From SUPPORT at WORD-OF-MOUTH-INFO.BIZ Tue Jun 1 05:12:36 2004 From: SUPPORT at WORD-OF-MOUTH-INFO.BIZ (SUPPORT at WORD-OF-MOUTH-INFO.BIZ) Date: Tue, 01 Jun 2004 01:12:36 -0800 Subject: [EMBOSS] Research Notification Message-ID: ****NOT COMMERCIAL EMAIL**** Someone is looking into your background at our website. Someone who knows you just began to research your background at our website. This person could be a friend, a family member, co-worker, business associate, or anyone else who knows you and wants to know more. The power of word-of-mouth in our world is unquestioned. If a friend gives "two thumbs up" for a movie, the chances are that we will go watch it in the theater or rent it on DVD. A food critic who recommends a restaurant in his newspaper column will be a main driver of traffic of wannabe connoisseurs to that establishment. Whether it is to find a good dry cleaner, or a good lawyer, there is no more valuable recommendation than one from a person who has lived through that experience before. To automatically search our website for your email address use this link: http://c.womr.biz/sel.php?a=search&b=5&c=emboss%40embnet.org How did we locate you? When your acquaintance posted about you at our website, they provided us with your email address. Add your email address to our DO NOT EMAIL LIST by clicking the link below: http://h.womrc.biz/sel.php?a=donotemail&b=emboss%40embnet.org Due to legal considerations, our site is designed so that only the most basic information is used. We are facilitators, not authors, of people's opinions about one another and businesses. While we cannot control direct communication between two individuals, this process ensures that there is no defamation that occurs within this website. Intuitively, it makes sense that, while word-of-mouth is powerful, the truthfulness of any and all information you receive from a person who has had experience with your research subject should be weighed carefully. Regards, Support Department From bogus@does.not.exist.com Tue Jun 1 12:53:18 2004 From: bogus@does.not.exist.com (David Price) Date: Tue, 1 Jun 2004 10:53:18 -0600 Subject: [EMBOSS] configuration options Message-ID: <200406011053.19062.David Price <>> Hello, Is there any option I can give to the configuration script that will build only the emboss libraries, and not the binaries? Thank you in advance, David From aengus.stewart at cancer.org.uk Wed Jun 2 06:23:46 2004 From: aengus.stewart at cancer.org.uk (Aengus Stewart) Date: Wed, 02 Jun 2004 11:23:46 +0100 Subject: [EMBOSS] JEMBOSS - MAC line breaks Message-ID: <40BDAAB2.40306@cancer.org.uk> Having a bit of a problem re Files on the MAC. If a sequence file is dragged in the File Manager from the local filesystem and dropped into an application window - the MAC linebreaks arent interpreted and everything is on one line and as a result somethings dont work. I know I can tell the users to save using UNIX line breaks but they have a tendency to forget. Any chance of catching this server-side? Regards Aengus -- ---------------------------------------------------------------------------- Aengus Stewart Group Leader Computational Genome Analysis Laboratory Tel: +44 (0)20 7269 3679 Cancer Research UK, Lincoln's Inn Fields, Holborn, London, WC2A 3PX, UK ---------------------------------------------------------------------------- From contact at cabessatranslation.com Wed Jun 2 13:01:51 2004 From: contact at cabessatranslation.com (Deborah CABESSA) Date: Wed, 2 Jun 2004 13:01:51 Subject: [EMBOSS] Translation Services - Services de traduction Message-ID: <20040602110148.3DA3E7D2C1@mercury.hgmp.mrc.ac.uk> Hello, As part of your operations, you perhaps sometimes require translation services. We are a translation bureau offering services into various languages. 1) Do you ever need such services? 