd5b40ff9e88@mail.gmail.com> Message-ID: <49A3BD43.7010300@vub.ac.be> Mohd Afiq Hazlami wrote: > But when > it comes to 'showdb' tutorial, the program returns this: Alas, the manual and tutorial are out-of-date. This is an unfortunate chronic disease of EMBOSS, even if for the rest EMBOSS is great. Before you can access 'public' sequences using the : syntax you must first define databases in the file /share/EMBOSS/emboss.default There is a file emboss.default.template with examples. To get a quick try using the EMBOSS tutorial data you could put the following in emboss.default : DB test_embl [ type: N comment: 'testset for EMBL' format: embl method: emblcd dir: /opt/sw/EMBOSS6/EMBOSS-6.0.1/test/embl ] Do replace /opt/sw/EMBOSS6/EMBOSS-6.0.1/test/embl by /test/embl You will note that this directory does contain sequences and indexes. You can then do showdb entret test_embl:Z11115 You can read more about it at http://emboss.sourceforge.net/docs/themes/Databases.html A question for the EMBOSS development team : what is the status of the new EMBOSS manual ? Regards, Guy Bottu, Belgian EMBnet Node From benys at usp.br Wed Feb 25 09:51:35 2009 From: benys at usp.br (Beny Spira) Date: Wed, 25 Feb 2009 11:51:35 -0300 Subject: [EMBOSS] emboss-explorer Message-ID: <21e884180902250651r54203c25x6003b0cc5df2721b@mail.gmail.com> Hi I was trying to install emboss-explorer using Debian binaries. Emboss installed fine, emboss-explorer also got installed fine in my desktop computer but not in my laptop. Both computers OS is Linux Debian Lenny and emboss version is 5.0.07. (One of) the recurrent errors in /var/log/apache2/error.log is: [Wed Feb 25 10:37:08 2009] [error] [client 127.0.0.1] File does not exist: /usr/share/emboss-explorer/html/output/949348, referer: http://localhost/cgi-bin/emboss/wossname Apache apparently runs OK. Any clue about what might be wrong? Beny -- Beny Spira Departamento de Microbiologia Instituto de Ci?ncias Biom?dicas Universidade de S?o Paulo Av. Prof. Lineu Prestes 1374 S?o Paulo-SP CEP:05508-900 Brasil Tel: 5511-3091-7347 FAX: 5511-3091-7354 E-mail: benys at usp.br Homepage: www.icb.usp.br/~benys From scott at cs.wits.ac.za Thu Feb 26 08:26:50 2009 From: scott at cs.wits.ac.za (Scott Hazelhurst) Date: Thu, 26 Feb 2009 15:26:50 +0200 Subject: [EMBOSS] fneighbor and dist programs Message-ID: <20090226132041.M96385@cs.wits.ac.za> Dear all, I am having problems using fneighbor with either fprotdist or fdnadist. The way the dist programs work is that when it prints the distance matrix, after every nine distance values a new line is printed. However, this seems to upset fneighbor which complains thus: Error: Distances file found 0 rows, expected 26 Error: Unable to read distances file 'ensmuscle2.fprotdist' Died: fneighbor terminated: Bad value for '-datafile' with -auto defined fneighbor exited with status 1... If I use a small number of sequences, then there's no problem. Or, if I manually edit the fprotdist file so as to remove the newlines, then it works fine. This is OK for me, but for the student lab it's a bit of a showstopper I looked in my archives and documentation but couldn't find anything on this. Am I missing something obvious? I am using Phylipnew 3.67, EMBOSS 6.0.1 Many thanks Scott

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From scott at cs.wits.ac.za Fri Feb 27 07:15:50 2009 From: scott at cs.wits.ac.za (Scott Hazelhurst) Date: Fri, 27 Feb 2009 14:15:50 +0200 Subject: [EMBOSS] fneighbor and dist programs In-Reply-To: <20090226132041.M96385@cs.wits.ac.za> References: <20090226132041.M96385@cs.wits.ac.za> Message-ID: <20090227121502.M74045@cs.wits.ac.za> Thanks to Peter and the EMBOSS team for the quick patch. My lab went well.

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From charles-listes-emboss at plessy.org Sat Feb 28 06:53:17 2009 From: charles-listes-emboss at plessy.org (Charles Plessy) Date: Sat, 28 Feb 2009 20:53:17 +0900 Subject: [EMBOSS] emboss-explorer In-Reply-To: <21e884180902250651r54203c25x6003b0cc5df2721b@mail.gmail.com> References: <21e884180902250651r54203c25x6003b0cc5df2721b@mail.gmail.com> Message-ID: <20090228115317.GI30418@kunpuu.plessy.org> Le Wed, Feb 25, 2009 at 11:51:35AM -0300, Beny Spira a ?crit : > (One of) the recurrent errors in /var/log/apache2/error.log is: > > [Wed Feb 25 10:37:08 2009] [error] [client 127.0.0.1] File does not exist: > /usr/share/emboss-explorer/html/output/949348, referer: > http://localhost/cgi-bin/emboss/wossname Dear Beny, there is probably a problem with /etc/emboss-explorer/emboss-explorer.conf (a Debian-specific file), that should contain something like: # path to the EMBOSS::GUI temporary output directory our $OUTPUT_PATH = "/var/lib/emboss-explorer/output"; In the worst case, just try to purge emboss-explorer and reinstall it, but before this save any change you made to the configuration, as it will be deleted. Have a nice day, -- Charles Plessy Debian Med packaging team, http://www.debian.org/devel/debian-med Tsurumi, Kanagawa, Japan From n.celik at pgrad.unimelb.edu.au Wed Feb 4 03:24:34 2009 From: n.celik at pgrad.unimelb.edu.au (Nermin Celik) Date: Wed, 04 Feb 2009 14:24:34 +1100 (EST) Subject: [EMBOSS] How to find protein sequences in a given genome using CDS information Message-ID: <28718.128.250.91.230.1233717874.squirrel@webmail.student.unimelb.edu.au> Hi, I have the CDS section of a feature table and a genome of an organism. Which EMBOSS program will allow me to extract the coding regions defined in the CDS file from the genome and then translate them to protein sequences? Example of CDS file: FT CDS 166..231 FT /systematic_id="ROD00001" FT CDS 313..2775 FT /systematic_id="ROD00011" FT CDS 2778..3707 Thank you. Nermin From gbottu at vub.ac.be Wed Feb 4 08:49:01 2009 From: gbottu at vub.ac.be (Guy Bottu) Date: Wed, 04 Feb 2009 09:49:01 +0100 Subject: [EMBOSS] How to find protein sequences in a given genome using CDS information In-Reply-To: <28718.128.250.91.230.1233717874.squirrel@webmail.student.unimelb.edu.au> References: <28718.128.250.91.230.1233717874.squirrel@webmail.student.unimelb.edu.au> Message-ID: <4989567D.7030402@vub.ac.be> Dear Nermin, You can do that with coderet. At the command line you can do : coderet AAA -cdsoutseq=XXX -translationoutseq=YYY -outfile=/dev/null -mrnaoutseq=/dev/null -restoutseq=/dev/null where AAA contains one or more sequences in EMBL or GenBank format. You will get the coding sequences in XXX and the protein sequences in YYY. How to do it in a GUI or dataflow system should be obvious to figure out. Regards, Guy Bottu, Belgian EMBnet Node From pmr at ebi.ac.uk Wed Feb 4 09:21:37 2009 From: pmr at ebi.ac.uk (Peter Rice) Date: Wed, 04 Feb 2009 09:21:37 +0000 Subject: [EMBOSS] How to find protein sequences in a given genome using CDS information In-Reply-To: <28718.128.250.91.230.1233717874.squirrel@webmail.student.unimelb.edu.au> References: <28718.128.250.91.230.1233717874.squirrel@webmail.student.unimelb.edu.au> Message-ID: <49895E21.1070303@ebi.ac.uk> Nermin Celik wrote: > Hi, > > I have the CDS section of a feature table and a genome of an organism. > Which EMBOSS program will allow me to extract the coding regions defined > in the CDS file from the genome and then translate them to protein > sequences? > > Example of CDS file: > FT CDS 166..231 > FT /systematic_id="ROD00001" > FT CDS 313..2775 > FT /systematic_id="ROD00011" > FT CDS 2778..3707 Ah, that highlights something we meant to fix. We have the application coderet that, in theory, will read the sequence and the feature table and do exactly what you want. Unfortunately the original author of coderet used a shortcut - it reads a sequence database entry and parses the feature table. Not good. However, what you can do is convert your genomic sequence and feature table into an EMBL entry: seqret -feature genomic.fasta -ufo embl::feature.table embl.entry coderet embl.entry GenBank entries also work in coderet. We will be working on coderet to fix this and read feature data normally. Any other suggestions for improvements are