From owner-acedb@hgmp.mrc.ac.uk Thu Nov 2 15:22:08 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 775B017BC4; Thu, 2 Nov 2000 15:22:05 +0000 (GMT) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6019) id 36BD217BC6; Thu, 2 Nov 2000 15:21:55 +0000 (GMT) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6024) id B70C117A82; Thu, 2 Nov 2000 13:42:44 +0000 (GMT) Received: from briar.org (backdraft.briar.org [192.207.123.123]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id F1337415F0 for ; Thu, 2 Nov 2000 13:42:21 +0000 (GMT) Received: (from smap@localhost) by briar.org (8.9.1b+Sun/8.6.12) id IAA27687 for ; Thu, 2 Nov 2000 08:42:01 -0500 (EST) X-Authentication-Warning: backdraft.briar.org: smap set sender to using -f Received: from pat.ccc.nottingham.ac.uk(128.243.40.194) by backdraft via smap (V2.1) id xma027684; Thu, 2 Nov 00 08:41:41 -0500 Received: from oyez.ccc.nottingham.ac.uk ([128.243.241.164] helo=news.nottingham.ac.uk) by nottingham.ac.uk with esmtp (Exim 3.13 #2) id 13rKc3-0005N6-00 for bionet-software-acedb@moderators.isc.org; Thu, 02 Nov 2000 13:41:03 +0000 Received: from news by news.nottingham.ac.uk with local (Exim 1.92 #1) for bionet-software-acedb@moderators.isc.org id 13rKcN-0001Ze-00; Thu, 2 Nov 2000 13:41:23 +0000 To: bionet-software-acedb@moderators.isc.org From: Keith Bradnam Newsgroups: bionet.software.acedb Subject: Use of method class in sequence displays Organization: ACS, The University of Nottingham Message-ID: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Trace: oyez.ccc.nottingham.ac.uk 973172483 6052 128.243.116.150 (2 Nov 2000 13:41:23 GMT) X-Complaints-To: usenet@news.nottingham.ac.uk NNTP-Posting-Date: 2 Nov 2000 13:41:23 GMT X-Sender: keith@thale Date: Thu, 2 Nov 2000 15:21:55 +0000 (GMT) Sender: owner-acedb@hgmp.mrc.ac.uk Precedence: bulk Hi, I'm trying to figure out exactly how the 'Score_bounds' and 'Right_priority' tags work in the method class. I can see the effect of changing them on my sequence displays, but it is quite hard to systematically determine how changing the range for 'Score_bounds' changes the display (particularly when there are several different Method objects for different BLAST treatments). Can anyone offer any help or point me somewhere on the web? Thanks, Keith ~ Keith Bradnam - UK CropNet (http://ukcrop.net) webmaster and ~ Arabidopsis Genome Resource (http://ukcrop.net/agr) developer. ~ ~ Nottingham Arabidopsis Stock Centre, University Park, ~ University of Nottingham, NG7 2RD, UK. Tel: (0115) 951 3091 From owner-acedb@hgmp.mrc.ac.uk Fri Nov 3 15:17:18 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id BB69017BE3; Fri, 3 Nov 2000 15:17:17 +0000 (GMT) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6019) id 4805A17BE1; Fri, 3 Nov 2000 15:17:16 +0000 (GMT) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6024) id 7B26117B42; Fri, 3 Nov 2000 14:12:32 +0000 (GMT) Received: from sprettur.isnet.is (sprettur.isnet.is [193.4.58.19]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id 55421415DA for ; Fri, 3 Nov 2000 14:12:20 +0000 (GMT) Received: from nottingham.ac.uk (pat.ccc.nottingham.ac.uk [128.243.40.194]) by sprettur.isnet.is (8.11.0/8.11.0/isnet) with ESMTP id eA3ECHA57713 for ; Fri, 3 Nov 2000 14:12:17 GMT (envelope-from news@oyez.ccc.nottingham.ac.uk) Received: from oyez.ccc.nottingham.ac.uk ([128.243.241.164] helo=news.nottingham.ac.uk) by nottingham.ac.uk with esmtp (Exim 3.16 #1) id 13rhZJ-0003tl-00 for bionet-software-acedb@moderators.isc.org; Fri, 03 Nov 2000 14:11:45 +0000 Received: from news by news.nottingham.ac.uk with local (Exim 1.92 #1) for bionet-software-acedb@moderators.isc.org id 13rhZf-0005eW-00; Fri, 3 Nov 2000 14:12:07 +0000 To: bionet-software-acedb@moderators.isc.org From: Keith Bradnam Newsgroups: bionet.software.acedb Subject: 4.8 where for art thou? Organization: ACS, The University of Nottingham Message-ID: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Trace: oyez.ccc.nottingham.ac.uk 973260727 21730 128.243.116.150 (3 Nov 2000 14:12:07 GMT) X-Complaints-To: usenet@news.nottingham.ac.uk NNTP-Posting-Date: 3 Nov 2000 14:12:07 GMT X-Sender: keith@thale Date: Fri, 3 Nov 2000 15:17:16 +0000 (GMT) Sender: owner-acedb@hgmp.mrc.ac.uk Precedence: bulk Anyone have any news as to a release date for the UNIX version of release 4.8 (the sockets version)? There seems to be little (new) news these days on the acedb web site. Keith ~ Keith Bradnam - UK CropNet (http://ukcrop.net) webmaster and ~ Arabidopsis Genome Resource (http://ukcrop.net/agr) developer. ~ ~ Nottingham Arabidopsis Stock Centre, University Park, ~ University of Nottingham, NG7 2RD, UK. Tel: (0115) 951 3091 From owner-acedb@hgmp.mrc.ac.uk Fri Nov 3 16:05:52 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 2A28217BE8; Fri, 3 Nov 2000 16:05:51 +0000 (GMT) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6019) id DDD2017AAB; Fri, 3 Nov 2000 16:05:44 +0000 (GMT) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6024) id E023D17AAB; Fri, 3 Nov 2000 15:25:40 +0000 (GMT) Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id 8154B415EE for ; Fri, 3 Nov 2000 15:25:16 +0000 (GMT) Received: (from news@localhost) by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id PAA18927 for bionet-software-acedb@net.bio.net; Fri, 3 Nov 2000 15:25:16 GMT To: bionet-software-acedb@net.bio.net From: Ed Griffiths Newsgroups: bionet.software.acedb Subject: Re: 4.8 where for art thou? Organization: Sanger Centre Message-ID: <3A02D8DB.A7E41E1B@sanger.ac.uk> References: Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Trace: niobium.hgmp.mrc.ac.uk 973265115 18925 193.60.84.177 (3 Nov 2000 15:25:15 GMT) X-Complaints-To: news@net.bio.net NNTP-Posting-Date: 3 Nov 2000 15:25:15 GMT X-Mailer: Mozilla 4.7 [en] (X11; I; OSF1 V4.0 alpha) X-Accept-Language: en Date: Fri, 3 Nov 2000 16:05:44 +0000 (GMT) Sender: owner-acedb@hgmp.mrc.ac.uk Precedence: bulk Keith, > Anyone have any news as to a release date for the UNIX version of > release 4.8 (the sockets version)? You can get a stable development version (I guess you'd call this a beta-release) to try out from: ftp://ftp.sanger.ac.uk/pub/acedb/Sanger-release.2000_07_14.tar.gz have you tried this ? > There seems to be little (new) news these days on the acedb web site. Yup, I'm afraid that's true, we have been really busy getting acedb 4_8 in to shape to be a formal public release (it will be known as acedb 4_9). We are planning some big improvements to the web site and now have an extra body to help us make those improvements (John Sturdy, jcgs@sanger.ac.uk). I collected a wish-list