From michael.watson at bbsrc.ac.uk Thu Oct 1 07:33:50 2009 From: michael.watson at bbsrc.ac.uk (michael watson (IAH-C)) Date: Thu, 1 Oct 2009 12:33:50 +0100 Subject: [EMBOSS] Trim polyA from fastq files Message-ID: <8D08960C647E64438CE5740657CBBDC5010D2AC6E2@iahcexch1.iah.bbsrc.ac.uk> Hello I have some Illumina reads which have varying lengths of polyAs at the ends. I want to trim these off. The data is in fastq format. Is this possible in EMBOSS? I have 6.0.1 and I tried trimest but it couldn't read my fastq file Thanks Mick Head of Bioinformatics Institute for Animal Health Compton Berks RG20 7NN 01635 578411 Please consider the environment and don't print this e-mail unless you really need to. The information contained in this message may be confidential or legally privileged and is intended solely for the addressee. If you have received this message in error please delete it & notify the originator immediately. 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The Institute is also a registered charity, Charity Commissioners Reference No. 228824 From pmr at ebi.ac.uk Thu Oct 1 08:09:48 2009 From: pmr at ebi.ac.uk (Peter Rice) Date: Thu, 01 Oct 2009 13:09:48 +0100 Subject: [EMBOSS] Trim polyA from fastq files In-Reply-To: <8D08960C647E64438CE5740657CBBDC5010D2AC6E2@iahcexch1.iah.bbsrc.ac.uk> References: <8D08960C647E64438CE5740657CBBDC5010D2AC6E2@iahcexch1.iah.bbsrc.ac.uk> Message-ID: <4AC49C0C.5010800@ebi.ac.uk> On 01/10/09 12:33, michael watson (IAH-C) wrote: > Hello > > I have some Illumina reads which have varying lengths of polyAs at the ends. I want to trim these off. The data is in fastq format. > > Is this possible in EMBOSS? I have 6.0.1 and I tried trimest but it couldn't read my fastq file Yes, but you need EMBOSS 6.1.0 to support FASTQ input. There are also a couple of patches that are needed for some FASTQ files. regards, Peter Rice From michael.watson at bbsrc.ac.uk Thu Oct 1 08:53:12 2009 From: michael.watson at bbsrc.ac.uk (michael watson (IAH-C)) Date: Thu, 1 Oct 2009 13:53:12 +0100 Subject: [EMBOSS] Trim polyA from fastq files In-Reply-To: <4AC49C0C.5010800@ebi.ac.uk> References: <8D08960C647E64438CE5740657CBBDC5010D2AC6E2@iahcexch1.iah.bbsrc.ac.uk> <4AC49C0C.5010800@ebi.ac.uk> Message-ID: <8D08960C647E64438CE5740657CBBDC5010D2AC6E9@iahcexch1.iah.bbsrc.ac.uk> Hi Peter Thanks for that. Is it possible to preserve the fastq format? My input was fastq, I also put .fastq as my output, but it only gave me straight fasta Thanks Mick -----Original Message----- From: Peter Rice [mailto:pmr at ebi.ac.uk] Sent: 01 October 2009 13:10 To: michael watson (IAH-C) Cc: 'emboss at emboss.open-bio.org' Subject: Re: [EMBOSS] Trim polyA from fastq files On 01/10/09 12:33, michael watson (IAH-C) wrote: > Hello > > I have some Illumina reads which have varying lengths of polyAs at the ends. I want to trim these off. The data is in fastq format. > > Is this possible in EMBOSS? I have 6.0.1 and I tried trimest but it couldn't read my fastq file Yes, but you need EMBOSS 6.1.0 to support FASTQ input. There are also a couple of patches that are needed for some FASTQ files. regards, Peter Rice From biopython at maubp.freeserve.co.uk Thu Oct 1 10:04:14 2009 From: biopython at maubp.freeserve.co.uk (Peter) Date: Thu, 1 Oct 2009 15:04:14 +0100 Subject: [EMBOSS] Trim polyA from fastq files In-Reply-To: <8D08960C647E64438CE5740657CBBDC5010D2AC6E9@iahcexch1.iah.bbsrc.ac.uk> References: <8D08960C647E64438CE5740657CBBDC5010D2AC6E2@iahcexch1.iah.bbsrc.ac.uk> <4AC49C0C.5010800@ebi.ac.uk> <8D08960C647E64438CE5740657CBBDC5010D2AC6E9@iahcexch1.iah.bbsrc.ac.uk> Message-ID: <320fb6e00910010704u648614d4wf48a6244a9c6aa6c@mail.gmail.com> On Thu, Oct 1, 2009 at 1:53 PM, michael watson (IAH-C) wrote: > > Hi Peter > > Thanks for that. > > Is it possible to preserve the fastq format? ?My input was fastq, I also put .fastq as my output, but it only gave me straight fasta > Use "fastq-sanger" (or a variant), not just "fastq" which means ignoring the qualities in EMBOSS. http://emboss.sourceforge.net/docs/themes/SequenceFormats.html#in Peter From pmr at ebi.ac.uk Thu Oct 1 10:31:15 2009 From: pmr at ebi.ac.uk (Peter Rice) Date: Thu, 01 Oct 2009 15:31:15 +0100 Subject: [EMBOSS] Trim polyA from fastq files In-Reply-To: <320fb6e00910010704u648614d4wf48a6244a9c6aa6c@mail.gmail.com> References: <8D08960C647E64438CE5740657CBBDC5010D2AC6E2@iahcexch1.iah.bbsrc.ac.uk> <4AC49C0C.5010800@ebi.ac.uk> <8D08960C647E64438CE5740657CBBDC5010D2AC6E9@iahcexch1.iah.bbsrc.ac.uk> <320fb6e00910010704u648614d4wf48a6244a9c6aa6c@mail.gmail.com> Message-ID: <4AC4BD33.7050201@ebi.ac.uk> On 01/10/09 15:04, Peter wrote: > On Thu, Oct 1, 2009 at 1:53 PM, michael watson (IAH-C) > wrote: >> Thanks for that. >> >> Is it possible to preserve the fastq format? My input was fastq, I also put .fastq as my output, but it only gave me straight fasta The filename can be anything. You need -osformat fastq-sanger on the command line to set the output format. regards, Peter Rice From jesse at libbench.com Wed Oct 14 13:22:37 2009 From: jesse at libbench.com (Jesse Erdmann) Date: Wed, 14 Oct 2009 12:22:37 -0500 Subject: [EMBOSS] vectorstrip: Died: Unknown qualifier --vectorfile Message-ID: <97174eb20910141022r14ccb771n94180883053c9b24@mail.gmail.com> I downloaded, compiled and installed EMBOSS' latest stable version this morning on my Mac OS X 10.5 so I could do some testing on my development machine. Currently, when I execute a command that works just fine on our production environment, I get "Died: Unknown qualifier -vectorfile". Removing -vectorfile works, but then I have to interactively respond to the prompt, whereas the Perl script would normally just run. To install, all I did was './configure; make; sudo make install'. Any suggestions as to what might be happening here? Thanks! -- Jesse Erdmann jesse at jesseerdmann.com Twitter: http://twitter.com/jesseerdmann Blog: http://blog.jesseerdmann.com/ From Richard.Rothery at ualberta.ca Wed Oct 14 13:46:21 2009 From: Richard.Rothery at ualberta.ca (Richard Rothery) Date: Wed, 14 Oct 2009 11:46:21 -0600 Subject: [EMBOSS] Seqret slowness..... Message-ID: <6061958B16EE43509AEF205B25657630@Nordegg> Hi, I have been trying to update my sequence datasets using the seqret program. Step 1 is that I blast my sequence against uniprot using the EXPASY server. Unfortunately, because the recent explosion of duplicate data ("environmental samples"), it is now necessary to download 1-2K sequences and then filter out the random "environmental" sample derived fragments etc. Step 2 is assembling a list in gnumeric, exporting it as a multiline text file of format "unpirot:accession" . Step 3 is using the command "seqret @filename.txt". This is extraordinarily slow. It takes >12 hours to download a fasta file containing 3K sequences. Is there a way of speeding this up? I used to be able to download directly from EXPASY, but the site now only allows about 200-odd sequences to be selected and downloaded at a time. Note that filtering sequence sets is very fast with the program cd-hit. This takes about 10 seconds on an old P4 machine to remove sequences from the set with >90% identity to any other, for example. I do not have the resources to install and index local databases. Thanks! Richard A. Rothery, Ph.D. Research Associate ______________________________________________ Membrane Protein Research Group, Department of Biochemistry, University of Alberta, Edmonton T6G 2H7 Ph. 780-492-2229 Fax. 780-492-0886 ______________________________________________ From uludag at ebi.ac.uk Wed Oct 14 15:22:33 2009 From: uludag at ebi.ac.uk (uludag at ebi.ac.uk) Date: Wed, 14 Oct 2009 20:22:33 +0100 (BST) Subject: [EMBOSS] vectorstrip: Died: Unknown qualifier --vectorfile In-Reply-To: <97174eb20910141022r14ccb771n94180883053c9b24@mail.gmail.com> References: <97174eb20910141022r14ccb771n94180883053c9b24@mail.gmail.com> Message-ID: <52060.78.105.201.225.1255548153.squirrel@webmail.ebi.ac.uk> > "Died: Unknown qualifier -vectorfile". Name of the qualifier looks like to be vectorsfile rather than vectorfile. Regards, Mahmut From jesse at libbench.com Wed Oct 14 15:28:18 2009 From: jesse at libbench.com (Jesse Erdmann) Date: Wed, 14 Oct 2009 14:28:18 -0500 Subject: [EMBOSS] vectorstrip: Died: Unknown qualifier --vectorfile In-Reply-To: <52060.78.105.201.225.1255548153.squirrel@webmail.ebi.ac.uk> References: <97174eb20910141022r14ccb771n94180883053c9b24@mail.gmail.com> <52060.78.105.201.225.1255548153.squirrel@webmail.ebi.ac.uk> Message-ID: <97174eb20910141228m5b158b4cn7615ba670bd9f4bf@mail.gmail.com> Actually there are both. According to http://emboss.bioinformatics.nl/cgi-bin/emboss/help/vectorstrip, the [-[no]vectorfile] option allows you to answer the question "Are your vector sequences in a file?" without having to interact with the program. This works as expected in a different environment, but it's not on my development environment, which means I have to manually intervene multiple times during our perl script that would otherwise run unattended. Thanks! Jesse On Wed, Oct 14, 2009 at 2:22 PM, wrote: > >> "Died: Unknown qualifier -vectorfile". > > Name of the qualifier looks like to be vectorsfile rather than vectorfile. > > Regards, > Mahmut > > > -- Jesse Erdmann jesse at jesseerdmann.com Twitter: http://twitter.com/jesseerdmann Blog: http://blog.jesseerdmann.com/ From uludag at ebi.ac.uk Wed Oct 14 15:38:14 2009 From: uludag at ebi.ac.uk (uludag at ebi.ac.uk) Date: Wed, 14 Oct 2009 20:38:14 +0100 (BST) Subject: [EMBOSS] vectorstrip: Died: Unknown qualifier --vectorfile In-Reply-To: <97174eb20910141228m5b158b4cn7615ba670bd9f4bf@mail.gmail.com> References: <97174eb20910141022r14ccb771n94180883053c9b24@mail.gmail.com> <52060.78.105.201.225.1255548153.squirrel@webmail.ebi.ac.uk> <97174eb20910141228m5b158b4cn7615ba670bd9f4bf@mail.gmail.com> Message-ID: <42610.78.105.201.225.1255549094.squirrel@webmail.ebi.ac.uk> > http://emboss.bioinformatics.nl/cgi-bin/emboss/help/vectorstrip, the > [-[no]vectorfile] option allows you to answer the question "Are your > vector sequences in a file?" Above site seems to be using EMBOSS-6.0.1. It looks like the 'vectorstrip' option has been renamed as 'readfile' in the latest release. http://emboss.open-bio.org/wiki/Appdoc:Vectorstrip#Command_line_arguments Mahmut From benys at usp.br Wed Oct 14 15:44:08 2009 From: benys at usp.br (Beny Spira) Date: Wed, 14 Oct 2009 16:44:08 -0300 Subject: [EMBOSS] fuzznuc Message-ID: <21e884180910141244m5976f7e5ke9543eb02cfe01ed@mail.gmail.com> Hi I am using EMBOSS 6.1.0 and I wonder why the '-mismatch' qualifier of fuzznuc is missing in the new EMBOSS version. Is there an alternative for fuzznuc for searching short DNA motifs? Cheers, 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 jesse at libbench.com Wed Oct 14 15:50:23 2009 From: jesse at libbench.com (Jesse Erdmann) Date: Wed, 14 Oct 2009 14:50:23 -0500 Subject: [EMBOSS] vectorstrip: Died: Unknown qualifier --vectorfile In-Reply-To: <42610.78.105.201.225.1255549094.squirrel@webmail.ebi.ac.uk> References: <97174eb20910141022r14ccb771n94180883053c9b24@mail.gmail.com> <52060.78.105.201.225.1255548153.squirrel@webmail.ebi.ac.uk> <97174eb20910141228m5b158b4cn7615ba670bd9f4bf@mail.gmail.com> <42610.78.105.201.225.1255549094.squirrel@webmail.ebi.ac.uk> Message-ID: <97174eb20910141250pc0ac7f7u6fdcc078d9ae1e40@mail.gmail.com> That would explain it! Thanks very much! Jesse On Wed, Oct 14, 2009 at 2:38 PM, wrote: > >> http://emboss.bioinformatics.nl/cgi-bin/emboss/help/vectorstrip, the >> [-[no]vectorfile] option allows you to answer the question "Are your >> vector sequences in a file?" > > Above site seems to be using EMBOSS-6.0.1. > > It looks like the 'vectorstrip' option has been renamed as 'readfile' in > the latest release. > > http://emboss.open-bio.org/wiki/Appdoc:Vectorstrip#Command_line_arguments > > Mahmut > > > > -- Jesse Erdmann jesse at jesseerdmann.com Twitter: http://twitter.com/jesseerdmann Blog: http://blog.jesseerdmann.com/ From uludag at ebi.ac.uk Wed Oct 14 16:05:27 2009 From: uludag at ebi.ac.uk (uludag at ebi.ac.uk) Date: Wed, 14 Oct 2009 21:05:27 +0100 (BST) Subject: [EMBOSS] vectorstrip: Died: Unknown qualifier --vectorfile In-Reply-To: <97174eb20910141250pc0ac7f7u6fdcc078d9ae1e40@mail.gmail.com> References: <97174eb20910141022r14ccb771n94180883053c9b24@mail.gmail.com> <52060.78.105.201.225.1255548153.squirrel@webmail.ebi.ac.uk> <97174eb20910141228m5b158b4cn7615ba670bd9f4bf@mail.gmail.com> <42610.78.105.201.225.1255549094.squirrel@webmail.ebi.ac.uk> <97174eb20910141250pc0ac7f7u6fdcc078d9ae1e40@mail.gmail.com> Message-ID: <35977.78.105.201.225.1255550727.squirrel@webmail.ebi.ac.uk> > That would explain it! I initially thought it would be a MAC issue. Glad that problem has been solved. vectorstrip has been implemented some years ago, if you think any new feature that would make it a more useful tool please let us know. Regards, Mahmut From uludag at ebi.ac.uk Wed Oct 14 16:25:07 2009 From: uludag at ebi.ac.uk (uludag at ebi.ac.uk) Date: Wed, 14 Oct 2009 21:25:07 +0100 (BST) Subject: [EMBOSS] fuzznuc In-Reply-To: <21e884180910141244m5976f7e5ke9543eb02cfe01ed@mail.gmail.com> References: <21e884180910141244m5976f7e5ke9543eb02cfe01ed@mail.gmail.com> Message-ID: <38921.78.105.201.225.1255551907.squirrel@webmail.ebi.ac.uk> > I am using EMBOSS 6.1.0 and I wonder why the '-mismatch' qualifier of > fuzznuc is missing in the new EMBOSS version. In latest EMBOSS releases the '-mismatch' option seems to be renamed as '-pmismatch' as it became one of the associated qualifiers of '-pattern' option. http://emboss.open-bio.org/wiki/Appdoc:Fuzznuc#Command_line_arguments > Is there an alternative for fuzznuc for searching short DNA motifs? Do you search your DNA motifs in one/few long sequence(s) or in several short sequences? Regards, Mahmut From uludag at ebi.ac.uk Wed Oct 14 16:38:36 2009 From: uludag at ebi.ac.uk (uludag at ebi.ac.uk) Date: Wed, 14 Oct 2009 21:38:36 +0100 (BST) Subject: [EMBOSS] Seqret slowness..... In-Reply-To: <6061958B16EE43509AEF205B25657630@Nordegg> References: <6061958B16EE43509AEF205B25657630@Nordegg> Message-ID: <49519.78.105.201.225.1255552716.squirrel@webmail.ebi.ac.uk> > file of format "unpirot:accession" . Step 3 is using the command "seqret > @filename.txt". This is extraordinarily slow. It takes >12 hours to download > a fasta file containing 3K sequences. Is there a way of speeding this up? It looks possible to get Uniprot entries from different servers, such as from uniprot.org or from the EBI either using dbfetch or SRS. You may try updating your EMBOSS uniprot db definition to point to alternative servers that may return uniprot entries faster than the current server you are using. Regards, Mahmut From pmr at ebi.ac.uk Thu Oct 15 06:47:55 2009 From: pmr at ebi.ac.uk (Peter Rice) Date: Thu, 15 Oct 2009 11:47:55 +0100 Subject: [EMBOSS] Seqret slowness..... In-Reply-To: <6061958B16EE43509AEF205B25657630@Nordegg> References: <6061958B16EE43509AEF205B25657630@Nordegg> Message-ID: <4AD6FDDB.10808@ebi.ac.uk> Richard Rothery wrote: > Hi, > > > > I have been trying to update my sequence datasets using the seqret program. > Step 1 is that I blast my sequence against uniprot using the EXPASY server. > Unfortunately, because the recent explosion of duplicate data > ("environmental samples"), it is now necessary to download 1-2K sequences > and then filter out the random "environmental" sample derived fragments etc. > Step 2 is assembling a list in gnumeric, exporting it as a multiline text > file of format "unpirot:accession" . Step 3 is using the command "seqret > @filename.txt". This is extraordinarily slow. It takes >12 hours to download > a fasta file containing 3K sequences. Is there a way of speeding this up? I > used to be able to download directly from EXPASY, but the site now only > allows about 200-odd sequences to be selected and downloaded at a time. Perhaps we can download in batches ... what is your EMBOSS database definition for uniprot? Also, how do you select the 1-2K sequences? > Note that filtering sequence sets is very fast with the program cd-hit. This > takes about 10 seconds on an old P4 machine to remove sequences from the set > with >90% identity to any other, for example. Would this be a useful addition to EMBOSS? For example an application that reads selected entries from a database (uniprot) and filters them. The output would be a sequence file containing the uniprot entries you need (so no need for the final seqret step retrieving sequences again). > I do not have the resources to install and index local databases. No problem - we try to support users in exactly your situation. regards, Peter Rice From belegdol at gmail.com Sat Oct 17 07:49:22 2009 From: belegdol at gmail.com (Julian Sikorski) Date: Sat, 17 Oct 2009 13:49:22 +0200 Subject: [EMBOSS] Fedora package review is complete Message-ID: Hi, after quite some time, the fedora package review for emboss is complete. Several minor issues have been pointed out: 1. Several files lack a license header. The list of these files is attached. 2. The destdir is missing in runJemboss.sh installation command. Patch fixing the problem is attached. 