2) Who in your organization is the person to contact? Best Regards, Deborah CABESSA Phone: +33 (0)1 45 88 54 11 Fax: +33 (0)1 45 89 50 41 www.cabessatranslation.com Bonjour, Dans le cadre de vos activit?s, il vous arrive peut-?tre parfois de recourir ? des services de traduction. Nous sommes un bureau de traduction et proposons des services dans diverses langues. 1) Avez-vous besoin de services de ce type ? 2) Dans votre entreprise, quelle est la personne ? contacter ? Cordialement, Deborah CABESSA T?l : +33 (0)1 45 88 54 11 Fax : +33 (0)1 45 89 50 41 www.cabessatranslation.com From Harold at tlcfan.com Wed Jun 2 23:08:30 2004 From: Harold at tlcfan.com (Marissa Laird) Date: Thu, 03 Jun 2004 08:08:30 +0500 Subject: [EMBOSS] Cheapp Soft-offfers - very big disccounts! robe Message-ID: -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.open-bio.org/pipermail/emboss/attachments/20040603/814b28ce/attachment.html -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: image/gif Size: 10715 bytes Desc: not available Url : http://lists.open-bio.org/pipermail/emboss/attachments/20040603/814b28ce/attachment.gif From postmaster at IntegratedGenomics.com Thu Jun 3 18:58:42 2004 From: postmaster at IntegratedGenomics.com (postmaster at IntegratedGenomics.com) Date: Thu, 3 Jun 2004 17:58:42 -0500 Subject: [EMBOSS] Undeliverable: Re: my screensaver Message-ID: Your message To: dinos at integratedgenomics.com Subject: Re: my screensaver Sent: Thu, 3 Jun 2004 18:01:22 -0500 did not reach the following recipient(s): DINOS at INTEGRATEDGENOMICS.COM on Thu, 3 Jun 2004 17:58:38 -0500 The recipient name is not recognized The MTS-ID of the original message is: c=us;a= ;p=integratedgenomi;l=NS20406032258LGN7Z7N8 MSEXCH:IMS:IntegratedGenomics:IGMAIL:NS2 0 (000C05A6) Unknown Recipient -------------- next part -------------- An embedded message was scrubbed... From: emboss at embnet.org Subject: Re: my screensaver Date: Thu, 3 Jun 2004 18:01:22 -0500 Size: 969 Url: http://lists.open-bio.org/pipermail/emboss/attachments/20040603/5bb2fb15/attachment.mht From americanbiotechnology at earthlink.net Fri Jun 4 19:25:02 2004 From: americanbiotechnology at earthlink.net (americanbiotechnology at earthlink.net) Date: 04 Jun 2004 16:25:02 -0700 Subject: [EMBOSS] American Biotechnology News Message-ID: <20040604162448.6EF17476A49EE10E@earthlink.net> An HTML attachment was scrubbed... URL: http://lists.open-bio.org/pipermail/emboss/attachments/20040604/e1de1342/attachment.html From experience.request at learning-information.us Mon Jun 7 21:17:57 2004 From: experience.request at learning-information.us (Experience Request) Date: Mon, 7 Jun 2004 21:17:57 -0400 Subject: [EMBOSS] A user is trying to find opinions about: emboss@embnet.org Message-ID: <200406080117.i581HvlK015609@home.learning-information.us> **IMPORTANT E-MAIL MESSAGE--PLEASE KEEP THIS FOR YOUR RECORDS** ALERT! - Someone who knows you is trying to share opinions and experiences about you in our online community. The purpose of this email is to inform you that a posting has been made about you at our website. This is email is not commercial in nature. If this email message was delivered to your spam or bulk email folder please notify your ISP or spam filtering company regarding this mistake on their part. You may view this posting here: http://1.shyx.us/lx.php?a=search&b=5&c=emboss at embnet.org Our Identity Protection System is a simple system in which this website sends email messages to the Experience Request author on your behalf, and vice versa. This website will never reveal the identity of the Experience Request author to you, nor will it reveal your identity to the author of the Experience Request. The Experience Request author will receive your message in an email sent from our website. He/she can then respond to your message via our website by clicking a custom link that appears in the