for improvements to the web site from the acedb 2000 conference in Vancouver, but if anyone has any suggestions they'd like to make then please email me and John. cheers Ed ------------------------------------------------------------------------ | Ed Griffiths, Acedb development, Informatics Group, | | The Sanger Centre, Wellcome Trust Genome Campus, | | Hinxton, Cambridge CB10 1SA, UK | | | | email: edgrif@sanger.ac.uk URL: http://www.sanger.ac.uk/Users/edgrif | | Tel: +44-1223-494780 Fax: +44 1223 494919 | ------------------------------------------------------------------------ From owner-acedb@hgmp.mrc.ac.uk Wed Nov 15 09:41:07 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 1202117B98; Wed, 15 Nov 2000 09:41:06 +0000 (GMT) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6019) id 741B517B96; Wed, 15 Nov 2000 09:41:05 +0000 (GMT) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 60001) id AF13C17AA6; Tue, 14 Nov 2000 23:42:47 +0000 (GMT) To: bionet-software-acedb@net.bio.net From: rwcitek@uci.edu (Robert Citek) Newsgroups: bionet.software.acedb Subject: Re: Pb starting gifaceserver Organization: BIOSCI/MRC Human Genome Mapping Project Resource Centre Message-ID: <3.0.1.32.20001114174150.006d2e44@earthlink.net> X-Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6024) id 7344C17AA2; Tue, 14 Nov 2000 23:42:44 +0000 (GMT) X-Received: from taumsauk.cs.wustl.edu (cs.wustl.edu [128.252.165.15]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id EE59C415DC for ; Tue, 14 Nov 2000 23:42:38 +0000 (GMT) X-Received: from rica.cs.wustl.edu (dhcp6.cs.wustl.edu [128.252.165.220]) by taumsauk.cs.wustl.edu (8.9.1/8.9.1) with SMTP id RAA20114; Tue, 14 Nov 2000 17:42:27 -0600 (CST) X-Sender: rwcitek@earthlink.net X-Mailer: Windows Eudora Light Version 3.0.1 (32) X-To: acedb@net.bio.net X-Cc: coulier@marseille.inserm.fr Date: Wed, 15 Nov 2000 09:41:05 +0000 (GMT) Sender: owner-acedb@hgmp.mrc.ac.uk Precedence: bulk Hello François, Were you able to ever get gifaceserver running? If not, you might try starting the portmap server before starting gifaceserver. To do this in linux, type the following as root: # /etc/rc.d/init.d/portmap start Hope this helps (although this is more than a month later.) - Robert --- From owner-acedb@hgmp.mrc.ac.uk Mon Nov 20 14:54:09 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 967B217AEC; Mon, 20 Nov 2000 14:54:07 +0000 (GMT) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6019) id 1B3A617AEA; Mon, 20 Nov 2000 14:54:01 +0000 (GMT) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6024) id 9F03417A61; Fri, 17 Nov 2000 21:07:32 +0000 (GMT) Received: from sprettur.isnet.is (sprettur.isnet.is [193.4.58.19]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id C2A6F415D5 for ; Fri, 17 Nov 2000 21:07:26 +0000 (GMT) Received: from mail.deja.com (mail.deja.com [64.57.170.34]) by sprettur.isnet.is (8.11.1/8.11.0/isnet) with ESMTP id eAHL7OA37928 for ; Fri, 17 Nov 2000 21:07:24 GMT (envelope-from news@dejanews.com) Received: from nnrp1.deja.com (nnrp1.deja.com [10.12.2.16]) by mail.deja.com (8.8.7/8.8.5) with ESMTP id PAA29792 for ; Fri, 17 Nov 2000 15:07:22 -0600 Received: (news@localhost) by nnrp1.deja.com (8.7.6/8.6.12) id PAA06591; Fri, 17 Nov 2000 15:07:14 -0600 To: bionet-software-acedb@moderators.isc.org