3. The reviewer has provided a patch which enables using the system-wide pcre. Patch attached. I would be very grateful if you could look into these issues, as well the exit call I mentioned earlier [1]. Best regards, Julian [1] http://article.gmane.org/gmane.science.biology.emboss/1412 -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: emboss-license-headers.txt URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: EMBOSS-6.1.0-destdir.patch Type: text/x-patch Size: 2135 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: EMBOSS-system-pcre.patch Type: text/x-patch Size: 7093 bytes Desc: not available URL: From maoj at helix.nih.gov Wed Oct 28 14:39:40 2009 From: maoj at helix.nih.gov (Jean Mao) Date: Wed, 28 Oct 2009 14:39:40 -0400 Subject: [EMBOSS] Question about showalign program Message-ID: <4AE88FEC.5010701@helix.nih.gov> Hi, A user of ours have a question regarding showaling. When running showalign with the input file (attached), the consensus (and parental) residue is Lysine (K) and one of her mutants residue is Glutamic acid (E). Lysine is basic and Glutamic acid is basic, which are opposites and shouldn't be similar. She was using all default setting which supposed to show (E) in the alignment output. But instead, it shows (e) which indicate similarity between Lysine and Glutamic acid. Can someone help? Thank you Jean Mao -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: test URL: From yanlinlin82 at gmail.com Thu Oct 29 03:55:27 2009 From: yanlinlin82 at gmail.com (Linlin Yan) Date: Thu, 29 Oct 2009 15:55:27 +0800 Subject: [EMBOSS] Question about showalign program In-Reply-To: <4AE88FEC.5010701@helix.nih.gov> References: <4AE88FEC.5010701@helix.nih.gov> Message-ID: <8d4c23b10910290055k7430470ege714e5cb32959cb3@mail.gmail.com> K and E are treated similar because they are both charged, according to the default matrix (EBLOSUM62), in which the score between K and E is positive 1. Maybe you could use parameter -matrix to set your specified score matrix. On Thu, Oct 29, 2009 at 2:39 AM, Jean Mao wrote: > Hi, > > A user of ours have a question regarding showaling. When running showalign > with the input file (attached), the consensus (and parental) residue is > Lysine (K) and one of her mutants residue is Glutamic acid (E). Lysine is > basic and Glutamic acid is basic, which are opposites and shouldn't be > similar. She was using all default setting which supposed to show (E) in the > alignment output. But instead, it shows (e) which indicate similarity > between Lysine and Glutamic acid. Can someone help? > > Thank you > > Jean Mao > > >>A1 > ASQMTQSPSSLSASVGDRVTITCRASQGIRNDLGWYQQKPGKAPKLLIYAASSLQSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCLQDYTYPWTFGQGTKLEIKRTGGGGSGGGGSGGGGSVQLLEQSGAEVKKPGESLKISCKGSGYSFTNYWIGWVRQMPGKGLEWMGIIYPDDSDTRYSPSSQGQVTISFDKSTNTAYLQWSSLKASDTAIYYCARALWFRDWGKVDVWGKGTTVTVSVD >>A2 > ASQMTQSPSSLSASVGDRVTITCRASQGIRNDLGWYQQKPGKAPKLLIYAASSLQSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCLQDYTYPWTFGQGTKLEIKRTGGGGSGGGGSGGGGSVQLLEQSGAEVKKPGESLKISCKGSGYSFTNYWIGWVRQMPGKGLEWMGIIYPDDSDTRYSPSFQGQVTISFDKSINTAYLQWSSLKASDTAIYYCARALRFRDWGKMDVWGKGTTVTVSVD >>A3 > ASQMTQSPSSLSASVGDRVTITCRASQGIRSDLGWYQQKPGKAPKLLIYAASSLQSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCLQDYTYPWTFGQGTKLEIKRTGGGGSGGGGSGGGGSVQLLEQSGAEVKKPGESLRISCKGSGYSFTNYWIGWVRQMPGKGLEWMGIIYPDDSDTRYSPSFQGQVTISFDKSINTAYLQWSSLKASDTAIYYCARALWFRDWGKMDVWGKGTAVTVSVD >>A4 > ASQMTQSPSSLSASVGDRVTITCRASQGIGNDLGWYQQKPGKAPKLLIYAASSLQSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCLQDYTYPWTFGQGTKLEIKRTGGGGSGGGGSGGGGSVQLLEQSGAEVKKPGESLKISCEGSGYSFTNYWIGWVRQMPGKGLEWMGIIYPDDSDTRYSPSFQGQVTISFDKSINTAYLQWSSLKASDTAIYYCARALRFRDWGKMDVWGKGTTVTVSVD >>A6 > ASQMTQSPSSLSASVGDRVTITCRASQGIRNDLGWYQQKPGKAPKLLIYAASSLQSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCLQDYTYPWTFGQGTKLEIKRTGGGGSGGGGSGGGGSVQLLEQSGAEVKKPGESLKISCKGSGYSFTNYWIGWVRQMPGKGLEWMGIIYPDDSDTRYSPSFQGQVTISFDKSINTAYLQWSSLRASDTAIYYCARALRFRDWGKMDVWGKGTTVTVSVD >>A7 > ASQMTQSPSSLSASVGDRVTITCRASQGIRNDLGWYQQKPGKAPKLLIYAASSLQSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCLQDYTYPWTFGQGTKLEIKRTGGGGSGGGGSGGGGSVQLLEQSGAEVKKPGESLKISCKGSGYSFTNYWIGWVRQMPGKGLEWMGIIYPDDSDTRYSPSFQGQVTISFDKSINTAYLQWSSLKASDTAIYYCARALRFRDWGKMDVWGKGTTVTVSVD >>A8 > ASQMTQSPSSLSASVGDRVTITCRASQGIRNDLGWYQQKPGKAPKLLIYAASSLQSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCLQDYTYPWTFGQGTKLEIKRTGGGGSGGGGSGGGGSVQLLEQSGAEVKKPGESLKISCKGSGHSFTNYWIGWVRQMPGKGLEWMGIIYPDDSDTRYSPSFQGQVTISFDKSINTAYLQWSSLKASDTAIYYCARVLWFRDWGKMDVWGKGTTVTVSVD >>A9 > ASQMTQSPSSLSASVGDRVTITCRASQGIRNGLGWYQQKPGKAPKLLIYAASSLQSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCLQDYTYPWTFGQGTKLEIKRTGGGGSGGGGSGGGGSVQLLEQSGAEVKKPGESLKISCKGSGYSFTNYWIGWVRQTPGKGLEWMGIIYPDGSDTRYGPSFQGQVTISFDKSIDTAYLQWSSLKASDTAIYYCARALWFRDWGKMDVWGKGTTVTVSVD >>B1 > ASQMAQSPSSLSASVGDRVTITCRASQGIRNDLGWYQQKPGKAPKLLIYAASSLQSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCLQDYTYPWTFGQGTKLEIKRTGGGGSGGGGSGGGGSVQLLEQSGAEVKKPGESLKISCKGSGYSFTNYWIGWVRQMPGKGLEWMGIIYPDDSDTRYSPSFQGQVTISFDKSINTAYLQWSSLKASDTAIYYCARALRFRDWGKMDVWGKGTTVTVS >>B2 > ASQMTQSPSSLSASVGDRVTITCRASQGIRNGLGWYQQKPGKAPKLLIYAASSLQSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCLQDYTYPWTFGQGTKLEIKRTGGGGSGGGGSGGGGSVQLLEQSGAEVKKPGESLKISCKGSGYSFTNYWIGWVRQMPGKGLEWMGIIYPDDSDTRYSPSFQGQVTISFDKSINTAYLQWSSLKASDTAIYYCARALRFRDWGKMDVWGKGTTVTVSVD >>B4 > ASQMTQSPSSLSASVGDRVAITCRVSQGIRNDLGWYQQKPGKAPKLLIYAASSLQSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCLQDYTYPWTFGQGTKLEIKRTGGGGSGGGGSGGGGSVQLLEQSGAEVKKPGESLKISCKGSGYNFTNYWIGWVRQMPGKGLEWMGIIYPDDSDTRYSPSFQGQVTISFDKSINTAYLQWSSLKASDTAIYYCARALWFRDWGKMDVWGKGTTVTVSVD >>B5 > ASQMTQSPSSLSASVGDRVTITCRASQGIGNDLGWYQQKPGKAPKLLIYAASSLQSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCLQGYTYPWTFGQGTKLEIKRTGGGGSGGGGSGGGGSVQLLEQSGAEVKKPGESLKISCKGSGHSFTNYWIGWVRQMPGKGLEWMGIIYPDDSDTRYSPSFQGQVTISFDKSINTAYLQWSSLKASDTAIYYCARALRFRDWGKMDVWGKGTTVTVSVD >>B6 > ASQMTQSPSSLSASVGDRVTITCRASQGIRNDLGWYQQKPGKAPKLLIYAASSLQSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCLQDYTYPWTFGQGTKLEIKRTGGGGSGGGGSGGGGSVQLLEQSGAEVKKPGESLKISCKGSGYSFTNYWIGWVRQMPGKGLEWMGAIYPDDSDTRYSPSFQGQVTISFDKSTNTAYLQWSSLKASDTAIYYCARALWFRDWGKMDVWGKGTTVTVSVD >>C1 > ASQMTQSPSSLSASVGDRVTITCRASQGIRNGLGWYQQKPGKAPKLLIYAASSLQSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCLQDYTYPWTFGQGTKLEIKRTGGGGSGGGGSGGGGSVQLLEQSGAEVKKPGESLKISCKGSGYSFTNYWIGWVRQMPGKGLEWMGIIYPDDSDTRYSPSFQGQVTISFDKSISTAYLQWSSLKASDTAIYYCARALWFRDWGKMDVWGKGTTVTVA >>C3 > ASQMTQSPSSLSASVGDRVTITCRASQGIRNNLGWYQQKPGEAPKLLIYAASSLQSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCLQDYTYPWTFGQGTKLEIKRTGGGGSGGGGSGGGGSVQLLEQSGAEVKKPGEPLKISCKGSGYSFTNYWIGWVRQMPGKGLEWMGIIYPDDSDTRYSPSFQGQVTISFDKSINTAYLQWSSLKASDTAIYYCARALWFRDWGKMDVWGKGTTVTVSA >>C4 > ASQMTQSPSSLPASVGDRVTITRRASQGIRNDLGWYQQKPGKAPKLLIYAASSLQSGVPSRFSGSGSGTDSTLTISSLQPEDFATYYCLQDYTYPRTFGQGTKLEIKRTGGGGSGGGGSGGGGSVQLLEQSGAEVKKPGESLKISCKGSGYSFTNYWIGWVRQMPGKGLEWMGIIYPDDSDTRYSPSFQGQVTISFDKSINTAYLQWSSLKASDTAIYYCARALWFRDWGKVDVWGKGTTVTVSVD >>C6 > ASQMTQSPSSLSASVGDRVTITCRASQGIRNGLGWYQQKPGEAPKLLIYAASSLQSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCLQDYTYPWTFGQGTKLEIKRTGGGGSGGGGSGGGGSAQLLEQSGAEVKKPGESLKISCKGSGYSFTNYWIGWVRQMPGKGLEWMGIIYPDDSDTRYSPSFQGQVTISFDKSINTAYLQWSSLKASDTAIYYCARALWFRDWGKMDVWGKGTTVTVSVD >>C8 > ASQMTQSPSSLSASVGDRVTITCRASQGIRNDLGWYQQKPGKAPKLLIYAASSLQSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCLQDYTYPWTFGQGTKLEIKRTGGGGSGGGGSGGGGSVQLLEQSGAEVKKPGESLKISCKGSGYSFTNYWIGWVRQMPGKGLEWMGIIYPDDSDTRYSPSFQGQVTISFDKSINTAYLQWSSLKASDTAIYYCARALRFRDWGKMDVWGKGTTVTVSVD >>D1 > ASQMTQSPSSLSASVGDRVTITCRASQGIRNDLGWYQQKPGKAPKLLIYAASSLQSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCLQDYTYPWTFGQGTKLEIKRTGGGGSGGGGSGGGGSVQLLEQSGAEVKKPGESLKISCKGSGYSFTNYWIGWVRQMPGKGLEWMGIIYPDDSDTRYSPSFQGQVTISFDKSINTAYLQWSSLKASDTATYYCARALRFRDWGKMDVWGRGTTVTVSVD >>D2 > ASQMTQSPSSLSASVGDRVTITCRASQGIRNDLGWYQQKPGKAPKLLIYAASSLQSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCLQGYTYPWTFGQGTKLEIKRTGGGGSGGGGSGGGGSVQLLEQSGAEVKKPGESLKISCKGSGYSFTNYWIGWVRQMPGKGLEWMGIIYPDDSDTRYSPSFQGQVTISFDKSINTAYLQWSSLKASDTAIYYCARALWFRDWGKMDVWGKGTTVTVSVD >>D3 > ASQMTQSPSSLSASVGDRVTITCRASQGIRNGLGWYQQKPGKAPKLLIYAASSLQSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCLQDHTYPWTFGQGTKLEIKRTGGGGSGGGGSGGGGSVQLLEQSGAEVKKPGESLKISCKGSGYSFANYWIGWVRQMPGKGLEWMGIIYPDDSDTRYSPSFQGQVTISFDKSINTAYLQWSSLEASDTAIYYCARALWFRDWGKMDVWGKGTTVTVSVD >>D7 > ASQMTQSPSSLSASVGDRVTITCRASQGIRNDLGWYQQKPGEAPKLLIYAASSLQSGVPSRFSGSGSGTDFTLTISSLQPEDSATYYCLQDYTYPWTFGQGTKLEIKRTGGGGSGGGGSGGGGSVQLLEQSGAEVKKPGESLKISCKGSGYSFTNYWIGWVRQMPGKGLEWMGIIYPDDSDTRYSPSFQGQVTISFDKSINTAYLQWSSLKASDTAIYYCARALWFRDWGKMDVWGKGTTVTVSVD >>D8 > ASQMTQSPSSLSASVGDRVTITCRASQGIRNDLGWYQQKPGKAPKLLIYAASSLQSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCLQDHTYPWTFGQGTKLEIKRTGGGGSGGGGSGGGGSVQLLEQSGAEVKKPGESLKISCKGSGYSFTNYWIGWVRQMPGKGLEWMGIIYPDDSDTRYSPSFQGQVTISFDKSINTAYLQWSSLKASDTAIYYCARALRFRDWGKMDVWGKGTTVTVSVD >>D9 > ASQMTQSPSSLSASVGDRVTITCRASQGIRNDLGWYQQKPGKAPKLLIYAASSLQSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCLQDYTYPWTFGQGTKLEIKRTGGGGSGGGGSGGGGSVQLLEQSGAEVKGPGESLKISCRGSGYSFTNYWIGWVRQMPGKGLEWMGIIYPDDSDTRYSPSFQGQVTISFDKSINTAYLQWSSLKASDTAIYYCARALWFRDWGKVDVWGKGTTVTVSVD >>E4 > ASQMTQSPSSLSASVGDRVTITCRASQGIRNGLGWYQQKPGKAPKLLIYAASSLQSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCLQDYTYPWTFGQGTKLEIKRTGGGGSGGGGSGGGGSVQLLEQSGAEVKKPGESLKISCKGSGYSFTNYWIGWVRQMPGKGLEWMGIIYPDDSDTRYSPSFQGQVTISFDKSINTAYLQWSSLKASDTAIYYCARALRFRDWGKMDVWGKGTTVTVSVD >>E9 > ASQMTQSPSSLSASVGDRVTITCRASQGIRNDLGWYQQKPGEAPKLLIYAASSLQSGVPSRFSGSGSGTDFTLTISSLQPEDSATYYCLQDYTYPWTFGQGTKLEIKRTGGGGSGGGGSGGGGSVQLLEQSGAEVKKPGESLKISCKGSGYSFTNYWIGWVRQMPGKGLEWMGIIYPDDSDTRYSPSFQGQVTISFDKSINTAYLQWSSLKASDTAIYYCARALWFRDWGKMDVWGKGTTVTVSVD >>E11 > ASQMTQSPSSLSASVGDRVTITCRASQGIRNGLGWYQQKPGKAPKLLIYAASSLQSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCLQDYAYPWTFGQGTKLEIKRTGGGGSGGGGSGGGGSVQLLEQSGAEVKKPGESLKISCKGSGYSFTNYWIGWVRQMPGKGLEWMGIIYPDDSDTRYSPSFQGQVTISFDKSINTAYLQWSSLKASDTAIYYCARALWLRDWGKMDVWGKGTTVTVSVD >>F1 > ASQMTQSPSSLSASVGDRVTITCRASQGIRSDLGWYQQKPGKAPKLLIYAASSLQSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCLQDYTYPWTFGQGTKLEIKRTGGGGSGGGGSGGGGSVQLLEQSGAEVKKPGESLRISCKGSGYSFTNYWIGWVRQMPGKGLEWMGIIYPDDSDTRYSPSFQGQVTISFDKSINTAYLQWSSLKASDTAIYYCARALWFRDWGKMDVWGKGTAVTVSVD >>F2 > ASQMTQSPSSLSASVGDRVTITCRASQGIRNGLGWYQQKPGEAPKLLIYAASSLQSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCLQDYTYPWTFGQGTKLEIKRTGGGGSGGGGSGGGGSAQLLEQSGAEVKKPGESLKISCKGSGYSFTNYWIGWVRQMPGKGLEWMGIIYPDDSDTRYSPSFQGQVTISFDKSINTAYLQWSSLKASDTAIYYCARALWFRDWGKMDVWGKGTTVTVSVD >>F3 > ASQMTQSPSSLSASVGDRVTITCRASQGIRNDLGWYQQKPGKAPKLLIYAASSLQSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCLQDYTYPWTFGQGTKLEIKRTGGGGSGGGGSGGGGSVQLLEQSGAEVKKPGESLKISCKGSGYSFTNYWIGWVRQMPGKGLEWMGIIYPDDSDTRYSPSFQGQVTISFDKSINTAYLQWSSLKASDTAIYYCARALRFRTGARWTSGAKGPRSPSPS >>F4 > ASQMTQSPSSLSASVGDRVTITCRASQGIRNGLGWYQQKPGKAPKLLIYAASSLQSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCLQDYTYPWTFGQGTKLEIKRTGGGGSGGGGSGGGGSVQLLEQSGAEVKKPGESLKISCKGSGYSSTNYWIGWVRQMPGKGLEWMGTIYPDDSDTRYSPSFQGQVTISFDKSINTAYLQWSSLKASDTAIYYCARALWFRDWGKMDVWGKGTTVTVSVD >>G1 > ASQMAQSPSSLSASVGDRVTITCRASQGIRNDLGWYQQKPGKAPKLLIYAASSLQSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCLQDYTYPWTFGQGTKLEIKRTGGGGSGGGGSGGGGSVQLLEQSGAEVKKPGESLKISCKGSGYSFTNYWIGWVRQMPGKGLEWMGIIYPDDSDTRYSPSFQGQVTISFDKSINTAYLQWSSLKASDTAIYYCARALRFRDWGKMDVWGKGTRSPSP >>G2 > QMTQSPSSLSASVGDRVTITCRASQGIRNNLGWYQQKPGEAPKLLIYAASSLQSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCLQDYTYPWTFGQGTKLEIKRTGGGGSGGGGSGGGGSVQLLEQSGAEVKKPGEPLKISCKGSGYSFTNYWIGWVRQMPGKGLEWMGIIYPDDSDTRYSPSFQGQVTISFDKSINTAYLQWSSLKASDTAIYYCARALWFRDWGKMDVWGKGTTVTVS >>G3 > ASQMTQSPSSLSASVGDRVTITCRASQGIRNGLGWYQQKPGKAPKLLIYAASSLQSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCLQDHTYPWTFGQGTKLEIKRTGGGGSGGGGSGGGGSVQLLEQSGAEVKKPGESLKISCKGSGYSFANYWIGWVRQMPGKGLEWMGIIYPDDSDTRYSPSFQGQVTISFDKSINTAYLQWSSLEASDTAIYYCARALWFRDWGKMDVWGKGTTVTVSVD >>G4 > ASQMTQSPSSLSASVGDRVTITCRASQGIRSDLGWYQQKPGKAPKLLIYAASSLQSGVPSRFSGSGSGTDFTLTISSLQPEDSATYYCLQGYTYPWTFGQGTKLEIKRTGGGGSGGGGSGGGGSVQLLEQSGAEVKKPGESLKISCKGSGYSFTNYWIGWVRQMPGKGLEWMGTIYPDDSDTRYGPSFRGQVTISFDKSINTAYLQWSSLKASDTAIYYCARALWFRDWGKMDVWGKGTTVTVPVD >>G5 > ASQMTQSPSSLSASVGDRVTITCRASQGIRNGLGWYQQKPGKAPKLLIYAASSLQSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCLQDYTYPWTFGQGTKLEIKRTGGGGSGGGGSGGGGSVQLLEQSGAGVKKPGESLKISCKGSGYSFTDYWIGWVRQMPGKGLEWMGIIYPDDSDTRYSPSFQGQVTISFDKSINTAYLQWSSLKASDTAIYYCARALWFRDWGKMDVWGKGTTVTVSVD >>G6 > ASQMTQSPSSLSASVGGRVTITCRASQGIRNDLGWYQQKPGKAPKLLIYAASSLQSGVPSRFSGSGSGTDFTLTISSLQPEDSATYYCLQDYTYPWTFGQGTKLEIKRTGGGGSGGGGSGGGGSVQLLEQSGAEVKKPGESLKISCKGSGYSFTNYWIGWVRQMPGKGLEWMGIIYPDDSDTRYSPSFQGQVTISFDKSINTAYLQWSSLKASDTAIYYCARASWFRDWGKMDVWGKGTTVTVSVD > > _______________________________________________ > EMBOSS mailing list > EMBOSS at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/emboss > > From mathog at caltech.edu Thu Oct 29 14:55:12 2009 From: mathog at caltech.edu (David Mathog) Date: Thu, 29 Oct 2009 11:55:12 -0700 Subject: [EMBOSS] 6.1.0 build warnings in PHYLIPNEW-3.68 Message-ID: In consense.c extern Char intreename[FNMLNGTH], intree2name[FNMLNGTH]; const char* outfilename; const char* outtreename; In cons.c Char outfilename[FNMLNGTH], intreename[FNMLNGTH], intree2name[FNMLNGTH], outtreename[FNMLNGTH]; which explains this: > ld: warning: symbol `outfilename' has differing sizes: > (file consense.o value=0x4; file cons.o value=0xc8); > cons.o definition taken > ld: warning: symbol `outtreename' has differing sizes: > (file consense.o value=0x4; file cons.o value=0xc8); > cons.o definition taken Which one needs to be change? Thanks, David Mathog mathog at caltech.edu Manager, Sequence Analysis Facility, Biology Division, Caltech From mathog at caltech.edu Thu Oct 29 14:46:53 2009 From: mathog at caltech.edu (David Mathog) Date: Thu, 29 Oct 2009 11:46:53 -0700 Subject: [EMBOSS] 6.1.0 build warnings in PHYLIPNEW-3.68 Message-ID: Downloaded 6.1.0, patched, built, but found four warnings as shown below in the logs for PHYLIPNEW-3.68. This was on Solaris 8 with gcc 3.4.6. Is this a known issue? libtool: link: gcc -O2 -o .libs/fconsense consense.o cons.o phylip.o ../../../nucleus/.libs/libnucleus.so ../../../ajax/.libs/libajax.so ../../../plplot/.libs/libeplplot.so -lXaw -lXt -lnsl -lsocket /usr/local/lib/libgd.so -L/usr/local/lib -L/usr/local/BerkeleyDB.4.2/lib -L/usr/local/ssl/lib -L/usr/openwin/lib -L/usr/lib -L/usr/openwin/llib -lXpm -lX11 /usr/local/lib/libjpeg.so /usr/local/lib/libfontconfig.so -L/usr/local/mysql/lib/mysql /usr/local/lib/libexpat.so /usr/local/lib/libfreetype.so -lpng12 -lpng -lz -lm /usr/local/lib/libiconv.so -R/usr/local/lib ld: warning: symbol `outfilename' has differing sizes: (file consense.o value=0x4; file cons.o value=0xc8); cons.o definition taken ld: warning: symbol `outtreename' has differing sizes: (file consense.o value=0x4; file cons.o value=0xc8); cons.o definition taken libtool: link: gcc -O2 -o .libs/ftreedist treedist.o cons.o phylip.o ../../../nucleus/.libs/libnucleus.so ../../../ajax/.libs/libajax.so ../../../plplot/.libs/libeplplot.so -lXaw -lXt -lnsl -lsocket /usr/local/lib/libgd.so -L/usr/local/lib -L/usr/local/BerkeleyDB.4.2/lib -L/usr/local/ssl/lib -L/usr/openwin/lib -L/usr/lib -L/usr/openwin/llib -lXpm -lX11 /usr/local/lib/libjpeg.so /usr/local/lib/libfontconfig.so -L/usr/local/mysql/lib/mysql /usr/local/lib/libexpat.so /usr/local/lib/libfreetype.so -lpng12 -lpng -lz -lm /usr/local/lib/libiconv.so -R/usr/local/lib ld: warning: symbol `outfilename' has differing sizes: (file treedist.o value=0x4; file cons.o value=0xc8); cons.o definition taken libtool: link: gcc -O2 -o .libs/ftreedistpair treedistpair.o cons.o phylip.o ../../../nucleus/.libs/libnucleus.so ../../../ajax/.libs/libajax.so ../../../plplot/.libs/libeplplot.so -lXaw -lXt -lnsl -lsocket /usr/local/lib/libgd.so -L/usr/local/lib -L/usr/local/BerkeleyDB.4.2/lib -L/usr/local/ssl/lib -L/usr/openwin/lib -L/usr/lib -L/usr/openwin/llib -lXpm -lX11 /usr/local/lib/libjpeg.so /usr/local/lib/libfontconfig.so -L/usr/local/mysql/lib/mysql /usr/local/lib/libexpat.so /usr/local/lib/libfreetype.so -lpng12 -lpng -lz -lm /usr/local/lib/libiconv.so -R/usr/local/lib ld: warning: symbol `outfilename' has differing sizes: (file treedistpair.o value=0x4; file cons.o value=0xc8); cons.o definition taken There were no other fail, error, or warn strings anywhere in the build. Thanks, David Mathog mathog at caltech.edu Manager, Sequence Analysis Facility, Biology Division, Caltech From mathog at caltech.edu Thu Oct 29 16:54:38 2009 From: mathog at caltech.edu (David Mathog) Date: Thu, 29 Oct 2009 13:54:38 -0700 Subject: [EMBOSS] 6.1.0 build warnings in PHYLIPNEW-3.68 Message-ID: Changing one line as shown below seems to have fixed it, at least it eliminate the warning. Don't know yet if it causes any problems when the program runs. This change is in line with the way the other programs in this directory are constructed. % diff cons.c cons.c.dist 6c6 < Char intreename[FNMLNGTH], intree2name[FNMLNGTH]; --- > Char outfilename[FNMLNGTH], intreename[FNMLNGTH], intree2name[FNMLNGTH], outtreename[FNMLNGTH]; Regards, David Mathog mathog at caltech.edu Manager, Sequence Analysis Facility, Biology Division, Caltech From pmr at ebi.ac.uk Fri Oct 30 06:12:24 2009 From: pmr at ebi.ac.uk (Peter Rice) Date: Fri, 30 Oct 2009 10:12:24 +0000 Subject: [EMBOSS] 6.1.0 build warnings in PHYLIPNEW-3.68 In-Reply-To: References: Message-ID: <4AEABC08.70607@ebi.ac.uk> On 29/10/09 20:54, David Mathog wrote: > Changing one line as shown below seems to have fixed it, at least it > eliminate the warning. Don't know yet if it causes any problems when > the program runs. This change is in line with the way the other > programs in this directory are constructed. > > % diff cons.c cons.c.dist > 6c6 > < Char intreename[FNMLNGTH], intree2name[FNMLNGTH]; > --- >> Char outfilename[FNMLNGTH], intreename[FNMLNGTH], > intree2name[FNMLNGTH], outtreename[FNMLNGTH]; Yes, that is the correct fix for the compiler warning. We do not use the original phylip 3.6 outfile name buffers. Thanks Peter From mathog at caltech.edu Fri Oct 30 17:43:53 2009 From: mathog at caltech.edu (David Mathog) Date: Fri, 30 Oct 2009 14:43:53 -0700 Subject: [EMBOSS] CBSTOOLS not installing help files, don't work with emboss explorer Message-ID: For some reason or other the CBSTOOLS package built its html and txt help files, but didn't install them on "make install". To work around this, they were copied manually to the proper directories, then tfm eyinoyang worked, but the help links in emboss explorer still didn't pick them up. Found where those were supposed to go eventually by poking around in /usr/local/share/EMBOSS/doc/html/embassy. Seems like a glitch in the CBSTOOLS install, but no errors or warnings were emitted. Is something supposed to generate /usr/local/share/EMBOSS/doc/html/embassy/index.html automatically, or must that be hand edited when the embassy packages change? There are no directions inside the embassy/CBSTOOLS directory for installing the actual programs that these are wrappers for. They can be downloaded one at a time from here: http://www.cbs.dtu.dk/services/ is there a way to get the lot of them all at once? Thanks, David Mathog mathog at caltech.edu Manager, Sequence Analysis Facility, Biology Division, Caltech From michael.watson at bbsrc.ac.uk Thu Oct 1 11:33:50 2009 From: michael.watson at bbsrc.ac.uk (michael watson (IAH-C)) Date: Thu, 1 Oct 2009 12:33:50 +0100 Subject: [EMBOSS] Trim polyA from fastq files Message-ID: <8D08960C647E64438CE5740657CBBDC5010D2AC6E2@iahcexch1.iah.bbsrc.ac.uk> Hello I have some Illumina reads which have varying lengths of polyAs at the ends. I want to trim these off. The data is in fastq format. Is this possible in EMBOSS? I have 6.0.1 and I tried trimest but it couldn't read my fastq file Thanks Mick Head of Bioinformatics Institute for Animal Health Compton Berks RG20 7NN 01635 578411 Please consider the environment and don't print this e-mail unless you really need to. The information contained in this message may be confidential or legally privileged and is intended solely for the addressee. 