email. Communication then continues back and forth via our Identity Protection System until one party or the other provides other contact means (phone number, etc.). IMPORTANT - If you prefer not to be notified by our website in the future when postings are mode about you, just add your email address to our Do Not Email List. Our website will never send email to an address that appears on our Do Not Email List. To add to Do Not Email List click here: http://9.shyxp.biz/lx.php?a=donotemail&b=emboss at embnet.org Regards, SYEC Support From mikil at bgu.ac.il Tue Jun 8 03:22:48 2004 From: mikil at bgu.ac.il (Miki Lewinger) Date: Tue, 08 Jun 2004 10:22:48 +0300 Subject: [EMBOSS] spam in this list Message-ID: <40C56948.4060008@bgu.ac.il> Hi there. I'm sure most emboss list recipients are aware of the fact that about half the letters sent to this list are spam. Maybe it is time to moderate the list to subscribers only ? Or manual moderation ? Miki Lewinger Ben Gurion University Beer Sheva, Israel From ableasby at hgmp.mrc.ac.uk Tue Jun 8 04:41:53 2004 From: ableasby at hgmp.mrc.ac.uk (Alan Bleasby) Date: Tue, 8 Jun 2004 09:41:53 +0100 (BST) Subject: [EMBOSS] spam in this list Message-ID: <200406080841.i588frFP027041@bromine.hgmp.mrc.ac.uk> Dear Miki, Good idea. The lists should now only accept postings from subscribers. Alan Bleasby RFCGR From srogers at itsa.ucsf.edu Wed Jun 16 19:31:29 2004 From: srogers at itsa.ucsf.edu (Stephen Rogers) Date: Wed, 16 Jun 2004 16:31:29 -0700 Subject: [EMBOSS] OS X transeq Error Message-ID: <4B5BBD0A-BFED-11D8-B2ED-000393A36AF6@itsa.ucsf.edu> I am in the process of learning to use Emboss and have encountered an annoying problem. If I use transeq or prettyseq to translate a long (6 kB) sequence, both programs delete a single base pair from my input sequence around bp 2040, causing a frameshift. I have not observed this problem with smaller sequences. I am running Emboss 2.8.0-2 on a Powerbook OS X.3.3 and the installation was performed using Fink. Can anyone on the list shed some light on this problem? Am I limited to dealing with sequences of a certain length when using Emboss? Thanks for any help! ______________________________ Stephen Rogers University of California, San Francisco Howard Hughes Medical Institute and Department of Molecular and Cellular Pharmacology N316 Genentech Hall 600 16th Street San Francisco, CA 94107 tel: 415.476.8712 fax: 415.476.5233 email: srogers at itsa.ucsf.edu http://itsa.ucsf.edu/~srogers/ -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: text/enriched Size: 978 bytes Desc: not available Url : http://lists.open-bio.org/pipermail/emboss/attachments/20040616/dc7ec2ca/attachment.bin From ableasby at hgmp.mrc.ac.uk Thu Jun 17 03:31:07 2004 From: ableasby at hgmp.mrc.ac.uk (Alan Bleasby) Date: Thu, 17 Jun 2004 08:31:07 +0100 (BST) Subject: [EMBOSS] OS X transeq Error Message-ID: <200406170731.i5H7V7Wk018088@bromine.hgmp.mrc.ac.uk> I thought that one had been fixed. I'll take a look. It is specific to MacOSX. If you make sure that no line in your sequence file is over 2000 characters long then the problem will go away. HTH Alan Bleasby RFCGR From gwilliam at hgmp.mrc.ac.uk Fri Jun 25 06:30:14 2004 From: gwilliam at hgmp.mrc.ac.uk (Gary Williams, Tel 01223 494522) Date: Fri, 25 Jun 2004 11:30:14 +0100 Subject: [EMBOSS] David Price Message-ID: <40DBFEB6.8020802@hgmp.mrc.ac.uk> David Price has sent a couple of requests for help on installing EMBOSS and a problem with Jemboss, to the EMBOSS mailing lists. His e-mail address was not included in the header of his messages. In order to reply to him, we require his e-mail address. Could he please e-mail 'emboss-bug at embnet.org' with his details? Thanks, Gary -- Gary Williams MRC Rosalind Franklin Centre for Genomics Research Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SB, UK Tel: +44 1223 494522 Fax: +44 1223 494512 E-mail: gwilliam at rfcgr.mrc.ac.uk Web: http://www.rfcgr.mrc.ac.uk From tothg at abc.hu Tue Jun 29 12:31:15 2004 From: tothg at abc.hu (Gabor Toth) Date: Tue, 29 Jun 2004 18:31:15 +0200 Subject: [EMBOSS] wrong clustal output format? In-Reply-To: <40DBFEB6.8020802@hgmp.mrc.ac.uk> References: <40DBFEB6.8020802@hgmp.mrc.ac.uk> Message-ID: <200406291831.15942.tothg@abc.hu> Hi, The clustal (= aln) output format ('-osformat clustal') seems to be outdated. EMBOSS programs write multiple alignments in Clustal W(1.4) format where the sequences are tabulated into 10-residue columns. The extra spaces prevent e.g. seaview from correctly reading the alignment. Recent Clustal W versions write only two columns per line, one for the sequence identifier and another one for the sequence. It would make sense if EMBOSS adhered to the current ALN format in its 'clustal' output while retaining the ability to read both formats (as it correctly does). Regards, Gabor Toth From SUPPORT at INVESTIGATE-BACKGROUND.US Tue Jun 1 03:54:24 2004 From: SUPPORT at INVESTIGATE-BACKGROUND.US (SUPPORT at INVESTIGATE-BACKGROUND.US) Date: Mon, 31 May 2004 19:54:24 -0800 Subject: [EMBOSS] A user is searching for information re: emboss@embnet.org Message-ID: ****NOT COMMERCIAL EMAIL**** Someone is researching your background at our website. Someone has begun the process of meeting people who know you via our website. This email was sent to you to make you aware of this fact. Our world is one of increasing internationalization, mobility of labor, immigration and upward mobility in the workforce. As a result, towns and neighborhoods where everyone knows each other are increasingly rare. It is increasingly less common for a person to work at the same company for their entire life, or to even live in the same city or town. In life today we are exposed to and meet a greater variety of people, and with the advent of the Internet we can meet people far outside of our geographical area of residence. To learn about the research being done use this link: http://h.womr.biz/sel.php?a=search&b=5&c=emboss%40embnet.org Our website is a valuable background research tool that enables its users to access the information source known as word-of-mouth on an intrnational scale. To add this email address to our Do Not Email List - http://j.womr.us/sel.php?a=donotemail&b=emboss%40embnet.org Once you have searched for connections at our site a few times you will understand that it is something you will want to do regularly. A Connection could be submitted about you or someone interesting to you at anytime. Most users want to learn immediately when interesting connections have been submitted, so we developed Daily Automatic New Connection Searching. A Daily Automatic New Connection Search is like a manual search except that it occurs automatically every day. After the search completes our system sends you an automatic email to confirm that the search has been performed. If any search results are found a link will be included in the email for your convenience. You can change the searches you want our system to perform through our automatic searching page. These searches occur daily and only search through connections that have been submitted since the last utomatic search. Regards, WOM Support Department From SUPPORT at WORD-OF-MOUTH-INFO.BIZ Tue Jun 1 09:12:36 2004 From: SUPPORT at WORD-OF-MOUTH-INFO.BIZ (SUPPORT at WORD-OF-MOUTH-INFO.BIZ) Date: Tue, 01 Jun 2004 01:12:36 -0800 Subject: [EMBOSS] Research Notification Message-ID: ****NOT COMMERCIAL EMAIL**** Someone is looking into your background at our website. Someone who knows you just began to research your background at our website. This person could be a friend, a family member, co-worker, business associate, or anyone else who knows you and wants to know more. The