welcome. regards, Peter Rice From rls at ebi.ac.uk Wed Feb 4 09:32:15 2009 From: rls at ebi.ac.uk (Rodrigo Lopez) Date: Wed, 04 Feb 2009 09:32:15 +0000 Subject: [EMBOSS] How to find protein sequences in a given genome using CDS information In-Reply-To: <28718.128.250.91.230.1233717874.squirrel@webmail.student.unimelb.edu.au> References: <28718.128.250.91.230.1233717874.squirrel@webmail.student.unimelb.edu.au> Message-ID: <4989609F.7000606@ebi.ac.uk> Hi Nermin, To complement Guy's reply: You could also use the EMBLCDS database. This one contains all CDSs in EMBL-Bank (soon to be called ENA = European Nucleotide Archive). This one is available via the EBI's ftp server at pub/databases/embl/cds. The identifiers in this database correspond to the protein_id feature in the EMBL-Bank Feature Table which maps each CDS to corresponding protein translation. These in turn can be identified in UniProtKB. Please see the README.txt file at: ftp.ebi.ac.uk/pub/databases/embl/cds/README.txt for further details. Further to the above, and depending on the proteome in question, you could have a look at the integr8 directory on the ftp server as well: ftp.ebi.ac.uk/pub/databases/integr8 In here you will find the proteomes of more than 1600 organisms, mainly bacteria and archea, but also human, rat, mouse, etc. R:) Nermin Celik wrote: > Hi, > > I have the CDS section of a feature table and a genome of an organism. > Which EMBOSS program will allow me to extract the coding regions defined > in the CDS file from the genome and then translate them to protein > sequences? > > Example of CDS file: > FT CDS 166..231 > FT /systematic_id="ROD00001" > FT CDS 313..2775 > FT /systematic_id="ROD00011" > FT CDS 2778..3707 > > Thank you. > Nermin > > _______________________________________________ > EMBOSS mailing list > EMBOSS at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/emboss From malabady at gmail.com Wed Feb 4 12:27:24 2009 From: malabady at gmail.com (Magdy Alabady) Date: Wed, 4 Feb 2009 06:27:24 -0600 Subject: [EMBOSS] How to find protein sequences in a given genome using CDS information In-Reply-To: <4989609F.7000606@ebi.ac.uk> References: <28718.128.250.91.230.1233717874.squirrel@webmail.student.unimelb.edu.au> <4989609F.7000606@ebi.ac.uk> Message-ID: <6967ac4e0902040427q26671bc0h1e3fd3e8140fcdd1@mail.gmail.com> Hi, How about using fastacmd. If you have your genome sequence formatted with formatdb (in blast algorithm), you can easily use fastacmd to retrieve any sequence you want : fastacmd -d (your formatted genome db) -s (sequence name) (location) On Wed, Feb 4, 2009 at 3:32 AM, Rodrigo Lopez wrote: > Hi Nermin, > > To complement Guy's reply: You could also use the EMBLCDS database. This > one contains all CDSs in EMBL-Bank (soon to be called ENA = European > Nucleotide Archive). This one is available via the EBI's ftp server at > pub/databases/embl/cds. The identifiers in this database correspond to the > protein_id feature in the EMBL-Bank Feature Table which maps each CDS to > corresponding protein translation. These in turn can be identified in > UniProtKB. Please see the README.txt file at: > > ftp.ebi.ac.uk/pub/databases/embl/cds/README.txt > > for further details. > > Further to the above, and depending on the proteome in question, you could > have a look at the integr8 directory on the ftp server as well: > > ftp.ebi.ac.uk/pub/databases/integr8 > > In here you will find the proteomes of more than 1600 organisms, mainly > bacteria and archea, but also human, rat, mouse, etc. > > R:) > > > > Nermin Celik wrote: > >> Hi, >> >> I have the CDS section of a feature table and a genome of an organism. >> Which EMBOSS program will allow me to extract the coding regions defined >> in the CDS file from the genome and then translate them to protein >> sequences? >> >> Example of CDS file: >> FT CDS 166..231 >> FT /systematic_id="ROD00001" >> FT CDS 313..2775 >> FT /systematic_id="ROD00011" >> FT CDS 2778..3707 >> >> Thank you. >> Nermin >> >> _______________________________________________ >> EMBOSS mailing list >> EMBOSS at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/emboss >> > _______________________________________________ > EMBOSS mailing list > EMBOSS at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/emboss > -- -------------------------------------------------------- Magdy S. Alabady, PhD Energy Bioscience Institute (EBI) Institute for Genome Biology (IGB) University of Illinois At Urbana-Champaign, Illinois ------------------------------------------------------ Imagination is more important than knowledge. For knowledge is limited, whereas imagination embraces the entire world, stimulating progress, giving birth to evolution.. .....Albert Einstein ------------------------------------------------------------- From karinlag at ifi.uio.no Wed Feb 4 15:29:21 2009 From: karinlag at ifi.uio.no (Karin Lagesen) Date: Wed, 04 Feb 2009 16:29:21 +0100 Subject: [EMBOSS] fdnadist output not accepted by fneighbor Message-ID: I am trying to use the phylipnew package. I have the following sequences in phylip format: 4 15 C ATGGCCGGGA GGTT- D ATGGCAGGGA GGTT- A ATGGCCGGAA GGTTA B ATGGCCGGTA GGGTA produced by clustal. I now input it into fdnadist and get this one out: 4 C 0.000000 0.083014 0.074877 0.174794 D 0.083014 0.000000 0.170786 0.310384 A 0.074877 0.170786 0.000000 0.155764 B 0.174794 0.310384 0.155764 0.000000 I next try to input this one into fneighbor: alanine[15:54]:/projects/karin/phyliptest> /site/bioinf/EMBOSS-6.0.1/bin/fneighbor Phylogenies from distance matrix by N-J or UPGMA method Phylip distance matrix file: a.fdnadist Error: Distances file found -1 rows, expected 4 Error: Unable to read distances file 'a.fdnadist' Phylip distance matrix file: alanine[15:54]:/projects/karin/phyliptest> I get the same thing when I try to input the file from the examples on the webpage for fneighbor: alanine[16:02]:/projects/karin/phyliptest> cat embosstest.dat 7 Bovine 0.0000 1.6866 1.7198 1.6606 1.5243 1.6043 1.5905 Mouse 1.6866 0.0000 1.5232 1.4841 1.4465 1.4389 1.4629 Gibbon 1.7198 1.5232 0.0000 0.7115 0.5958 0.6179 0.5583 Orang 1.6606 1.4841 0.7115 0.0000 0.4631 0.5061 0.4710 Gorilla 1.5243 1.4465 0.5958 0.4631 0.0000 0.3484 0.3083 Chimp 1.6043 1.4389 0.6179 0.5061 0.3484 0.0000 0.2692 Human 1.5905 1.4629 0.5583 0.4710 0.3083 0.2692 0.0000 alanine[16:02]:/projects/karin/phyliptest> /site/bioinf/EMBOSS-6.0.1/bin/fneighbor Phylogenies from distance matrix by N-J or UPGMA method Phylip distance matrix file: embosstest.dat Error: Distances file found -1 rows, expected 7 Error: Unable to read distances file 'embosstest.dat' Phylip distance matrix file: Error: Distances file is required Died: fneighbor terminated: Bad value for '-datafile' and no more retries alanine[16:02]:/projects/karin/phyliptest> What am I doing wrong here? Have I misunderstood things completely? Thanks! Karin -- Karin Lagesen, Ph.D. karin.lagesen at medisin.uio.no http://folk.uio.no/karinlag From jeedward at yahoo.com Wed Feb 4 21:36:59 2009 From: jeedward at yahoo.com (John Edward) Date: Wed, 4 Feb 2009 13:36:59 -0800 (PST) Subject: [EMBOSS] Draft paper submission deadline extended: BCBGC-09 Message-ID: <103222.42756.qm@web45913.mail.sp1.yahoo.com> Draft paper submission deadline extended: BCBGC-09 ? The deadline for draft paper submission at the 2009 International Conference on Bioinformatics, Computational Biology, Genomics and Chemoinformatics (BCBGC-09) (website: http://www.PromoteResearch.org ) is extended due to numerous requests from the authors. The conference 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 aengus.stewart at cancer.org.uk Fri Feb 6 16:11:10 2009 From: aengus.stewart at cancer.org.uk (Aengus Stewart) Date: Fri, 06 Feb 2009 16:11:10 +0000 Subject: [EMBOSS] Align 12bp DNA back to genome In-Reply-To: References: Message-ID: <498C611E.7010700@cancer.org.uk> Hi all, This isnt an EMBOSS question per se but I thought it would go to the right audience. After trimming a bunch of illumina reads I have sequences that are 12bp long and "we" want to find their genomic location Before anyone even says "Why do you want to do that?" can I suggest 1) Treat it as a hypothetical case 2) because the scientist who asked me wants it :-) I have both a perl regex and fuzznuc running now for oh about a week.......... I have also attempted to build/configure/run without success maq soap blat So can anyone suggest anything else to try (probably I have missed the obvious) before the regex and fuzznuc finish? This completes the Friday pm puzzler........ Cheers Aengus -- ----------------------------------------------------------------------- Aengus Stewart Head of Bioinformatics and BioStatistics Bioinformatics and BioStatistics Tel: +44 (0)20 7269 3679 Cancer Research UK, Lincoln's Inn Fields, Holborn, London, WC2A 3PX, UK ----------------------------------------------------------------------- This electronic message contains information which may be privileged and confidential. The information is intended to be for the use of the individual(s) or entity named above. Be aware that any third party disclosure, distribution, copying or use of this communication, without prior permission, is strictly prohibited. This communication is from Cancer Research UK. Our website is at www.cancerresearchuk.org. We are a charity registered under number 1089464 and a company limited by guarantee registered in England & Wales under number 4325234. Our registered address is 61 Lincoln's Inn Fields, London WC2A 3PX. Our central telephone number is 020 7242 0200. This communication and any attachments contain information which is confidential and may also be privileged. It is for the exclusive use of the intended recipient(s). If you are not the intended recipient(s) please note that any form of disclosure, distribution, copying or use of this communication or the information in it or in any attachments is strictly prohibited and may be unlawful. If you have received this communication in error, please notify the sender and delete the email and destroy any copies of it. E-mail communications cannot be guaranteed to be secure or error free, as information could be intercepted, corrupted, amended, lost, destroyed, arrive late or incomplete, or contain viruses. We do not accept liability for any such matters or their consequences. Anyone who communicates with us by e-mail is taken to accept the risks in doing so. From pmr at ebi.ac.uk Fri Feb 6 16:42:27 2009 From: pmr at ebi.ac.uk (Peter Rice) Date: Fri, 06 Feb 2009 16:42:27 +0000 Subject: [EMBOSS] Align 12bp DNA back to genome In-Reply-To: <498C611E.7010700@cancer.org.uk> References: <498C611E.7010700@cancer.org.uk> Message-ID: <498C6873.6040304@ebi.ac.uk> Aengus Stewart wrote: > After trimming a bunch of illumina reads I have sequences that are 12bp > long and "we" want to find their genomic location Can you say that they should match exactly (depending on the size of genome, and the accuracy of the reads)? A word matching algorithm should work well. How many reads do you have? This is actually a problem we are very interested in writing EMBOSS applications for. regards, Peter From malabady at gmail.com Fri Feb 6 16:49:41 2009 From: malabady at gmail.com (Magdy Alabady) Date: Fri, 6 Feb 2009 10:49:41 -0600 Subject: [EMBOSS] Align 12bp DNA back to genome In-Reply-To: <498C6873.6040304@ebi.ac.uk> References: <498C611E.7010700@cancer.org.uk> <498C6873.6040304@ebi.ac.uk> Message-ID: <6967ac4e0902060849w33ccb487x2ab9c6643166869@mail.gmail.com> Hi, I have used GMap to exactly what you are asking for but with little longer reads (sRNA). It worked well. You might want to try GMap. magdy On Fri, Feb 6, 2009 at 10:42 AM, Peter Rice wrote: > Aengus Stewart wrote: > >> After trimming a bunch of illumina reads I have sequences that are 12bp >> long and "we" want to find their genomic location >> > > Can you say that they should match exactly (depending on the size of > genome, and the accuracy of the reads)? > > A word matching algorithm should work well. > > How many reads do you have? > > This is actually a problem we are very interested in writing EMBOSS > applications for. > > regards, > > Peter > > _______________________________________________ > EMBOSS mailing list > EMBOSS at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/emboss > -- -------------------------------------------------------- Magdy S. Alabady, PhD Energy Bioscience Institute (EBI) Institute for Genome Biology (IGB) University of Illinois At Urbana-Champaign, Illinois ------------------------------------------------------ Imagination is more important than knowledge. For knowledge is limited, whereas imagination embraces the entire world, stimulating progress, giving birth to evolution.. .....Albert Einstein ------------------------------------------------------------- From aengus.stewart at cancer.org.uk Fri Feb 6 17:12:10 2009 From: aengus.stewart at cancer.org.uk (Aengus Stewart) Date: Fri, 06 Feb 2009 17:12:10 +0000 Subject: [EMBOSS] Align 12bp DNA back to genome In-Reply-To: <498C611E.7010700@cancer.org.uk> References: <498C611E.7010700@cancer.org.uk> Message-ID: <498C6F6A.8010205@cancer.org.uk> hmmmmmm bowtie is on the list to build and test, but not for this problem. Can you assure me that both bowtie and GMap will work with 12bp sequences? Regards Aengus -- ----------------------------------------------------------------------- Aengus Stewart Head of Bioinformatics and BioStatistics Bioinformatics and BioStatistics Tel: +44 (0)20 7269 3679 Cancer Research UK, Lincoln's Inn Fields, Holborn, London, WC2A 3PX, UK ----------------------------------------------------------------------- This electronic message contains information which may be privileged and confidential. The information is intended to be for the use of the individual(s) or entity named above. Be aware that any third party disclosure, distribution, copying or use of this communication, without prior permission, is strictly prohibited. This communication is from Cancer Research UK. Our website is at www.cancerresearchuk.org. We are a charity registered under number 1089464 and a company limited by guarantee registered in England & Wales under number 4325234. Our registered address is 61 Lincoln's Inn Fields, London WC2A 3PX. Our central telephone number is 020 7242 0200. This communication and any attachments contain information which is confidential and may also be privileged. It is for the exclusive use of the intended recipient(s). If you are not the intended recipient(s) please note that any form of disclosure, distribution, copying or use of this communication or the information in it or in any attachments is strictly prohibited and may be unlawful. If you have received this communication in error, please notify the sender and delete the email and destroy any copies of it. E-mail communications cannot be guaranteed to be secure or error free, as information could be intercepted, corrupted, amended, lost, destroyed, arrive late or incomplete, or contain viruses. We do not accept liability for any such matters or their consequences. Anyone who communicates with us by e-mail is taken to accept the risks in doing so. From David.Lapointe at umassmed.edu Fri Feb 6 16:47:53 2009 From: David.Lapointe at umassmed.edu (Lapointe, David) Date: Fri, 6 Feb 2009 11:47:53 -0500 Subject: [EMBOSS] Align 12bp DNA back to genome In-Reply-To: <498C611E.7010700@cancer.org.uk> References: <498C611E.7010700@cancer.org.uk> Message-ID: <5ECA525B88314B48870E4AC72E3B9AF20246A225@EDUNIVMAIL05.ad.umassmed.edu> Aengus, You might try looking here for other software. Maq, soap, rmap, etc are relatively fast but still time-consuming. http://seqanswers.com/forums/showthread.php?t=43 David -----Original Message----- From: emboss-bounces at lists.open-bio.org [mailto:emboss-bounces at lists.open-bio.org] On Behalf Of Aengus Stewart Sent: Friday, February 06, 2009 11:11 AM To: emboss at lists.open-bio.org Subject: [EMBOSS] Align 12bp DNA back to genome Hi all, This isnt an EMBOSS question per se but I thought it would go to the right audience. After trimming a bunch of illumina reads I have sequences that are 12bp long and "we" want to find their genomic location Before anyone even says "Why do you want to do that?" can I suggest 1) Treat it as a hypothetical case 2) because the scientist who asked me wants it :-) I have both a perl regex and fuzznuc running now for oh about a week.......... I have also attempted to build/configure/run without success maq soap blat So can anyone suggest anything else to try (probably I have missed the obvious) before the regex and fuzznuc finish? This completes the Friday pm puzzler........ Cheers Aengus -- ----------------------------------------------------------------------- Aengus Stewart Head of Bioinformatics and BioStatistics Bioinformatics and BioStatistics Tel: +44 (0)20 7269 3679 Cancer Research UK, Lincoln's Inn Fields, Holborn, London, WC2A 3PX, UK ----------------------------------------------------------------------- This electronic message contains information which may be privileged and confidential. The information is intended to be for the use of the individual(s) or entity named above. Be aware that any third party disclosure, distribution, copying or use of this communication, without prior permission, is strictly prohibited. This communication is from Cancer Research UK. Our website is at www.cancerresearchuk.org. We are a charity registered under number 1089464 and a company limited by guarantee registered in England & Wales under number 4325234. Our registered address is 61 Lincoln's Inn Fields, London WC2A 3PX. Our central telephone number is 020 7242 0200. This communication and any attachments contain information which is confidential and may also be privileged. It is for the exclusive use of the intended recipient(s). If you are not the intended recipient(s) please note that any form of disclosure, distribution, copying or use of this communication or the information in it or in any attachments is strictly prohibited and may be unlawful. If you have received this communication in error, please notify the sender and delete the email and destroy any copies of it. E-mail communications cannot be guaranteed to be secure or error free, as information could be intercepted, corrupted, amended, lost, destroyed, arrive late or incomplete, or contain viruses. We do not accept liability for any such matters or their consequences. Anyone who communicates with us by e-mail is taken to accept the risks in doing so. _______________________________________________ EMBOSS mailing list EMBOSS at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/emboss From malabady at gmail.com Fri Feb 6 17:56:18 2009 From: malabady at gmail.com (Magdy Alabady) Date: Fri, 6 Feb 2009 11:56:18 -0600 Subject: [EMBOSS] Align 12bp DNA back to genome In-Reply-To: <498C6F6A.8010205@cancer.org.uk> References: <498C611E.7010700@cancer.org.uk> <498C6F6A.8010205@cancer.org.uk> Message-ID: <6967ac4e0902060956w268ea749pe1af52b0576823a@mail.gmail.com> I haven't use bowite before, sorry. I used GMap extensivly to map sRNA to genomes like rice, and it works fine. bear in mind that sRNA is around 20 bp. I don't a problem in your case, but a trial is needed to judge it On Fri, Feb 6, 2009 at 11:12 AM, Aengus Stewart < aengus.stewart at cancer.org.uk> wrote: > > hmmmmmm > > bowtie is on the list to build and test, but not for this problem. > > Can you assure me that both bowtie and GMap will work with 12bp sequences? > > > Regards > > Aengus > > -- > ----------------------------------------------------------------------- > Aengus Stewart > Head of Bioinformatics and BioStatistics > Bioinformatics and BioStatistics Tel: +44 (0)20 7269 3679 > Cancer Research UK, Lincoln's Inn Fields, Holborn, London, WC2A 3PX, UK > ----------------------------------------------------------------------- > > This electronic message contains information which may be privileged and > confidential. The information is intended to be for the use of the > individual(s) or entity named above. Be aware that any third party > disclosure, distribution, copying or use of this communication, without > prior permission, is strictly prohibited. > > This communication is from Cancer Research UK. Our website is at > www.cancerresearchuk.org. We are a charity registered under number 1089464 > and a company limited by guarantee registered in England & Wales under > number 4325234. Our registered address is 61 Lincoln's Inn Fields, London > WC2A 3PX. Our central telephone number is 020 7242 0200. > > This communication and any attachments contain information which is > confidential and may also be privileged. It is for the exclusive use of > the intended recipient(s). If you are not the intended recipient(s) please > note that any form of disclosure, distribution, copying or use of this > communication or the information in it or in any attachments is strictly > prohibited and may be unlawful. If you have received this communication in > error, please notify the sender and delete the email and destroy any copies > of it. > > E-mail communications cannot be guaranteed to be secure or error free, as > information could be intercepted, corrupted, amended, lost, destroyed, > arrive late or incomplete, or contain viruses. We do not accept liability > for any such matters or their consequences. Anyone who communicates with us > by e-mail is taken to accept the risks in doing so. > _______________________________________________ > EMBOSS mailing list > EMBOSS at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/emboss > -- -------------------------------------------------------- Magdy S. Alabady, PhD Energy Bioscience Institute (EBI) Institute for Genome Biology (IGB) University of Illinois At Urbana-Champaign, Illinois ------------------------------------------------------ Imagination is more important than knowledge. For knowledge is limited, whereas imagination embraces the entire world, stimulating progress, giving birth to evolution.. .....Albert Einstein ------------------------------------------------------------- From mathog at caltech.edu Fri Feb 6 19:56:45 2009 From: mathog at caltech.edu (David Mathog) Date: Fri, 06 Feb 2009 11:56:45 -0800 Subject: [EMBOSS] Align 12bp DNA back to genome Message-ID: > After trimming a bunch of illumina reads I have sequences that are 12bp long and "we" want to find > their genomic location location(S!) > > I have both a perl regex and fuzznuc running now for oh about a week.......... It shouldn't take that long. Assuming the words are perfectly known (so identity match only), and you have more than one of these words to do, the fastest way would be to break the genome(s) down into words, sort that form, and then just pull out matching word positions from the resulting table(s). If on the other hand, you are allowing mismatches, well, ugh. 12 is pretty small to start with... > > I have also attempted to build/configure/run without success > maq > soap > blat Here is a tool which is very simple to get you started: http://saf.bio.caltech.edu/pub/software/molbio/fastatuples.c Do fastatuples -h to see the options. Run it like (for instance) fastatuples -n -w 12 -d -p -s References: <498C611E.7010700@cancer.org.uk> <5ECA525B88314B48870E4AC72E3B9AF20246A225@EDUNIVMAIL05.ad.umassmed.edu> Message-ID: <5aa3b3570902070657h4238c57fwf349ce000915df7c@mail.gmail.com> On 2/6/09, Lapointe, David wrote: > Aengus, > > You might try looking here for other software. Maq, soap, rmap, etc are > relatively fast but still time-consuming. > > http://seqanswers.com/forums/showthread.php?t=43 > > David > > -----Original Message----- > From: emboss-bounces at lists.open-bio.org > [mailto:emboss-bounces at lists.open-bio.org] On Behalf Of Aengus Stewart > Sent: Friday, February 06, 2009 11:11 AM > To: emboss at lists.open-bio.org > Subject: [EMBOSS] Align 12bp DNA back to genome > > > Hi all, > > This isnt an EMBOSS question per se but I thought it would go to the > right audience. > > After trimming a bunch of illumina reads I have sequences that are 12bp > long and "we" want to find > their genomic location I think 12 bp is too short to obtain good results. How much big is the genome that you want to search? Have you calculated the probability that your 12 bp sequences match to a random location in the genome? Or to two distinct positions? The human genome is not homogenously sequenced: there are still regions full of errors and of 'N's. What if one of your sequences falls in such a zone? Moreover, the genomic sequence that you are working with could not be the same as the one from which you have extracted your seqs. > > Before anyone even says "Why do you want to do that?" can I suggest > > 1) Treat it as a hypothetical case > 2) because the scientist who asked me wants it > > :-) > > I have both a perl regex and fuzznuc running now for oh about a > week.......... > > I have also attempted to build/configure/run without success > > maq > soap > blat > > So can anyone suggest anything else to try (probably I have missed the > obvious) before the regex and > fuzznuc finish? > > This completes the Friday pm puzzler........ > > > > Cheers > Aengus > > -- > ----------------------------------------------------------------------- > Aengus Stewart > Head of Bioinformatics and BioStatistics > Bioinformatics and BioStatistics Tel: +44 (0)20 7269 3679 > Cancer Research UK, Lincoln's Inn Fields, Holborn, London, WC2A 3PX, UK > ----------------------------------------------------------------------- > > This electronic message contains information which may be privileged and > confidential. The information is intended to be for the use of the > individual(s) or entity named above. Be aware that any third party > disclosure, distribution, copying or use of this communication, without > prior permission, is strictly prohibited. > > This communication is from Cancer Research UK. Our website is at > www.cancerresearchuk.org. We are a charity registered under number > 1089464 and a company limited by guarantee registered in England & Wales > under number 4325234. Our registered address is 61 Lincoln's Inn Fields, > London WC2A 3PX. Our central telephone number is 020 7242 0200. > > This communication and any attachments contain information which is > confidential and may also be privileged. It is for the exclusive use > of the intended recipient(s). If you are not the intended recipient(s) > please note that any form of disclosure, distribution, copying or use of > this communication or the information in it or in any attachments is > strictly prohibited and may be unlawful. If you have received this > communication in error, please notify the sender and delete the email > and destroy any copies of it. > > E-mail communications cannot be guaranteed to be secure or error free, > as information could be intercepted, corrupted, amended, lost, > destroyed, arrive late or incomplete, or contain viruses. We do not > accept liability for any such matters or their consequences. Anyone who > communicates with us by e-mail is taken to accept the risks in doing so. > _______________________________________________ > EMBOSS mailing list > EMBOSS at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/emboss > > > > _______________________________________________ > EMBOSS mailing list > EMBOSS at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/emboss > -- My blog on bioinformatics (now in English): http://bioinfoblog.it From charles-listes-emboss at plessy.org Sat Feb 14 02:04:39 2009 From: charles-listes-emboss at plessy.org (Charles Plessy) Date: Sat, 14 Feb 2009 11:04:39 +0900 Subject: [EMBOSS] www.emboss.org or emboss.sourceforge.org ? Message-ID: <20090214020439.GA24788@kunpuu.plessy.org> Dear EMBOSS developers, I was just wondering what is the canonical URL for the EMBOSS homepage. Is it emboss.sourceforge.net, emboss.org, or www.emboss.org ? There seems to be a problem with at least www.emboss.org, as the IP address 66.150.161.133 does not answer. Have a nice day, -- Charles Plessy http://charles.plessy.org Tsurumi, Kanagawa, Japan From ajb at ebi.ac.uk Sat Feb 14 09:53:28 2009 From: ajb at ebi.ac.uk (ajb at ebi.ac.uk) Date: Sat, 14 Feb 2009 09:53:28 -0000 (GMT) Subject: [EMBOSS] www.emboss.org or emboss.sourceforge.org ? In-Reply-To: <20090214020439.GA24788@kunpuu.plessy.org> References: <20090214020439.GA24788@kunpuu.plessy.org> Message-ID: <36342.86.9.126.186.1234605208.squirrel@webmail.ebi.ac.uk> Dear Charles, At the moment it is officially emboss.sourceforge.net. However, just to confuse things further, in the near future it is likely to change to emboss.open-bio.org (but we'll redirect sourceforge when that is done). Alan > Dear EMBOSS developers, > > I was just wondering what is the canonical URL for the EMBOSS homepage. Is > it > emboss.sourceforge.net, emboss.org, or www.emboss.org ? > > There seems to be a problem with at least www.emboss.org, as the IP > address > 66.150.161.133 does not answer. > > Have a nice day, > > -- > Charles Plessy > http://charles.plessy.org > Tsurumi, Kanagawa, Japan > _______________________________________________ > EMBOSS mailing list > EMBOSS at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/emboss > From stephen.taylor at imm.ox.ac.uk Mon Feb 16 13:45:07 2009 From: stephen.taylor at imm.ox.ac.uk (Steve Taylor) Date: Mon, 16 Feb 2009 13:45:07 +0000 Subject: [EMBOSS] Diversity / p-distance Message-ID: <49996DE3.7060807@imm.ox.ac.uk> Hi, Is there an EMBOSS tool that that can calculate p-distance as defined in http://evolgen.biol.metro-u.ac.jp/MEGA/manual/Distance.html? I can probably code something to do it but I thought I would ask first.:-) Kind regards and thanks, Steve ------------------------------------------------------------------ Medical Sciences Division Weatherall Institute of Molecular Medicine/Sir William Dunn School Oxford University From jerome.laroche at bioinfo.ulaval.ca Mon Feb 16 16:54:35 2009 From: jerome.laroche at bioinfo.ulaval.ca (=?ISO-8859-1?Q?J=E9r=F4me_Laroche?=) Date: Mon, 16 Feb 2009 11:54:35 -0500 Subject: [EMBOSS] error message with charge and pepstats Message-ID: <54FE4DF2-DFE2-406F-B03F-18C27F5357B7@bioinfo.ulaval.ca> Hi, I get the following error message when using the programs "charge" and "pepstats": EMBOSS An error in embprop.c at line 114: Incorrect (old?) format amino data file I work with EMBOSS 6.0.1 Files tested are in fasta format. Other programs read these files very well. Thanks. J?r?me Laroche Responsable de travaux pratiques et de recherche Centre de bioinformatique et de biologie computationnelle Universit? Laval From ajb at ebi.ac.uk Mon Feb 16 18:03:42 2009 From: ajb at ebi.ac.uk (ajb at ebi.ac.uk) Date: Mon, 16 Feb 2009 18:03:42 -0000 (GMT) Subject: [EMBOSS] error message with charge and pepstats In-Reply-To: <54FE4DF2-DFE2-406F-B03F-18C27F5357B7@bioinfo.ulaval.ca> References: <54FE4DF2-DFE2-406F-B03F-18C27F5357B7@bioinfo.ulaval.ca> Message-ID: <47313.86.9.126.186.1234807422.squirrel@webmail.ebi.ac.uk> Hi J?r?me, The programs aren't complaining about your FASTA files. The error is because the programs are not picking up the correct EMBOSS data file 'Eamino.dat'. That sort of error can happen if you've installed a new version of EMBOSS but, for whatever reason, have set an environment variable (EMBOSS_DATA) pointing to EMBOSS data files from a previous release. Alternatively, an incorrect Eamino.dat file could be being found in your current directory, your home directory or a '.embossdata' subdirectory of your home or current directory. To find out what Eamino.dat is being used by EMBOSS you can type: embossdata Eamino.dat That should give you some clue where to look for the problem. HTH Alan > Hi, > > I get the following error message when using the programs "charge" and > "pepstats": > > EMBOSS An error in embprop.c at line 114: > Incorrect (old?) format amino data file > > I work with EMBOSS 6.0.1 > > Files tested are in fasta format. Other programs read these files very > well. > > > Thanks. > > > > J?r?me Laroche > > Responsable de travaux pratiques et de recherche > Centre de bioinformatique et de biologie computationnelle > Universit? Laval > > > > > _______________________________________________ > EMBOSS mailing list > EMBOSS at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/emboss > From jison at ebi.ac.uk Tue Feb 17 13:46:07 2009 From: jison at ebi.ac.uk (Jon Ison) Date: Tue, 17 Feb 2009 13:46:07 -0000 (GMT) Subject: [EMBOSS] Diversity / p-distance In-Reply-To: <49996DE3.7060807@imm.ox.ac.uk> References: <49996DE3.7060807@imm.ox.ac.uk> Message-ID: <52021.84.92.187.247.1234878367.squirrel@webmail.ebi.ac.uk> Hi Steve I don't think so. You could have a look at: http://emboss.sourceforge.net/apps/cvs/embassy/phylipnew/ Any maybe: http://emboss.sourceforge.net/apps/cvs/emboss/apps/distmat.html If you do write something new in C, please let's have the code so it can be incorporated. Cheers Jon > Hi, > > Is there an EMBOSS tool that that can calculate p-distance as defined in > http://evolgen.biol.metro-u.ac.jp/MEGA/manual/Distance.html? > > I can probably code something to do it but I thought I would ask first.:-) > > Kind regards and thanks, > > Steve > ------------------------------------------------------------------ > Medical Sciences Division > Weatherall Institute of Molecular Medicine/Sir William Dunn School > Oxford University > _______________________________________________ > EMBOSS mailing list > EMBOSS at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/emboss > From stephen.taylor at imm.ox.ac.uk Tue Feb 17 15:56:26 2009 From: stephen.taylor at imm.ox.ac.uk (Steve Taylor) Date: Tue, 17 Feb 2009 15:56:26 +0000 Subject: [EMBOSS] Diversity / p-distance In-Reply-To: <52021.84.92.187.247.1234878367.squirrel@webmail.ebi.ac.uk> References: <49996DE3.7060807@imm.ox.ac.uk> <52021.84.92.187.247.1234878367.squirrel@webmail.ebi.ac.uk> Message-ID: <499ADE2A.9010007@imm.ox.ac.uk> Hi Jon, > > I don't think so. You could have a look at: > http://emboss.sourceforge.net/apps/cvs/embassy/phylipnew/ > > Any maybe: > http://emboss.sourceforge.net/apps/cvs/emboss/apps/distmat.html > Aha from distmat Looks like D = uncorrected distance = p-distance = 1-S > If you do write something new in C, please let's have the code > so it can be incorporated. > Steve ------------------------------------------------------------------ Medical Sciences Division Weatherall Institute of Molecular Medicine/Sir William Dunn School Oxford University From sea99.wang at gmail.com Thu Feb 19 07:43:29 2009 From: sea99.wang at gmail.com (Sea) Date: Thu, 19 Feb 2009 15:43:29 +0800 Subject: [EMBOSS] How to disable jemboss authorization function? Message-ID: <4f3a50530902182343v150c949cj825f7a11d4b4f331@mail.gmail.com> Hi, I installed jemboss on a unix server few years ago and enable the authorization function. (It's a window to login id and pwd before running the jemboss) Now I want to disable this function and run the jemboss directly, but have no idea how to do this. Does somebody have the same experience and have any good suggestions to disable the authorization function? If it is, give me some hints please, thanks a lot! :-) Sea From uludag at ebi.ac.uk Thu Feb 19 17:43:30 2009 From: uludag at ebi.ac.uk (uludag at ebi.ac.uk) Date: Thu, 19 Feb 2009 17:43:30 -0000 (GMT) Subject: [EMBOSS] How to disable jemboss authorization function? In-Reply-To: <4f3a50530902182343v150c949cj825f7a11d4b4f331@mail.gmail.com> References: <4f3a50530902182343v150c949cj825f7a11d4b4f331@mail.gmail.com> Message-ID: <50988.130.88.47.86.1235065410.squirrel@webmail.ebi.ac.uk> > I installed jemboss on a unix server few years ago and enable the > authorization function. > (It's a window to login id and pwd before running the jemboss) > Now I want to disable this function and run the jemboss directly, > but have no idea how to do this. i tested this with my jemboss installation after i have the following setting on the server side jemboss.properties file user.auth=false and the following settings on the client side jemboss.properties file then jemboss doesn't ask user name/password and able to communicate with the server user.auth=false service.public=JembossServer service.private=JembossServer Regards, Mahmut From charles-listes-emboss at plessy.org Fri Feb 20 14:51:06 2009 From: charles-listes-emboss at plessy.org (Charles Plessy) Date: Fri, 20 Feb 2009 23:51:06 +0900 Subject: [EMBOSS] RootDirectory and BaseDirectory hardcoded at build time ? Message-ID: <20090220145106.GA16170@kunpuu.plessy.org> Dear EMBOSS developers, I realised some time ago that when using the Debian 'emboss' package, embossversion would report wrong RootDirectory and BaseDirectory because the binaries are built in a temporary location before being moved in the package and installed on downstream computers: aqwa?~?$ embossversion -full Writes the current EMBOSS version number to a file PackageName: EMBOSS LibraryVersion: 6.0.1 InstallDirectory: /usr RootDirectory: /tmp/buildd/emboss-6.0.1/emboss BaseDirectory: /tmp/buildd/emboss-6.0.1/ Using 'strace' and 'strings', I figured out that this information is hard-coded in libajax. Is there a way to indicate the final location (/usr/share/EMBOSS?) at build time? Have a nice day, -- Charles Plessy http://charles.plessy.org Tsurumi, Kanagawa, Japan From jeedward at yahoo.com Fri Feb 20 15:19:59 2009 From: jeedward at yahoo.com (John Edward) Date: Fri, 20 Feb 2009 07:19:59 -0800 (PST) Subject: [EMBOSS] Draft paper submission deadline extended: BCBGC-09 Message-ID: <988357.6613.qm@web45903.mail.sp1.yahoo.com> Draft paper submission deadline extended: BCBGC-09 ? The deadline for draft paper submission at the 2009 International Conference on Bioinformatics, Computational Biology, Genomics and Chemoinformatics (BCBGC-09) (website: http://www.PromoteResearch.org ) is extended due to numerous requests from the authors. The conference 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 pmr at ebi.ac.uk Fri Feb 20 15:27:37 2009 From: pmr at ebi.ac.uk (Peter Rice) Date: Fri, 20 Feb 2009 15:27:37 +0000 Subject: [EMBOSS] RootDirectory and BaseDirectory hardcoded at build time ? In-Reply-To: <20090220145106.GA16170@kunpuu.plessy.org> References: <20090220145106.GA16170@kunpuu.plessy.org> Message-ID: <499ECBE9.5030409@ebi.ac.uk> Charles Plessy wrote: > Dear EMBOSS developers, > > I realised some time ago that when using the Debian 'emboss' package, > embossversion would report wrong RootDirectory and BaseDirectory because the > binaries are built in a temporary location before being moved in the package > and installed on downstream computers: > > aqwa$ embossversion -full > Writes the current EMBOSS version number to a file > PackageName: EMBOSS > LibraryVersion: 6.0.1 > InstallDirectory: /usr > RootDirectory: /tmp/buildd/emboss-6.0.1/emboss > BaseDirectory: /tmp/buildd/emboss-6.0.1/ > > Using 'strace' and 'strings', I figured out that this information is hard-coded > in libajax. Is there a way to indicate the final location (/usr/share/EMBOSS?) > at build time? The values are defined at build time. You can override them with settings in emboss.defaults (the easiest way) as EMBOSS_ROOT (the base directory is simply one level up). embossversion will report these values. This is the usual way where EMBOSS installations have been moved. The directories are defined from the --prefix setting when you run ./configure and we have not needed to define alternatives as the above method works. Of course, you could try hard coding any value you like in ajnam.c but we wouldn't recommend that! Hope that helps, Peter From georgios at biotek.uio.no Fri Feb 20 15:38:47 2009 From: georgios at biotek.uio.no (George Magklaras) Date: Fri, 20 Feb 2009 16:38:47 +0100 Subject: [EMBOSS] RootDirectory and BaseDirectory hardcoded at build time ? In-Reply-To: <20090220145106.GA16170@kunpuu.plessy.org> References: <20090220145106.GA16170@kunpuu.plessy.org> Message-ID: <499ECE87.7030703@biotek.uio.no> In the Makefile, shouldn't they be a: AJAX_FIXED_ROOT directive? I am not exactly familiar with the Debian package process, but at my (manually built) leftovers from the sources, I did a: georgie at slartibartfast# fgrep -i root config.log ... AJAX_FIXED_ROOT='\"/site/sources/EMBOSS-6.0.1/emboss\"' datadir='${datarootdir}' datarootdir='${prefix}/share' docdir='${datarootdir}/doc/${PACKAGE}' infodir='${datarootdir}/info' localedir='${datarootdir}/locale' mandir='${datarootdir}/man' ...... and the location was passed by configure with the --prefix switch. Does the Debian package dist specify a location that way? -- -- George Magklaras BSc Hons MPhil RHCE:805008309135525 Senior Computer Systems Engineer/UNIX-Linux Systems Administrator EMBnet Technical Management Board The Biotechnology Centre of Oslo, University of Oslo http://folk.uio.no/georgios Charles Plessy wrote: > Dear EMBOSS developers, > > I realised some time ago that when using the Debian 'emboss' package, > embossversion would report wrong RootDirectory and BaseDirectory because the > binaries are built in a temporary location before being moved in the package > and installed on downstream computers: > > aqwa?