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The Institute is also a registered charity, Charity Commissioners Reference No. 228824 From pmr at ebi.ac.uk Thu Oct 1 12:09:48 2009 From: pmr at ebi.ac.uk (Peter Rice) Date: Thu, 01 Oct 2009 13:09:48 +0100 Subject: [EMBOSS] Trim polyA from fastq files In-Reply-To: <8D08960C647E64438CE5740657CBBDC5010D2AC6E2@iahcexch1.iah.bbsrc.ac.uk> References: <8D08960C647E64438CE5740657CBBDC5010D2AC6E2@iahcexch1.iah.bbsrc.ac.uk> Message-ID: <4AC49C0C.5010800@ebi.ac.uk> On 01/10/09 12:33, michael watson (IAH-C) wrote: > Hello > > I have some Illumina reads which have varying lengths of polyAs at the ends. I want to trim these off. The data is in fastq format. > > Is this possible in EMBOSS? I have 6.0.1 and I tried trimest but it couldn't read my fastq file Yes, but you need EMBOSS 6.1.0 to support FASTQ input. There are also a couple of patches that are needed for some FASTQ files. regards, Peter Rice From michael.watson at bbsrc.ac.uk Thu Oct 1 12:53:12 2009 From: michael.watson at bbsrc.ac.uk (michael watson (IAH-C)) Date: Thu, 1 Oct 2009 13:53:12 +0100 Subject: [EMBOSS] Trim polyA from fastq files In-Reply-To: <4AC49C0C.5010800@ebi.ac.uk> References: <8D08960C647E64438CE5740657CBBDC5010D2AC6E2@iahcexch1.iah.bbsrc.ac.uk> <4AC49C0C.5010800@ebi.ac.uk> Message-ID: <8D08960C647E64438CE5740657CBBDC5010D2AC6E9@iahcexch1.iah.bbsrc.ac.uk> Hi Peter Thanks for that. Is it possible to preserve the fastq format? My input was fastq, I also put .fastq as my output, but it only gave me straight fasta Thanks Mick -----Original Message----- From: Peter Rice [mailto:pmr at ebi.ac.uk] Sent: 01 October 2009 13:10 To: michael watson (IAH-C) Cc: 'emboss at emboss.open-bio.org' Subject: Re: [EMBOSS] Trim polyA from fastq files On 01/10/09 12:33, michael watson (IAH-C) wrote: > Hello > > I have some Illumina reads which have varying lengths of polyAs at the ends. I want to trim these off. The data is in fastq format. > > Is this possible in EMBOSS? I have 6.0.1 and I tried trimest but it couldn't read my fastq file Yes, but you need EMBOSS 6.1.0 to support FASTQ input. There are also a couple of patches that are needed for some FASTQ files. regards, Peter Rice From biopython at maubp.freeserve.co.uk Thu Oct 1 14:04:14 2009 From: biopython at maubp.freeserve.co.uk (Peter) Date: Thu, 1 Oct 2009 15:04:14 +0100 Subject: [EMBOSS] Trim polyA from fastq files In-Reply-To: <8D08960C647E64438CE5740657CBBDC5010D2AC6E9@iahcexch1.iah.bbsrc.ac.uk> References: <8D08960C647E64438CE5740657CBBDC5010D2AC6E2@iahcexch1.iah.bbsrc.ac.uk> <4AC49C0C.5010800@ebi.ac.uk> <8D08960C647E64438CE5740657CBBDC5010D2AC6E9@iahcexch1.iah.bbsrc.ac.uk> Message-ID: <320fb6e00910010704u648614d4wf48a6244a9c6aa6c@mail.gmail.com> On Thu, Oct 1, 2009 at 1:53 PM, michael watson (IAH-C) wrote: > > Hi Peter > > Thanks for that. > > Is it possible to preserve the fastq format? ?My input was fastq, I also put .fastq as my output, but it only gave me straight fasta > Use "fastq-sanger" (or a variant), not just "fastq" which means ignoring the qualities in EMBOSS. http://emboss.sourceforge.net/docs/themes/SequenceFormats.html#in Peter From pmr at ebi.ac.uk Thu Oct 1 14:31:15 2009 From: pmr at ebi.ac.uk (Peter Rice) Date: Thu, 01 Oct 2009 15:31:15 +0100 Subject: [EMBOSS] Trim polyA from fastq files In-Reply-To: <320fb6e00910010704u648614d4wf48a6244a9c6aa6c@mail.gmail.com> References: <8D08960C647E64438CE5740657CBBDC5010D2AC6E2@iahcexch1.iah.bbsrc.ac.uk> <4AC49C0C.5010800@ebi.ac.uk> <8D08960C647E64438CE5740657CBBDC5010D2AC6E9@iahcexch1.iah.bbsrc.ac.uk> <320fb6e00910010704u648614d4wf48a6244a9c6aa6c@mail.gmail.com> Message-ID: <4AC4BD33.7050201@ebi.ac.uk> On 01/10/09 15:04, Peter wrote: > On Thu, Oct 1, 2009 at 1:53 PM, michael watson (IAH-C) > wrote: >> Thanks for that. >> >> Is it possible to preserve the fastq format? My input was fastq, I also put .fastq as my output, but it only gave me straight fasta The filename can be anything. You need -osformat fastq-sanger on the command line to set the output format. regards, Peter Rice From jesse at libbench.com Wed Oct 14 17:22:37 2009 From: jesse at libbench.com (Jesse Erdmann) Date: Wed, 14 Oct 2009 12:22:37 -0500 Subject: [EMBOSS] vectorstrip: Died: Unknown qualifier --vectorfile Message-ID: <97174eb20910141022r14ccb771n94180883053c9b24@mail.gmail.com> I downloaded, compiled and installed EMBOSS' latest stable version this morning on my Mac OS X 10.5 so I could do some testing on my development machine. Currently, when I execute a command that works just fine on our production environment, I get "Died: Unknown qualifier -vectorfile". Removing -vectorfile works, but then I have to interactively respond to the prompt, whereas the Perl script would normally just run. To install, all I did was './configure; make; sudo make install'. Any suggestions as to what might be happening here? Thanks! -- Jesse Erdmann jesse at jesseerdmann.com Twitter: http://twitter.com/jesseerdmann Blog: http://blog.jesseerdmann.com/ From Richard.Rothery at ualberta.ca Wed Oct 14 17:46:21 2009 From: Richard.Rothery at ualberta.ca (Richard Rothery) Date: Wed, 14 Oct 2009 11:46:21 -0600 Subject: [EMBOSS] Seqret slowness..... Message-ID: <6061958B16EE43509AEF205B25657630@Nordegg> Hi, I have been trying to update my sequence datasets using the seqret program. Step 1 is that I blast my sequence against uniprot using the EXPASY server. Unfortunately, because the recent explosion of duplicate data ("environmental samples"), it is now necessary to download 1-2K sequences and then filter out the random "environmental" sample derived fragments etc. Step 2 is assembling a list in gnumeric, exporting it as a multiline text file of format "unpirot:accession" . Step 3 is using the command "seqret @filename.txt". This is extraordinarily slow. It takes >12 hours to download a fasta file containing 3K sequences. Is there a way of speeding this up? I used to be able to download directly from EXPASY, but the site now only allows about 200-odd sequences to be selected and downloaded at a time. Note that filtering sequence sets is very fast with the program cd-hit. This takes about 10 seconds on an old P4 machine to remove sequences from the set with >90% identity to any other, for example. I do not have the resources to install and index local databases. Thanks! Richard A. Rothery, Ph.D. Research Associate ______________________________________________ Membrane Protein Research Group, Department of Biochemistry, University of Alberta, Edmonton T6G 2H7 Ph. 780-492-2229 Fax. 780-492-0886 ______________________________________________ From uludag at ebi.ac.uk Wed Oct 14 19:22:33 2009 From: uludag at ebi.ac.uk (uludag at ebi.ac.uk) Date: Wed, 14 Oct 2009 20:22:33 +0100 (BST) Subject: [EMBOSS] vectorstrip: Died: Unknown qualifier --vectorfile In-Reply-To: <97174eb20910141022r14ccb771n94180883053c9b24@mail.gmail.com> References: <97174eb20910141022r14ccb771n94180883053c9b24@mail.gmail.com> Message-ID: <52060.78.105.201.225.1255548153.squirrel@webmail.ebi.ac.uk> > "Died: Unknown qualifier -vectorfile". Name of the qualifier looks like to be vectorsfile rather than vectorfile. Regards, Mahmut From jesse at libbench.com Wed Oct 14 19:28:18 2009 From: jesse at libbench.com (Jesse Erdmann) Date: Wed, 14 Oct 2009 14:28:18 -0500 Subject: [EMBOSS] vectorstrip: Died: Unknown qualifier --vectorfile In-Reply-To: <52060.78.105.201.225.1255548153.squirrel@webmail.ebi.ac.uk> References: <97174eb20910141022r14ccb771n94180883053c9b24@mail.gmail.com> <52060.78.105.201.225.1255548153.squirrel@webmail.ebi.ac.uk> Message-ID: <97174eb20910141228m5b158b4cn7615ba670bd9f4bf@mail.gmail.com> Actually there are both. According to http://emboss.bioinformatics.nl/cgi-bin/emboss/help/vectorstrip, the [-[no]vectorfile] option allows you to answer the question "Are your vector sequences in a file?" without having to interact with the program. This works as expected in a different environment, but it's not on my development environment, which means I have to manually intervene multiple times during our perl script that would otherwise run unattended. Thanks! Jesse On Wed, Oct 14, 2009 at 2:22 PM, wrote: > >> "Died: Unknown qualifier -vectorfile". > > Name of the