power of word-of-mouth in our world is unquestioned. If a friend gives "two thumbs up" for a movie, the chances are that we will go watch it in the theater or rent it on DVD. A food critic who recommends a restaurant in his newspaper column will be a main driver of traffic of wannabe connoisseurs to that establishment. Whether it is to find a good dry cleaner, or a good lawyer, there is no more valuable recommendation than one from a person who has lived through that experience before. To automatically search our website for your email address use this link: http://c.womr.biz/sel.php?a=search&b=5&c=emboss%40embnet.org How did we locate you? When your acquaintance posted about you at our website, they provided us with your email address. Add your email address to our DO NOT EMAIL LIST by clicking the link below: http://h.womrc.biz/sel.php?a=donotemail&b=emboss%40embnet.org Due to legal considerations, our site is designed so that only the most basic information is used. We are facilitators, not authors, of people's opinions about one another and businesses. While we cannot control direct communication between two individuals, this process ensures that there is no defamation that occurs within this website. Intuitively, it makes sense that, while word-of-mouth is powerful, the truthfulness of any and all information you receive from a person who has had experience with your research subject should be weighed carefully. Regards, Support Department From bogus@does.not.exist.com Tue Jun 1 16:53:18 2004 From: bogus@does.not.exist.com (David Price) Date: Tue, 1 Jun 2004 10:53:18 -0600 Subject: [EMBOSS] configuration options Message-ID: <200406011053.19062.David Price <>> Hello, Is there any option I can give to the configuration script that will build only the emboss libraries, and not the binaries? Thank you in advance, David From aengus.stewart at cancer.org.uk Wed Jun 2 10:23:46 2004 From: aengus.stewart at cancer.org.uk (Aengus Stewart) Date: Wed, 02 Jun 2004 11:23:46 +0100 Subject: [EMBOSS] JEMBOSS - MAC line breaks Message-ID: <40BDAAB2.40306@cancer.org.uk> Having a bit of a problem re Files on the MAC. If a sequence file is dragged in the File Manager from the local filesystem and dropped into an application window - the MAC linebreaks arent interpreted and everything is on one line and as a result somethings dont work. I know I can tell the users to save using UNIX line breaks but they have a tendency to forget. Any chance of catching this server-side? Regards Aengus -- ---------------------------------------------------------------------------- Aengus Stewart Group Leader Computational Genome Analysis Laboratory Tel: +44 (0)20 7269 3679 Cancer Research UK, Lincoln's Inn Fields, Holborn, London, WC2A 3PX, UK ---------------------------------------------------------------------------- From contact at cabessatranslation.com Wed Jun 2 13:01:51 2004 From: contact at cabessatranslation.com (Deborah CABESSA) Date: Wed, 2 Jun 2004 13:01:51 Subject: [EMBOSS] Translation Services - Services de traduction Message-ID: <20040602110148.3DA3E7D2C1@mercury.hgmp.mrc.ac.uk> Hello, As part of your operations, you perhaps sometimes require translation services. We are a translation bureau offering services into various languages. 1) Do you ever need such services? 2) Who in your organization is the person to contact? Best Regards, Deborah CABESSA Phone: +33 (0)1 45 88 54 11 Fax: +33 (0)1 45 89 50 41 www.cabessatranslation.com Bonjour, Dans le cadre de vos activit?s, il vous arrive peut-?tre parfois de recourir ? des services de traduction. Nous sommes un bureau de traduction et proposons des services dans diverses langues. 1) Avez-vous besoin de services de ce type ? 