~?$ embossversion -full > Writes the current EMBOSS version number to a file > PackageName: EMBOSS > LibraryVersion: 6.0.1 > InstallDirectory: /usr > RootDirectory: /tmp/buildd/emboss-6.0.1/emboss > BaseDirectory: /tmp/buildd/emboss-6.0.1/ > > Using 'strace' and 'strings', I figured out that this information is hard-coded > in libajax. Is there a way to indicate the final location (/usr/share/EMBOSS?) > at build time? > > Have a nice day, > From pmr at ebi.ac.uk Fri Feb 20 16:12:30 2009 From: pmr at ebi.ac.uk (Peter Rice) Date: Fri, 20 Feb 2009 16:12:30 +0000 Subject: [EMBOSS] RootDirectory and BaseDirectory hardcoded at build time ? In-Reply-To: <499ECBE9.5030409@ebi.ac.uk> References: <20090220145106.GA16170@kunpuu.plessy.org> <499ECBE9.5030409@ebi.ac.uk> Message-ID: <499ED66E.6070506@ebi.ac.uk> Peter Rice wrote: > Charles Plessy wrote: >> Dear EMBOSS developers, >> >> I realised some time ago that when using the Debian 'emboss' package, >> embossversion would report wrong RootDirectory and BaseDirectory >> because the >> binaries are built in a temporary location before being moved in the >> package >> and installed on downstream computers: >> >> aqwa$ embossversion -full >> Writes the current EMBOSS version number to a file >> PackageName: EMBOSS >> LibraryVersion: 6.0.1 >> InstallDirectory: /usr >> RootDirectory: /tmp/buildd/emboss-6.0.1/emboss >> BaseDirectory: /tmp/buildd/emboss-6.0.1/ >> >> Using 'strace' and 'strings', I figured out that this information is >> hard-coded >> in libajax. Is there a way to indicate the final location >> (/usr/share/EMBOSS?) >> at build time? > > The values are defined at build time. You can override them with > settings in emboss.defaults (the easiest way) as EMBOSS_ROOT (the base > directory is simply one level up). embossversion will report > these values. This is the usual way where EMBOSS installations have been > moved. Oops, wrong answer! It is not possible to define it in emboss.default (the correct name) because the values are set before emboss.default is read (they are needed to find the possible locations of emboss.default). That leaves setenv EMBOSS_ROOT as the way to define the values (in csh syntax) but that is not so easy to implement globally. Does the embossversion output give you any other problems? Or do the values give problems for any other EMBOSS applications? Where does the source get moved to? Or is it removed? Peter From pmr at ebi.ac.uk Fri Feb 20 16:16:51 2009 From: pmr at ebi.ac.uk (Peter Rice) Date: Fri, 20 Feb 2009 16:16:51 +0000 Subject: [EMBOSS] RootDirectory and BaseDirectory hardcoded at build time ? In-Reply-To: <499ECE87.7030703@biotek.uio.no> References: <20090220145106.GA16170@kunpuu.plessy.org> <499ECE87.7030703@biotek.uio.no> Message-ID: <499ED773.1020405@ebi.ac.uk> George Magklaras wrote: > In the Makefile, shouldn't they be a: > > AJAX_FIXED_ROOT directive? > > I am not exactly familiar with the Debian package process, but at my > (manually built) leftovers from the sources, I did a: > georgie at slartibartfast# fgrep -i root config.log > ... > AJAX_FIXED_ROOT='\"/site/sources/EMBOSS-6.0.1/emboss\"' > datadir='${datarootdir}' > datarootdir='${prefix}/share' > docdir='${datarootdir}/doc/${PACKAGE}' > infodir='${datarootdir}/info' > localedir='${datarootdir}/locale' > mandir='${datarootdir}/man' > ...... > > and the location was passed by configure with the --prefix switch. Does > the Debian package dist specify a location that way? AJAX_FIXED_ROOT is originally defined in configure.in in the top level directory. > #dnl Define where the EMBOSS package is located > AC_SUBST(AJAX_FIXED_ROOT) > AJAX_FIXED_ROOT="\\\"`pwd`/emboss\\\"" > AC_SUBST(EMBOSS_TOP) > EMBOSS_TOP=`pwd` The values then are used to build ./configure and get copied to config.log when it runs. Peter P.S. I liked the "georgie at slartibartfast" :-) From gbottu at vub.ac.be Fri Feb 20 17:31:48 2009 From: gbottu at vub.ac.be (Guy Bottu) Date: Fri, 20 Feb 2009 18:31:48 +0100 Subject: [EMBOSS] wEMBOSS multiple login problem fixed Message-ID: <499EE904.9050209@vub.ac.be> Dear all, As those of you who use wEMBOSS will have noticed, with recent versions of Web browsers a problem had appeared : you had to type in your username/password for each frame separately (up to 4 times). This problem has been fixed by a change in the login procedure that makes you must again login just once. We have released a new subversion 1.8.1 with the fix and some further minor changes, see http://sourceforge.net/project/shownotes.php?release_id=662615&group_id=170030 http://sourceforge.net/project/shownotes.php?release_id=662578&group_id=170030 Regards, Guy Bottu, Belgian EMBnet Node - wEMBOSS development team From charles-listes-emboss at plessy.org Sat Feb 21 05:22:24 2009 From: charles-listes-emboss at plessy.org (Charles Plessy) Date: Sat, 21 Feb 2009 14:22:24 +0900 Subject: [EMBOSS] RootDirectory and BaseDirectory hardcoded at build time ? In-Reply-To: <499ED773.1020405@ebi.ac.uk> References: <20090220145106.GA16170@kunpuu.plessy.org> <499ECE87.7030703@biotek.uio.no> <499ED773.1020405@ebi.ac.uk> Message-ID: <20090221052224.GA29289@kunpuu.plessy.org> Le Fri, Feb 20, 2009 at 04:16:51PM +0000, Peter Rice a ?crit : > George Magklaras wrote: >> In the Makefile, shouldn't they be a: >> >> AJAX_FIXED_ROOT directive? >> >> I am not exactly familiar with the Debian package process, but at my >> (manually built) leftovers from the sources, I did a: >> georgie at slartibartfast# fgrep -i root config.log >> ... >> AJAX_FIXED_ROOT='\"/site/sources/EMBOSS-6.0.1/emboss\"' >> datadir='${datarootdir}' >> datarootdir='${prefix}/share' >> docdir='${datarootdir}/doc/${PACKAGE}' >> infodir='${datarootdir}/info' >> localedir='${datarootdir}/locale' >> mandir='${datarootdir}/man' >> ...... >> >> and the location was passed by configure with the --prefix switch. Does >> the Debian package dist specify a location that way? > > AJAX_FIXED_ROOT is originally defined in configure.in in the top level > directory. Thanks for all your anwers, I solved the problem by passing AJAX_FIXED_ROOT=\\\"/usr/share/EMBOSS\\\" to the make command. This hardcodes the root to /usr/share/EMBOSS, where all the data files are installed by the Debian package 'emboss-data'. It was not a big problem that embossversion --full reported the directories where EMBOSS was built, but just in case a user would rely on this, I prefer to correct it. Have a nice day, -- Charles From afikolami at gmail.com Tue Feb 24 01:28:51 2009 From: afikolami at gmail.com (Mohd Afiq Hazlami) Date: Tue, 24 Feb 2009 09:28:51 +0800 Subject: [EMBOSS] Problem with showdb and seqret Message-ID: <4e53edca0902231728o2fb9a389gbde8fd5b40ff9e88@mail.gmail.com> Hello, I'm new to EMBOSS and I have a problem that I can't figure out. I have configured and installed EMBOSS-6.0.1 on my Ubuntu machine and I tried doing the exercises according to the tutorial. There's nothing wrong when I typed 'wossname' and the program works fine, just like in the tutorial. But when it comes to 'showdb' tutorial, the program returns this: afiq at peregrin:~/EMBOSS-6.0.1$ showdb Displays information on configured databases # Name Type ID Qry All