qualifier looks like to be vectorsfile rather than vectorfile. > > Regards, > Mahmut > > > -- Jesse Erdmann jesse at jesseerdmann.com Twitter: http://twitter.com/jesseerdmann Blog: http://blog.jesseerdmann.com/ From uludag at ebi.ac.uk Wed Oct 14 19:38:14 2009 From: uludag at ebi.ac.uk (uludag at ebi.ac.uk) Date: Wed, 14 Oct 2009 20:38:14 +0100 (BST) Subject: [EMBOSS] vectorstrip: Died: Unknown qualifier --vectorfile In-Reply-To: <97174eb20910141228m5b158b4cn7615ba670bd9f4bf@mail.gmail.com> References: <97174eb20910141022r14ccb771n94180883053c9b24@mail.gmail.com> <52060.78.105.201.225.1255548153.squirrel@webmail.ebi.ac.uk> <97174eb20910141228m5b158b4cn7615ba670bd9f4bf@mail.gmail.com> Message-ID: <42610.78.105.201.225.1255549094.squirrel@webmail.ebi.ac.uk> > http://emboss.bioinformatics.nl/cgi-bin/emboss/help/vectorstrip, the > [-[no]vectorfile] option allows you to answer the question "Are your > vector sequences in a file?" Above site seems to be using EMBOSS-6.0.1. It looks like the 'vectorstrip' option has been renamed as 'readfile' in the latest release. http://emboss.open-bio.org/wiki/Appdoc:Vectorstrip#Command_line_arguments Mahmut From benys at usp.br Wed Oct 14 19:44:08 2009 From: benys at usp.br (Beny Spira) Date: Wed, 14 Oct 2009 16:44:08 -0300 Subject: [EMBOSS] fuzznuc Message-ID: <21e884180910141244m5976f7e5ke9543eb02cfe01ed@mail.gmail.com> Hi I am using EMBOSS 6.1.0 and I wonder why the '-mismatch' qualifier of fuzznuc is missing in the new EMBOSS version. Is there an alternative for fuzznuc for searching short DNA motifs? Cheers, 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 jesse at libbench.com Wed Oct 14 19:50:23 2009 From: jesse at libbench.com (Jesse Erdmann) Date: Wed, 14 Oct 2009 14:50:23 -0500 Subject: [EMBOSS] vectorstrip: Died: Unknown qualifier --vectorfile In-Reply-To: <42610.78.105.201.225.1255549094.squirrel@webmail.ebi.ac.uk> References: <97174eb20910141022r14ccb771n94180883053c9b24@mail.gmail.com> <52060.78.105.201.225.1255548153.squirrel@webmail.ebi.ac.uk> <97174eb20910141228m5b158b4cn7615ba670bd9f4bf@mail.gmail.com> <42610.78.105.201.225.1255549094.squirrel@webmail.ebi.ac.uk> Message-ID: <97174eb20910141250pc0ac7f7u6fdcc078d9ae1e40@mail.gmail.com> That would explain it! Thanks very much! Jesse On Wed, Oct 14, 2009 at 2:38 PM, wrote: > >> http://emboss.bioinformatics.nl/cgi-bin/emboss/help/vectorstrip, the >> [-[no]vectorfile] option allows you to answer the question "Are your >> vector sequences in a file?" > > Above site seems to be using EMBOSS-6.0.1. > > It looks like the 'vectorstrip' option has been renamed as 'readfile' in > the latest release. > > http://emboss.open-bio.org/wiki/Appdoc:Vectorstrip#Command_line_arguments > > Mahmut > > > > -- Jesse Erdmann jesse at jesseerdmann.com Twitter: http://twitter.com/jesseerdmann Blog: http://blog.jesseerdmann.com/ From uludag at ebi.ac.uk Wed Oct 14 20:05:27 2009 From: uludag at ebi.ac.uk (uludag at ebi.ac.uk) Date: Wed, 14 Oct 2009 21:05:27 +0100 (BST) Subject: [EMBOSS] vectorstrip: Died: Unknown qualifier --vectorfile In-Reply-To: <97174eb20910141250pc0ac7f7u6fdcc078d9ae1e40@mail.gmail.com> References: <97174eb20910141022r14ccb771n94180883053c9b24@mail.gmail.com> <52060.78.105.201.225.1255548153.squirrel@webmail.ebi.ac.uk> <97174eb20910141228m5b158b4cn7615ba670bd9f4bf@mail.gmail.com> <42610.78.105.201.225.1255549094.squirrel@webmail.ebi.ac.uk> <97174eb20910141250pc0ac7f7u6fdcc078d9ae1e40@mail.gmail.com> Message-ID: <35977.78.105.201.225.1255550727.squirrel@webmail.ebi.ac.uk> > That would explain it! I initially thought it would be a MAC issue. Glad that problem has been solved. vectorstrip has been implemented some years ago, if you think any new feature that would make it a more useful tool please let us know. Regards, Mahmut From uludag at ebi.ac.uk Wed Oct 14 20:25:07 2009 From: uludag at ebi.ac.uk (uludag at ebi.ac.uk) Date: Wed, 14 Oct 2009 21:25:07 +0100 (BST) Subject: [EMBOSS] fuzznuc In-Reply-To: <21e884180910141244m5976f7e5ke9543eb02cfe01ed@mail.gmail.com> References: <21e884180910141244m5976f7e5ke9543eb02cfe01ed@mail.gmail.com> Message-ID: <38921.78.105.201.225.1255551907.squirrel@webmail.ebi.ac.uk> > I am using EMBOSS 6.1.0 and I wonder why the '-mismatch' qualifier of > fuzznuc is missing in the new EMBOSS version. In latest EMBOSS releases the '-mismatch' option seems to be renamed as '-pmismatch' as it became one of the associated qualifiers of '-pattern' option. http://emboss.open-bio.org/wiki/Appdoc:Fuzznuc#Command_line_arguments > Is there an alternative for fuzznuc for searching short DNA motifs? Do you search your DNA motifs in one/few long sequence(s) or in several short sequences? Regards, Mahmut From uludag at ebi.ac.uk Wed Oct 14 20:38:36 2009 From: uludag at ebi.ac.uk (uludag at ebi.ac.uk) Date: Wed, 14 Oct 2009 21:38:36 +0100 (BST) Subject: [EMBOSS] Seqret slowness..... In-Reply-To: <6061958B16EE43509AEF205B25657630@Nordegg> References: <6061958B16EE43509AEF205B25657630@Nordegg> Message-ID: <49519.78.105.201.225.1255552716.squirrel@webmail.ebi.ac.uk> > file of format "unpirot:accession" . Step 3 is using the command "seqret > @filename.txt". This is extraordinarily slow. It takes >12 hours to download > a fasta file containing 3K sequences. Is there a way of speeding this up? It looks possible to get Uniprot entries from different servers, such as from uniprot.org or from the EBI either using dbfetch or SRS. You may try updating your EMBOSS uniprot db definition to point to alternative servers that may return uniprot entries faster than the current server you are using. Regards, Mahmut From pmr at ebi.ac.uk Thu Oct 15 10:47:55 2009 From: pmr at ebi.ac.uk (Peter Rice) Date: Thu, 15 Oct 2009 11:47:55 +0100 Subject: [EMBOSS] Seqret slowness..... In-Reply-To: <6061958B16EE43509AEF205B25657630@Nordegg> References: <6061958B16EE43509AEF205B25657630@Nordegg> Message-ID: <4AD6FDDB.10808@ebi.ac.uk> Richard Rothery wrote: > Hi, > > > > I have been trying to update my sequence datasets using the seqret program. > Step 1 is that I blast my sequence against uniprot using the EXPASY server. > Unfortunately, because the recent explosion of duplicate data > ("environmental samples"), it is now necessary to download 1-2K sequences > and then filter out the random "environmental" sample derived fragments etc. > Step 2 is assembling a list in gnumeric, exporting it as a multiline text > file of format "unpirot:accession" . Step 3 is using the command "seqret > @filename.txt". This is extraordinarily slow. It takes >12 hours to download > a fasta file containing 3K sequences. Is there a way of speeding this up? I > used to be able to download directly from EXPASY, but the site now only > allows about 200-odd sequences to be selected and downloaded at a time. Perhaps we can download in batches ... what is your EMBOSS database definition for uniprot? Also, how do you select the 1-2K sequences? > Note that filtering sequence sets is very fast with the program cd-hit. This > takes about 10 seconds on an old P4 machine to remove sequences from the set > with >90% identity to any other, for example. Would this be a useful addition to EMBOSS? For example an application that reads selected entries from a database (uniprot) and filters them. The output would be a sequence file containing the uniprot entries you need (so no need for the final seqret step retrieving sequences again). > I do not have the resources to install and index local databases. No problem - we try to support users in exactly your situation. regards, Peter Rice From belegdol at gmail.com Sat Oct 17 11:49:22 2009 From: belegdol at gmail.com (Julian Sikorski) Date: Sat, 17 Oct 2009 13:49:22 +0200 Subject: [EMBOSS] Fedora package review is complete Message-ID: Hi, after quite some time, the fedora package review for emboss is complete. Several minor issues have been pointed out: 1. Several files lack a license header. The list of these files is attached. 2. The destdir is missing in runJemboss.sh installation command. Patch fixing the problem is attached. 