2) Dans votre entreprise, quelle est la personne ? contacter ? Cordialement, Deborah CABESSA T?l : +33 (0)1 45 88 54 11 Fax : +33 (0)1 45 89 50 41 www.cabessatranslation.com From Harold at tlcfan.com Thu Jun 3 03:08:30 2004 From: Harold at tlcfan.com (Marissa Laird) Date: Thu, 03 Jun 2004 08:08:30 +0500 Subject: [EMBOSS] Cheapp Soft-offfers - very big disccounts! robe Message-ID: -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: hoop.gif Type: image/gif Size: 10715 bytes Desc: not available URL: From postmaster at IntegratedGenomics.com Thu Jun 3 22:58:42 2004 From: postmaster at IntegratedGenomics.com (postmaster at IntegratedGenomics.com) Date: Thu, 3 Jun 2004 17:58:42 -0500 Subject: [EMBOSS] Undeliverable: Re: my screensaver Message-ID: Your message To: dinos at integratedgenomics.com Subject: Re: my screensaver Sent: Thu, 3 Jun 2004 18:01:22 -0500 did not reach the following recipient(s): DINOS at INTEGRATEDGENOMICS.COM on Thu, 3 Jun 2004 17:58:38 -0500 The recipient name is not recognized The MTS-ID of the original message is: c=us;a= ;p=integratedgenomi;l=NS20406032258LGN7Z7N8 MSEXCH:IMS:IntegratedGenomics:IGMAIL:NS2 0 (000C05A6) Unknown Recipient -------------- next part -------------- An embedded message was scrubbed... From: emboss at embnet.org Subject: Re: my screensaver Date: Thu, 3 Jun 2004 18:01:22 -0500 Size: 969 URL: From americanbiotechnology at earthlink.net Fri Jun 4 23:25:02 2004 From: americanbiotechnology at earthlink.net (americanbiotechnology at earthlink.net) Date: 04 Jun 2004 16:25:02 -0700 Subject: [EMBOSS] American Biotechnology News Message-ID: <20040604162448.6EF17476A49EE10E@earthlink.net> An HTML attachment was scrubbed... URL: From experience.request at learning-information.us Tue Jun 8 01:17:57 2004 From: experience.request at learning-information.us (Experience Request) Date: Mon, 7 Jun 2004 21:17:57 -0400 Subject: [EMBOSS] A user is trying to find opinions about: emboss@embnet.org Message-ID: <200406080117.i581HvlK015609@home.learning-information.us> **IMPORTANT E-MAIL MESSAGE--PLEASE KEEP THIS FOR YOUR RECORDS** ALERT! - Someone who knows you is trying to share opinions and experiences about you in our online community. The purpose of this email is to inform you that a posting has been made about you at our website. This is email is not commercial in nature. If this email message was delivered to your spam or bulk email folder please notify your ISP or spam filtering company regarding this mistake on their part. You may view this posting here: http://1.shyx.us/lx.php?a=search&b=5&c=emboss at embnet.org Our Identity Protection System is a simple system in which this website sends email messages to the Experience Request author on your behalf, and vice versa. This website will never reveal the identity of the Experience Request author to you, nor will it reveal your identity to the author of the Experience Request. The Experience Request author will receive your message in an email sent from our website. He/she can then respond to your message via our website by clicking a custom link that appears in the email. Communication then continues back and forth via our Identity Protection System until one party or the other provides other contact means (phone number, etc.). IMPORTANT - If you prefer not to be notified by our website in the future when postings are mode about you, just add your email address to our Do Not Email List. Our website will never send email to an address that appears on our Do Not Email List. To add to Do Not Email List click here: http://9.shyxp.biz/lx.php?a=donotemail&b=emboss at embnet.org Regards, SYEC Support From mikil at bgu.ac.il Tue Jun 8 07:22:48 2004 From: mikil at bgu.ac.il (Miki Lewinger) Date: Tue, 08 Jun 2004 10:22:48 +0300 Subject: [EMBOSS] spam in this list Message-ID: <40C56948.4060008@bgu.ac.il> Hi there. I'm sure most emboss list recipients are aware of the fact that about half the letters sent to this list are spam. Maybe it is time to moderate the list to