Comment # ============ ==== == === === ======= afiq at peregrin:~/EMBOSS-6.0.1$ which is totally different from the tutorial where it shows some database names. Is this normal? Then, when I tried to use seqret as in the tutorial given (using xlrhodop), the program returns this: afiq at peregrin:~/EMBOSS-6.0.1$ seqret Reads and writes (returns) sequences Input (gapped) sequence(s): embl:xlrhodop Error: Failed to open filename 'embl' Error: Unable to read sequence 'embl:xlrhodop' Input (gapped) sequence(s): which is really confusing. Can anybody tell me what's wrong? From emno72 at gmail.com Tue Feb 24 03:26:03 2009 From: emno72 at gmail.com (Mohd Noor Mat Isa) Date: Tue, 24 Feb 2009 11:26:03 +0800 Subject: [EMBOSS] Problem with showdb and seqret In-Reply-To: <4e53edca0902231728o2fb9a389gbde8fd5b40ff9e88@mail.gmail.com> References: <4e53edca0902231728o2fb9a389gbde8fd5b40ff9e88@mail.gmail.com> Message-ID: <2e2159f50902231926x78b43697v13b4fd01e3bffe88@mail.gmail.com> Dear Mohd Afiq, I'm not an expert also on EMBOSS installation but I can give you some clues on your problems: First, showdb does not give you any db list as you need to index all the databases that you requires to show. You can get further info here http://emboss.sourceforge.net/docs/adminguide/node56.html on how to index databases. as for seqret you should tell the seqret you input format as *embl::xlrhodop * not embl*:*xlrhodop. Regards Mohd Noor Malaysia Genome Institute On Tue, Feb 24, 2009 at 9:28 AM, Mohd Afiq Hazlami wrote: > Hello, > I'm new to EMBOSS and I have a problem that I can't figure out. I have > configured and installed EMBOSS-6.0.1 on my Ubuntu machine and I tried > doing > the exercises according to the tutorial. There's nothing wrong when I typed > 'wossname' and the program works fine, just like in the tutorial. But when > it comes to 'showdb' tutorial, the program returns this: > > > afiq at peregrin:~/EMBOSS-6.0.1$ showdb > Displays information on configured databases > # Name Type ID Qry All Comment > # ============ ==== == === === ======= > afiq at peregrin:~/EMBOSS-6.0.1$ > > which is totally different from the tutorial where it shows some database > names. Is this normal? > > Then, when I tried to use seqret as in the tutorial given (using xlrhodop), > the program returns this: > > afiq at peregrin:~/EMBOSS-6.0.1$ seqret > Reads and writes (returns) sequences > Input (gapped) sequence(s): embl:xlrhodop > Error: Failed to open filename 'embl' > Error: Unable to read sequence 'embl:xlrhodop' > Input (gapped) sequence(s): > > which is really confusing. Can anybody tell me what's wrong? > _______________________________________________ > EMBOSS mailing list > EMBOSS at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/emboss > From gbottu at vub.ac.be Tue Feb 24 09:26:27 2009 From: gbottu at vub.ac.be (Guy Bottu) Date: Tue, 24 Feb 2009 10:26:27 +0100 Subject: [EMBOSS] Problem with showdb and seqret In-Reply-To: <4e53edca0902231728o2fb9a389gbde8fd5b40ff9e88@mail.gmail.com> References: <4e53edca0902231728o2fb9a389gbde8fd5b40ff9e88@mail.gmail.com> Message-ID: <49A3BD43.7010300@vub.ac.be> Mohd Afiq Hazlami wrote: > But when > it comes to 'showdb' tutorial, the program returns this: Alas, the manual and tutorial are out-of-date. This is an unfortunate chronic disease of EMBOSS, even if for the rest EMBOSS is great. Before you can access 'public' sequences using the : syntax you must first define databases in the file /share/EMBOSS/emboss.default There is a file emboss.default.template with examples. To get a quick try using the EMBOSS tutorial data you could put the following in emboss.default : DB test_embl [ type: N comment: 'testset for EMBL' format: embl method: emblcd dir: /opt/sw/EMBOSS6/EMBOSS-6.0.1/test/embl ] Do replace /opt/sw/EMBOSS6/EMBOSS-6.0.1/test/embl by /test/embl You will note that this directory does contain sequences and indexes. You can then do showdb entret test_embl:Z11115 You can read more about it at http://emboss.sourceforge.net/docs/themes/Databases.html A question for the EMBOSS development team : what is the status of the new EMBOSS manual ? Regards, Guy Bottu, Belgian EMBnet Node From benys at usp.br Wed Feb 25 14:51:35 2009 From: benys at usp.br (Beny Spira) Date: Wed, 25 Feb 2009 11:51:35 -0300 Subject: [EMBOSS] emboss-explorer Message-ID: <21e884180902250651r54203c25x6003b0cc5df2721b@mail.gmail.com> Hi I was trying to install emboss-explorer using Debian binaries. Emboss installed fine, emboss-explorer also got installed fine in my desktop computer but not in my laptop. Both computers OS is Linux Debian Lenny and emboss version is 5.0.07. (One of) the recurrent errors in /var/log/apache2/error.log is: [Wed Feb 25 10:37:08 2009] [error] [client 127.0.0.1] File does not exist: /usr/share/emboss-explorer/html/output/949348, referer: http://localhost/cgi-bin/emboss/wossname Apache apparently runs OK. Any clue about what might be wrong? Beny -- Beny Spira Departamento de Microbiologia Instituto de Ci?ncias Biom?dicas Universidade de S?o Paulo Av. Prof. Lineu Prestes 1374 S?o Paulo-SP CEP:05508-900 Brasil Tel: 5511-3091-7347 FAX: 5511-3091-7354 E-mail: benys at usp.br Homepage: www.icb.usp.br/~benys From scott at cs.wits.ac.za Thu Feb 26 13:26:50 2009 From: scott at cs.wits.ac.za (Scott Hazelhurst) Date: Thu, 26 Feb 2009 15:26:50 +0200 Subject: [EMBOSS] fneighbor and dist programs Message-ID: <20090226132041.M96385@cs.wits.ac.za> Dear all, I am having problems using fneighbor with either fprotdist or fdnadist. The way the dist programs work is that when it prints the distance matrix, after every nine distance values a new line is printed. However, this seems to upset fneighbor which complains thus: Error: Distances file found 0 rows, expected 26 Error: Unable to read distances file 'ensmuscle2.fprotdist' Died: fneighbor terminated: Bad value for '-datafile' with -auto defined fneighbor exited with status 1... If I use a small number of sequences, then there's no problem. Or, if I manually edit the fprotdist file so as to remove the newlines, then it works fine. This is OK for me, but for the student lab it's a bit of a showstopper I looked in my archives and documentation but couldn't find anything on this. Am I missing something obvious? I am using Phylipnew 3.67, EMBOSS 6.0.1 Many thanks Scott

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From scott at cs.wits.ac.za Fri Feb 27 12:15:50 2009 From: scott at cs.wits.ac.za (Scott Hazelhurst) Date: Fri, 27 Feb 2009 14:15:50 +0200 Subject: [EMBOSS] fneighbor and dist programs In-Reply-To: <20090226132041.M96385@cs.wits.ac.za> References: <20090226132041.M96385@cs.wits.ac.za> Message-ID: <20090227121502.M74045@cs.wits.ac.za> Thanks to Peter and the EMBOSS team for the quick patch. My lab went well.

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From charles-listes-emboss at plessy.org Sat Feb 28 11:53:17 2009 From: charles-listes-emboss at plessy.org (Charles Plessy) Date: Sat, 28 Feb 2009 20:53:17 +0900 Subject: [EMBOSS] emboss-explorer In-Reply-To: <21e884180902250651r54203c25x6003b0cc5df2721b@mail.gmail.com> References: <21e884180902250651r54203c25x6003b0cc5df2721b@mail.gmail.com> Message-ID: <20090228115317.GI30418@kunpuu.plessy.org> Le Wed, Feb 25, 2009 at 11:51:35AM -0300, Beny Spira a ?crit : > (One of) the recurrent errors in /var/log/apache2/error.log is: > > [Wed Feb 25 10:37:08 2009] [error] [client 127.0.0.1] File does not exist: > /usr/share/emboss-explorer/html/output/949348, referer: > http://localhost/cgi-bin/emboss/wossname Dear Beny, there is probably a problem with /etc/emboss-explorer/emboss-explorer.conf (a Debian-specific file), that should contain something like: # path to the EMBOSS::GUI temporary output directory our $OUTPUT_PATH = "/var/lib/emboss-explorer/output"; In the worst case, just try to purge emboss-explorer and reinstall it, but before this save any change you made to the configuration, as it will be deleted. Have a nice day, -- Charles Plessy Debian Med packaging team, http://www.debian.org/devel/debian-med Tsurumi, Kanagawa, Japan