3. The reviewer has provided a patch which enables using the system-wide pcre. Patch attached. I would be very grateful if you could look into these issues, as well the exit call I mentioned earlier [1]. Best regards, Julian [1] http://article.gmane.org/gmane.science.biology.emboss/1412 -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: emboss-license-headers.txt URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: EMBOSS-6.1.0-destdir.patch Type: text/x-patch Size: 2135 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: EMBOSS-system-pcre.patch Type: text/x-patch Size: 7093 bytes Desc: not available URL: From maoj at helix.nih.gov Wed Oct 28 18:39:40 2009 From: maoj at helix.nih.gov (Jean Mao) Date: Wed, 28 Oct 2009 14:39:40 -0400 Subject: [EMBOSS] Question about showalign program Message-ID: <4AE88FEC.5010701@helix.nih.gov> Hi, A user of ours have a question regarding showaling. When running showalign with the input file (attached), the consensus (and parental) residue is Lysine (K) and one of her mutants residue is Glutamic acid (E). Lysine is basic and Glutamic acid is basic, which are opposites and shouldn't be similar. She was using all default setting which supposed to show (E) in the alignment output. But instead, it shows (e) which indicate similarity between Lysine and Glutamic acid. Can someone help? Thank you Jean Mao -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: test URL: From yanlinlin82 at gmail.com Thu Oct 29 07:55:27 2009 From: yanlinlin82 at gmail.com (Linlin Yan) Date: Thu, 29 Oct 2009 15:55:27 +0800 Subject: [EMBOSS] Question about showalign program In-Reply-To: <4AE88FEC.5010701@helix.nih.gov> References: <4AE88FEC.5010701@helix.nih.gov> Message-ID: <8d4c23b10910290055k7430470ege714e5cb32959cb3@mail.gmail.com> K and E are treated similar because they are both charged, according to the default matrix (EBLOSUM62), in which the score between K and E is positive 1. Maybe you could use parameter -matrix to set your specified score matrix. On Thu, Oct 29, 2009 at 2:39 AM, Jean Mao wrote: > Hi, > > A user of ours have a question regarding showaling. When running showalign > with the input file (attached), the consensus (and parental) residue is > Lysine (K) and one of her mutants residue is Glutamic acid (E). Lysine is > basic and Glutamic acid is basic, which are opposites and shouldn't be > similar. She was using all default setting which supposed to show (E) in the > alignment output. But instead, it shows (e) which indicate similarity > between Lysine and Glutamic acid. Can someone help? > > Thank you > > Jean Mao > > >>A1 > ASQMTQSPSSLSASVGDRVTITCRASQGIRNDLGWYQQKPGKAPKLLIYAASSLQSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCLQDYTYPWTFGQGTKLEIKRTGGGGSGGGGSGGGGSVQLLEQSGAEVKKPGESLKISCKGSGYSFTNYWIGWVRQMPGKGLEWMGIIYPDDSDTRYSPSSQGQVTISFDKSTNTAYLQWSSLKASDTAIYYCARALWFRDWGKVDVWGKGTTVTVSVD >>A2 > ASQMTQSPSSLSASVGDRVTITCRASQGIRNDLGWYQQKPGKAPKLLIYAASSLQSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCLQDYTYPWTFGQGTKLEIKRTGGGGSGGGGSGGGGSVQLLEQSGAEVKKPGESLKISCKGSGYSFTNYWIGWVRQMPGKGLEWMGIIYPDDSDTRYSPSFQGQVTISFDKSINTAYLQWSSLKASDTAIYYCARALRFRDWGKMDVWGKGTTVTVSVD >>A3 > ASQMTQSPSSLSASVGDRVTITCRASQGIRSDLGWYQQKPGKAPKLLIYAASSLQSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCLQDYTYPWTFGQGTKLEIKRTGGGGSGGGGSGGGGSVQLLEQSGAEVKKPGESLRISCKGSGYSFTNYWIGWVRQMPGKGLEWMGIIYPDDSDTRYSPSFQGQVTISFDKSINTAYLQWSSLKASDTAIYYCARALWFRDWGKMDVWGKGTAVTVSVD >>A4 > ASQMTQSPSSLSASVGDRVTITCRASQGIGNDLGWYQQKPGKAPKLLIYAASSLQSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCLQDYTYPWTFGQGTKLEIKRTGGGGSGGGGSGGGGSVQLLEQSGAEVKKPGESLKISCEGSGYSFTNYWIGWVRQMPGKGLEWMGIIYPDDSDTRYSPSFQGQVTISFDKSINTAYLQWSSLKASDTAIYYCARALRFRDWGKMDVWGKGTTVTVSVD >>A6 > ASQMTQSPSSLSASVGDRVTITCRASQGIRNDLGWYQQKPGKAPKLLIYAASSLQSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCLQDYTYPWTFGQGTKLEIKRTGGGGSGGGGSGGGGSVQLLEQSGAEVKKPGESLKISCKGSGYSFTNYWIGWVRQMPGKGLEWMGIIYPDDSDTRYSPSFQGQVTISFDKSINTAYLQWSSLRASDTAIYYCARALRFRDWGKMDVWGKGTTVTVSVD >>A7 > ASQMTQSPSSLSASVGDRVTITCRASQGIRNDLGWYQQKPGKAPKLLIYAASSLQSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCLQDYTYPWTFGQGTKLEIKRTGGGGSGGGGSGGGGSVQLLEQSGAEVKKPGESLKISCKGSGYSFTNYWIGWVRQMPGKGLEWMGIIYPDDSDTRYSPSFQGQVTISFDKSINTAYLQWSSLKASDTAIYYCARALRFRDWGKMDVWGKGTTVTVSVD >>A8 > ASQMTQSPSSLSASVGDRVTITCRASQGIRNDLGWYQQKPGKAPKLLIYAASSLQSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCLQDYTYPWTFGQGTKLEIKRTGGGGSGGGGSGGGGSVQLLEQSGAEVKKPGESLKISCKGSGHSFTNYWIGWVRQMPGKGLEWMGIIYPDDSDTRYSPSFQGQVTISFDKSINTAYLQWSSLKASDTAIYYCARVLWFRDWGKMDVWGKGTTVTVSVD >>A9 > ASQMTQSPSSLSASVGDRVTITCRASQGIRNGLGWYQQKPGKAPKLLIYAASSLQSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCLQDYTYPWTFGQGTKLEIKRTGGGGSGGGGSGGGGSVQLLEQSGAEVKKPGESLKISCKGSGYSFTNYWIGWVRQTPGKGLEWMGIIYPDGSDTRYGPSFQGQVTISFDKSIDTAYLQWSSLKASDTAIYYCARALWFRDWGKMDVWGKGTTVTVSVD >>B1 > ASQMAQSPSSLSASVGDRVTITCRASQGIRNDLGWYQQKPGKAPKLLIYAASSLQSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCLQDYTYPWTFGQGTKLEIKRTGGGGSGGGGSGGGGSVQLLEQSGAEVKKPGESLKISCKGSGYSFTNYWIGWVRQMPGKGLEWMGIIYPDDSDTRYSPSFQGQVTISFDKSINTAYLQWSSLKASDTAIYYCARALRFRDWGKMDVWGKGTTVTVS >>B2 > ASQMTQSPSSLSASVGDRVTITCRASQGIRNGLGWYQQKPGKAPKLLIYAASSLQSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCLQDYTYPWTFGQGTKLEIKRTGGGGSGGGGSGGGGSVQLLEQSGAEVKKPGESLKISCKGSGYSFTNYWIGWVRQMPGKGLEWMGIIYPDDSDTRYSPSFQGQVTISFDKSINTAYLQWSSLKASDTAIYYCARALRFRDWGKMDVWGKGTTVTVSVD >>B4 > ASQMTQSPSSLSASVGDRVAITCRVSQGIRNDLGWYQQKPGKAPKLLIYAASSLQSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCLQDYTYPWTFGQGTKLEIKRTGGGGSGGGGSGGGGSVQLLEQSGAEVKKPGESLKISCKGSGYNFTNYWIGWVRQMPGKGLEWMGIIYPDDSDTRYSPSFQGQVTISFDKSINTAYLQWSSLKASDTAIYYCARALWFRDWGKMDVWGKGTTVTVSVD >>B5 > ASQMTQSPSSLSASVGDRVTITCRASQGIGNDLGWYQQKPGKAPKLLIYAASSLQSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCLQGYTYPWTFGQGTKLEIKRTGGGGSGGGGSGGGGSVQLLEQSGAEVKKPGESLKISCKGSGHSFTNYWIGWVRQMPGKGLEWMGIIYPDDSDTRYSPSFQGQVTISFDKSINTAYLQWSSLKASDTAIYYCARALRFRDWGKMDVWGKGTTVTVSVD >>B6 > ASQMTQSPSSLSASVGDRVTITCRASQGIRNDLGWYQQKPGKAPKLLIYAASSLQSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCLQDYTYPWTFGQGTKLEIKRTGGGGSGGGGSGGGGSVQLLEQSGAEVKKPGESLKISCKGSGYSFTNYWIGWVRQMPGKGLEWMGAIYPDDSDTRYSPSFQGQVTISFDKSTNTAYLQWSSLKASDTAIYYCARALWFRDWGKMDVWGKGTTVTVSVD >>C1 > ASQMTQSPSSLSASVGDRVTITCRASQGIRNGLGWYQQKPGKAPKLLIYAASSLQSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCLQDYTYPWTFGQGTKLEIKRTGGGGSGGGGSGGGGSVQLLEQSGAEVKKPGESLKISCKGSGYSFTNYWIGWVRQMPGKGLEWMGIIYPDDSDTRYSPSFQGQVTISFDKSISTAYLQWSSLKASDTAIYYCARALWFRDWGKMDVWGKGTTVTVA >>C3 > ASQMTQSPSSLSASVGDRVTITCRASQGIRNNLGWYQQKPGEAPKLLIYAASSLQSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCLQDYTYPWTFGQGTKLEIKRTGGGGSGGGGSGGGGSVQLLEQSGAEVKKPGEPLKISCKGSGYSFTNYWIGWVRQMPGKGLEWMGIIYPDDSDTRYSPSFQGQVTISFDKSINTAYLQWSSLKASDTAIYYCARALWFRDWGKMDVWGKGTTVTVSA >>C4 > ASQMTQSPSSLPASVGDRVTITRRASQGIRNDLGWYQQKPGKAPKLLIYAASSLQSGVPSRFSGSGSGTDSTLTISSLQPEDFATYYCLQDYTYPRTFGQGTKLEIKRTGGGGSGGGGSGGGGSVQLLEQSGAEVKKPGESLKISCKGSGYSFTNYWIGWVRQMPGKGLEWMGIIYPDDSDTRYSPSFQGQVTISFDKSINTAYLQWSSLKASDTAIYYCARALWFRDWGKVDVWGKGTTVTVSVD >>C6 > ASQMTQSPSSLSASVGDRVTITCRASQGIRNGLGWYQQKPGEAPKLLIYAASSLQSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCLQDYTYPWTFGQGTKLEIKRTGGGGSGGGGSGGGGSAQLLEQSGAEVKKPGESLKISCKGSGYSFTNYWIGWVRQMPGKGLEWMGIIYPDDSDTRYSPSFQGQVTISFDKSINTAYLQWSSLKASDTAIYYCARALWFRDWGKMDVWGKGTTVTVSVD >>C8 > ASQMTQSPSSLSASVGDRVTITCRASQGIRNDLGWYQQKPGKAPKLLIYAASSLQSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCLQDYTYPWTFGQGTKLEIKRTGGGGSGGGGSGGGGSVQLLEQSGAEVKKPGESLKISCKGSGYSFTNYWIGWVRQMPGKGLEWMGIIYPDDSDTRYSPSFQGQVTISFDKSINTAYLQWSSLKASDTAIYYCARALRFRDWGKMDVWGKGTTVTVSVD >>D1 > ASQMTQSPSSLSASVGDRVTITCRASQGIRNDLGWYQQKPGKAPKLLIYAASSLQSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCLQDYTYPWTFGQGTKLEIKRTGGGGSGGGGSGGGGSVQLLEQSGAEVKKPGESLKISCKGSGYSFTNYWIGWVRQMPGKGLEWMGIIYPDDSDTRYSPSFQGQVTISFDKSINTAYLQWSSLKASDTATYYCARALRFRDWGKMDVWGRGTTVTVSVD >>D2 > ASQMTQSPSSLSASVGDRVTITCRASQGIRNDLGWYQQKPGKAPKLLIYAASSLQSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCLQGYTYPWTFGQGTKLEIKRTGGGGSGGGGSGGGGSVQLLEQSGAEVKKPGESLKISCKGSGYSFTNYWIGWVRQMPGKGLEWMGIIYPDDSDTRYSPSFQGQVTISFDKSINTAYLQWSSLKASDTAIYYCARALWFRDWGKMDVWGKGTTVTVSVD >>D3 > ASQMTQSPSSLSASVGDRVTITCRASQGIRNGLGWYQQKPGKAPKLLIYAASSLQSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCLQDHTYPWTFGQGTKLEIKRTGGGGSGGGGSGGGGSVQLLEQSGAEVKKPGESLKISCKGSGYSFANYWIGWVRQMPGKGLEWMGIIYPDDSDTRYSPSFQGQVTISFDKSINTAYLQWSSLEASDTAIYYCARALWFRDWGKMDVWGKGTTVTVSVD >>D7 > ASQMTQSPSSLSASVGDRVTITCRASQGIRNDLGWYQQKPGEAPKLLIYAASSLQSGVPSRFSGSGSGTDFTLTISSLQPEDSATYYCLQDYTYPWTFGQGTKLEIKRTGGGGSGGGGSGGGGSVQLLEQSGAEVKKPGESLKISCKGSGYSFTNYWIGWVRQMPGKGLEWMGIIYPDDSDTRYSPSFQGQVTISFDKSINTAYLQWSSLKASDTAIYYCARALWFRDWGKMDVWGKGTTVTVSVD >>D8 > ASQMTQSPSSLSASVGDRVTITCRASQGIRNDLGWYQQKPGKAPKLLIYAASSLQSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCLQDHTYPWTFGQGTKLEIKRTGGGGSGGGGSGGGGSVQLLEQSGAEVKKPGESLKISCKGSGYSFTNYWIGWVRQMPGKGLEWMGIIYPDDSDTRYSPSFQGQVTISFDKSINTAYLQWSSLKASDTAIYYCARALRFRDWGKMDVWGKGTTVTVSVD >>D9 > ASQMTQSPSSLSASVGDRVTITCRASQGIRNDLGWYQQKPGKAPKLLIYAASSLQSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCLQDYTYPWTFGQGTKLEIKRTGGGGSGGGGSGGGGSVQLLEQSGAEVKGPGESLKISCRGSGYSFTNYWIGWVRQMPGKGLEWMGIIYPDDSDTRYSPSFQGQVTISFDKSINTAYLQWSSLKASDTAIYYCARALWFRDWGKVDVWGKGTTVTVSVD >>E4 > ASQMTQSPSSLSASVGDRVTITCRASQGIRNGLGWYQQKPGKAPKLLIYAASSLQSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCLQDYTYPWTFGQGTKLEIKRTGGGGSGGGGSGGGGSVQLLEQSGAEVKKPGESLKISCKGSGYSFTNYWIGWVRQMPGKGLEWMGIIYPDDSDTRYSPSFQGQVTISFDKSINTAYLQWSSLKASDTAIYYCARALRFRDWGKMDVWGKGTTVTVSVD >>E9 > ASQMTQSPSSLSASVGDRVTITCRASQGIRNDLGWYQQKPGEAPKLLIYAASSLQSGVPSRFSGSGSGTDFTLTISSLQPEDSATYYCLQDYTYPWTFGQGTKLEIKRTGGGGSGGGGSGGGGSVQLLEQSGAEVKKPGESLKISCKGSGYSFTNYWIGWVRQMPGKGLEWMGIIYPDDSDTRYSPSFQGQVTISFDKSINTAYLQWSSLKASDTAIYYCARALWFRDWGKMDVWGKGTTVTVSVD >>E11 > ASQMTQSPSSLSASVGDRVTITCRASQGIRNGLGWYQQKPGKAPKLLIYAASSLQSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCLQDYAYPWTFGQGTKLEIKRTGGGGSGGGGSGGGGSVQLLEQSGAEVKKPGESLKISCKGSGYSFTNYWIGWVRQMPGKGLEWMGIIYPDDSDTRYSPSFQGQVTISFDKSINTAYLQWSSLKASDTAIYYCARALWLRDWGKMDVWGKGTTVTVSVD >>F1 > ASQMTQSPSSLSASVGDRVTITCRASQGIRSDLGWYQQKPGKAPKLLIYAASSLQSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCLQDYTYPWTFGQGTKLEIKRTGGGGSGGGGSGGGGSVQLLEQSGAEVKKPGESLRISCKGSGYSFTNYWIGWVRQMPGKGLEWMGIIYPDDSDTRYSPSFQGQVTISFDKSINTAYLQWSSLKASDTAIYYCARALWFRDWGKMDVWGKGTAVTVSVD >>F2 > ASQMTQSPSSLSASVGDRVTITCRASQGIRNGLGWYQQKPGEAPKLLIYAASSLQSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCLQDYTYPWTFGQGTKLEIKRTGGGGSGGGGSGGGGSAQLLEQSGAEVKKPGESLKISCKGSGYSFTNYWIGWVRQMPGKGLEWMGIIYPDDSDTRYSPSFQGQVTISFDKSINTAYLQWSSLKASDTAIYYCARALWFRDWGKMDVWGKGTTVTVSVD >>F3 > ASQMTQSPSSLSASVGDRVTITCRASQGIRNDLGWYQQKPGKAPKLLIYAASSLQSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCLQDYTYPWTFGQGTKLEIKRTGGGGSGGGGSGGGGSVQLLEQSGAEVKKPGESLKISCKGSGYSFTNYWIGWVRQMPGKGLEWMGIIYPDDSDTRYSPSFQGQVTISFDKSINTAYLQWSSLKASDTAIYYCARALRFRTGARWTSGAKGPRSPSPS >>F4 > ASQMTQSPSSLSASVGDRVTITCRASQGIRNGLGWYQQKPGKAPKLLIYAASSLQSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCLQDYTYPWTFGQGTKLEIKRTGGGGSGGGGSGGGGSVQLLEQSGAEVKKPGESLKISCKGSGYSSTNYWIGWVRQMPGKGLEWMGTIYPDDSDTRYSPSFQGQVTISFDKSINTAYLQWSSLKASDTAIYYCARALWFRDWGKMDVWGKGTTVTVSVD >>G1 > ASQMAQSPSSLSASVGDRVTITCRASQGIRNDLGWYQQKPGKAPKLLIYAASSLQSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCLQDYTYPWTFGQGTKLEIKRTGGGGSGGGGSGGGGSVQLLEQSGAEVKKPGESLKISCKGSGYSFTNYWIGWVRQMPGKGLEWMGIIYPDDSDTRYSPSFQGQVTISFDKSINTAYLQWSSLKASDTAIYYCARALRFRDWGKMDVWGKGTRSPSP >>G2 > QMTQSPSSLSASVGDRVTITCRASQGIRNNLGWYQQKPGEAPKLLIYAASSLQSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCLQDYTYPWTFGQGTKLEIKRTGGGGSGGGGSGGGGSVQLLEQSGAEVKKPGEPLKISCKGSGYSFTNYWIGWVRQMPGKGLEWMGIIYPDDSDTRYSPSFQGQVTISFDKSINTAYLQWSSLKASDTAIYYCARALWFRDWGKMDVWGKGTTVTVS >>G3 > ASQMTQSPSSLSASVGDRVTITCRASQGIRNGLGWYQQKPGKAPKLLIYAASSLQSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCLQDHTYPWTFGQGTKLEIKRTGGGGSGGGGSGGGGSVQLLEQSGAEVKKPGESLKISCKGSGYSFANYWIGWVRQMPGKGLEWMGIIYPDDSDTRYSPSFQGQVTISFDKSINTAYLQWSSLEASDTAIYYCARALWFRDWGKMDVWGKGTTVTVSVD >>G4 > ASQMTQSPSSLSASVGDRVTITCRASQGIRSDLGWYQQKPGKAPKLLIYAASSLQSGVPSRFSGSGSGTDFTLTISSLQPEDSATYYCLQGYTYPWTFGQGTKLEIKRTGGGGSGGGGSGGGGSVQLLEQSGAEVKKPGESLKISCKGSGYSFTNYWIGWVRQMPGKGLEWMGTIYPDDSDTRYGPSFRGQVTISFDKSINTAYLQWSSLKASDTAIYYCARALWFRDWGKMDVWGKGTTVTVPVD >>G5 > ASQMTQSPSSLSASVGDRVTITCRASQGIRNGLGWYQQKPGKAPKLLIYAASSLQSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCLQDYTYPWTFGQGTKLEIKRTGGGGSGGGGSGGGGSVQLLEQSGAGVKKPGESLKISCKGSGYSFTDYWIGWVRQMPGKGLEWMGIIYPDDSDTRYSPSFQGQVTISFDKSINTAYLQWSSLKASDTAIYYCARALWFRDWGKMDVWGKGTTVTVSVD >>G6 > ASQMTQSPSSLSASVGGRVTITCRASQGIRNDLGWYQQKPGKAPKLLIYAASSLQSGVPSRFSGSGSGTDFTLTISSLQPEDSATYYCLQDYTYPWTFGQGTKLEIKRTGGGGSGGGGSGGGGSVQLLEQSGAEVKKPGESLKISCKGSGYSFTNYWIGWVRQMPGKGLEWMGIIYPDDSDTRYSPSFQGQVTISFDKSINTAYLQWSSLKASDTAIYYCARASWFRDWGKMDVWGKGTTVTVSVD > > _______________________________________________ > EMBOSS mailing list > EMBOSS at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/emboss > > From mathog at caltech.edu Thu Oct 29 18:55:12 2009 From: mathog at caltech.edu (David Mathog) Date: Thu, 29 Oct 2009 11:55:12 -0700 Subject: [EMBOSS] 6.1.0 build warnings in PHYLIPNEW-3.68 Message-ID: In consense.c extern Char intreename[FNMLNGTH], intree2name[FNMLNGTH]; const char* outfilename; const char* outtreename; In cons.c Char outfilename[FNMLNGTH], intreename[FNMLNGTH], intree2name[FNMLNGTH], outtreename[FNMLNGTH]; which explains this: > ld: warning: symbol `outfilename' has differing sizes: > (file consense.o value=0x4; file cons.o value=0xc8); > cons.o definition taken > ld: warning: symbol `outtreename' has differing sizes: > (file consense.o value=0x4; file cons.o value=0xc8); > cons.o definition taken Which one needs to be change? Thanks, David Mathog mathog at caltech.edu Manager, Sequence Analysis Facility, Biology Division, Caltech From mathog at caltech.edu Thu Oct 29 18:46:53 2009 From: mathog at caltech.edu (David Mathog) Date: Thu, 29 Oct 2009 11:46:53 -0700 Subject: [EMBOSS] 6.1.0 build warnings in PHYLIPNEW-3.68 Message-ID: Downloaded 6.1.0, patched, built, but found four warnings as shown below in the logs for PHYLIPNEW-3.68. This was on Solaris 8 with gcc 3.4.6. Is this a known issue? libtool: link: gcc -O2 -o .libs/fconsense consense.o cons.o phylip.o ../../../nucleus/.libs/libnucleus.so ../../../ajax/.libs/libajax.so ../../../plplot/.libs/libeplplot.so -lXaw -lXt -lnsl -lsocket /usr/local/lib/libgd.so -L/usr/local/lib -L/usr/local/BerkeleyDB.4.2/lib -L/usr/local/ssl/lib -L/usr/openwin/lib -L/usr/lib -L/usr/openwin/llib -lXpm -lX11 /usr/local/lib/libjpeg.so /usr/local/lib/libfontconfig.so -L/usr/local/mysql/lib/mysql /usr/local/lib/libexpat.so /usr/local/lib/libfreetype.so -lpng12 -lpng -lz -lm /usr/local/lib/libiconv.so -R/usr/local/lib ld: warning: symbol `outfilename' has differing sizes: (file consense.o value=0x4; file cons.o value=0xc8); cons.o definition taken ld: warning: symbol `outtreename' has differing sizes: (file consense.o value=0x4; file cons.o value=0xc8); cons.o definition taken libtool: link: gcc -O2 -o .libs/ftreedist treedist.o cons.o phylip.o ../../../nucleus/.libs/libnucleus.so ../../../ajax/.libs/libajax.so ../../../plplot/.libs/libeplplot.so -lXaw -lXt -lnsl -lsocket /usr/local/lib/libgd.so -L/usr/local/lib -L/usr/local/BerkeleyDB.4.2/lib -L/usr/local/ssl/lib -L/usr/openwin/lib -L/usr/lib -L/usr/openwin/llib -lXpm -lX11 /usr/local/lib/libjpeg.so /usr/local/lib/libfontconfig.so -L/usr/local/mysql/lib/mysql /usr/local/lib/libexpat.so /usr/local/lib/libfreetype.so -lpng12 -lpng -lz -lm /usr/local/lib/libiconv.so -R/usr/local/lib ld: warning: symbol `outfilename' has differing sizes: (file treedist.o value=0x4; file cons.o value=0xc8); cons.o definition taken libtool: link: gcc -O2 -o .libs/ftreedistpair treedistpair.o cons.o phylip.o ../../../nucleus/.libs/libnucleus.so ../../../ajax/.libs/libajax.so ../../../plplot/.libs/libeplplot.so -lXaw -lXt -lnsl -lsocket /usr/local/lib/libgd.so -L/usr/local/lib -L/usr/local/BerkeleyDB.4.2/lib -L/usr/local/ssl/lib -L/usr/openwin/lib -L/usr/lib -L/usr/openwin/llib -lXpm -lX11 /usr/local/lib/libjpeg.so /usr/local/lib/libfontconfig.so -L/usr/local/mysql/lib/mysql /usr/local/lib/libexpat.so /usr/local/lib/libfreetype.so -lpng12 -lpng -lz -lm /usr/local/lib/libiconv.so -R/usr/local/lib ld: warning: symbol `outfilename' has differing sizes: (file treedistpair.o value=0x4; file cons.o value=0xc8); cons.o definition taken There were no other fail, error, or warn strings anywhere in the build. Thanks, David Mathog mathog at caltech.edu Manager, Sequence Analysis Facility, Biology Division, Caltech From mathog at caltech.edu Thu Oct 29 20:54:38 2009 From: mathog at caltech.edu (David Mathog) Date: Thu, 29 Oct 2009 13:54:38 -0700 Subject: [EMBOSS] 6.1.0 build warnings in PHYLIPNEW-3.68 Message-ID: Changing one line as shown below seems to have fixed it, at least it eliminate the warning. Don't know yet if it causes any problems when the program runs. This change is in line with the way the other programs in this directory are constructed. % diff cons.c cons.c.dist 6c6 < Char intreename[FNMLNGTH], intree2name[FNMLNGTH]; --- > Char outfilename[FNMLNGTH], intreename[FNMLNGTH], intree2name[FNMLNGTH], outtreename[FNMLNGTH]; Regards, David Mathog mathog at caltech.edu Manager, Sequence Analysis Facility, Biology Division, Caltech From pmr at ebi.ac.uk Fri Oct 30 10:12:24 2009 From: pmr at ebi.ac.uk (Peter Rice) Date: Fri, 30 Oct 2009 10:12:24 +0000 Subject: [EMBOSS] 6.1.0 build warnings in PHYLIPNEW-3.68 In-Reply-To: References: Message-ID: <4AEABC08.70607@ebi.ac.uk> On 29/10/09 20:54, David Mathog wrote: > Changing one line as shown below seems to have fixed it, at least it > eliminate the warning. Don't know yet if it causes any problems when > the program runs. This change is in line with the way the other > programs in this directory are constructed. > > % diff cons.c cons.c.dist > 6c6 > < Char intreename[FNMLNGTH], intree2name[FNMLNGTH]; > --- >> Char outfilename[FNMLNGTH], intreename[FNMLNGTH], > intree2name[FNMLNGTH], outtreename[FNMLNGTH]; Yes, that is the correct fix for the compiler warning. We do not use the original phylip 3.6 outfile name buffers. Thanks Peter From mathog at caltech.edu Fri Oct 30 21:43:53 2009 From: mathog at caltech.edu (David Mathog) Date: Fri, 30 Oct 2009 14:43:53 -0700 Subject: [EMBOSS] CBSTOOLS not installing help files, don't work with emboss explorer Message-ID: For some reason or other the CBSTOOLS package built its html and txt help files, but didn't install them on "make install". To work around this, they were copied manually to the proper directories, then tfm eyinoyang worked, but the help links in emboss explorer still didn't pick them up. Found where those were supposed to go eventually by poking around in /usr/local/share/EMBOSS/doc/html/embassy. Seems like a glitch in the CBSTOOLS install, but no errors or warnings were emitted. Is something supposed to generate /usr/local/share/EMBOSS/doc/html/embassy/index.html automatically, or must that be hand edited when the embassy packages change? There are no directions inside the embassy/CBSTOOLS directory for installing the actual programs that these are wrappers for. They can be downloaded one at a time from here: http://www.cbs.dtu.dk/services/ is there a way to get the lot of them all at once? Thanks, David Mathog mathog at caltech.edu Manager, Sequence Analysis Facility, Biology Division, Caltech