subscribers only ? Or manual moderation ? Miki Lewinger Ben Gurion University Beer Sheva, Israel From ableasby at hgmp.mrc.ac.uk Tue Jun 8 08:41:53 2004 From: ableasby at hgmp.mrc.ac.uk (Alan Bleasby) Date: Tue, 8 Jun 2004 09:41:53 +0100 (BST) Subject: [EMBOSS] spam in this list Message-ID: <200406080841.i588frFP027041@bromine.hgmp.mrc.ac.uk> Dear Miki, Good idea. The lists should now only accept postings from subscribers. Alan Bleasby RFCGR From srogers at itsa.ucsf.edu Wed Jun 16 23:31:29 2004 From: srogers at itsa.ucsf.edu (Stephen Rogers) Date: Wed, 16 Jun 2004 16:31:29 -0700 Subject: [EMBOSS] OS X transeq Error Message-ID: <4B5BBD0A-BFED-11D8-B2ED-000393A36AF6@itsa.ucsf.edu> I am in the process of learning to use Emboss and have encountered an annoying problem. If I use transeq or prettyseq to translate a long (6 kB) sequence, both programs delete a single base pair from my input sequence around bp 2040, causing a frameshift. I have not observed this problem with smaller sequences. I am running Emboss 2.8.0-2 on a Powerbook OS X.3.3 and the installation was performed using Fink. Can anyone on the list shed some light on this problem? Am I limited to dealing with sequences of a certain length when using Emboss? Thanks for any help! ______________________________ Stephen Rogers University of California, San Francisco Howard Hughes Medical Institute and Department of Molecular and Cellular Pharmacology N316 Genentech Hall 600 16th Street San Francisco, CA 94107 tel: 415.476.8712 fax: 415.476.5233 email: srogers at itsa.ucsf.edu http://itsa.ucsf.edu/~srogers/ -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: text/enriched Size: 978 bytes Desc: not available URL: From ableasby at hgmp.mrc.ac.uk Thu Jun 17 07:31:07 2004 From: ableasby at hgmp.mrc.ac.uk (Alan Bleasby) Date: Thu, 17 Jun 2004 08:31:07 +0100 (BST) Subject: [EMBOSS] OS X transeq Error Message-ID: <200406170731.i5H7V7Wk018088@bromine.hgmp.mrc.ac.uk> I thought that one had been fixed. I'll take a look. It is specific to MacOSX. If you make sure that no line in your sequence file is over 2000 characters long then the problem will go away. HTH Alan Bleasby RFCGR From gwilliam at hgmp.mrc.ac.uk Fri Jun 25 10:30:14 2004 From: gwilliam at hgmp.mrc.ac.uk (Gary Williams, Tel 01223 494522) Date: Fri, 25 Jun 2004 11:30:14 +0100 Subject: [EMBOSS] David Price Message-ID: <40DBFEB6.8020802@hgmp.mrc.ac.uk> David Price has sent a couple of requests for help on installing EMBOSS and a problem with Jemboss, to the EMBOSS mailing lists. His e-mail address was not included in the header of his messages. In order to reply to him, we require his e-mail address. Could he please e-mail 'emboss-bug at embnet.org' with his details? Thanks, Gary -- Gary Williams MRC Rosalind Franklin Centre for Genomics Research Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SB, UK Tel: +44 1223 494522 Fax: +44 1223 494512 E-mail: gwilliam at rfcgr.mrc.ac.uk Web: http://www.rfcgr.mrc.ac.uk From tothg at abc.hu Tue Jun 29 16:31:15 2004 From: tothg at abc.hu (Gabor Toth) Date: Tue, 29 Jun 2004 18:31:15 +0200 Subject: [EMBOSS] wrong clustal output format? In-Reply-To: <40DBFEB6.8020802@hgmp.mrc.ac.uk> References: <40DBFEB6.8020802@hgmp.mrc.ac.uk> Message-ID: <200406291831.15942.tothg@abc.hu> Hi, The clustal (= aln) output format ('-osformat clustal') seems to be outdated. EMBOSS programs write multiple alignments in Clustal W(1.4) format where the sequences are tabulated into 10-residue columns. The extra spaces prevent e.g. seaview from correctly reading the alignment. Recent Clustal W versions write only two columns per line, one for the sequence identifier and another one for the sequence. It would make sense if EMBOSS adhered to the current ALN format in its 'clustal' output while retaining the ability to read both formats (as it correctly does). Regards, Gabor Toth