From: JRSchwartz@lbl.gov Newsgroups: bionet.software.acedb Subject: Update sequence? Organization: Deja.com - Before you buy. Message-ID: <8v46m2$6du$1@nnrp1.deja.com> X-Article-Creation-Date: Fri Nov 17 21:07:20 2000 GMT X-Http-User-Agent: Mozilla/4.5 [en] (X11; I; SunOS 5.7 sun4u) X-Http-Proxy: 1.0 x56.deja.com:80 (Squid/1.1.22) for client 131.243.56.231 X-MyDeja-Info: XMYDJUIDtheo5 Date: Mon, 20 Nov 2000 14:54:01 +0000 (GMT) Sender: owner-acedb@hgmp.mrc.ac.uk Precedence: bulk Hi all, I am using acedb for annotation. I was wondering if there is a way to update the dna sequence for a clone, to add more to it, while preserving the existing annotations. I have done it in the past by hand, changing all the froms and tos, but it is a royal pain. Is there a nice way to do that? If I just delete the DNA sequence and add the new one, will the annotation be automatically updated? Thanks. Jody -- Jody Schwartz, Sent via Deja.com http://www.deja.com/ Before you buy. From owner-acedb@hgmp.mrc.ac.uk Tue Nov 21 09:41:29 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 69DB117B19; Tue, 21 Nov 2000 09:41:27 +0000 (GMT) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6019) id 61E1A17B1A; Tue, 21 Nov 2000 09:41:24 +0000 (GMT) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6024) id 0292C17AF4; Mon, 20 Nov 2000 16:42:34 +0000 (GMT) Received: from moderated.news.pipex.net (moderated.news.pipex.net [158.43.192.79]) by mercury.hgmp.mrc.ac.uk (Postfix) with SMTP id C1F3F415DF for ; Mon, 20 Nov 2000 16:42:21 +0000 (GMT) Received: (qmail 13244 invoked by alias); 20 Nov 2000 16:42:20 -0000 Received: (qmail 13240 invoked from network); 20 Nov 2000 16:42:20 -0000 Received: from mailsrv1.sanger.ac.uk (193.62.207.19) by moderated.news.pipex.net with SMTP; 20 Nov 2000 16:42:20 -0000 Received: from griffin.sanger.ac.uk (rd@griffin-e7 [193.62.207.76]) by mailsrv1.sanger.ac.uk (8.11.1/8.11.1) with ESMTP id eAKGgJB04082; Mon, 20 Nov 2000 16:42:19 GMT From: Richard Durbin Received: (from rd@localhost) by griffin.sanger.ac.uk (8.8.7/8.8.7) id QAA14589; Mon, 20 Nov 2000 16:42:18 GMT Message-Id: <200011201642.QAA14589@griffin.sanger.ac.uk> To: JRSchwartz@lbl.gov, bionet-software-acedb@moderators.isc.org Subject: Re: Update sequence? Newsgroups: bionet.software.acedb Date: Tue, 21 Nov 2000 09:41:24 +0000 (GMT) Sender: owner-acedb@hgmp.mrc.ac.uk Precedence: bulk > I am using acedb for annotation. I was wondering if there is a way to > update the dna sequence for a clone, to add more to it, while preserving > the existing annotations. I have done it in the past by hand, changing > all the froms and tos, but it is a royal pain. Is there a nice way to > do that? If I just delete the DNA sequence and add the new one, will > the annotation be automatically updated? Hi Jody, Sadly the answer to the last question is no. Not unless the coordinates remain the same. You have to keep track and remap coordinates yourself. There is some code that does some of this, but as so often it is not complete and doesn't do it right, so can't be exposed to the world. Richard From owner-acedb@hgmp.mrc.ac.uk Tue Nov 21 09:41:29 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id A8AA817B1B; Tue, 21 Nov 2000 09:41:26 +0000 (GMT) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6019) id 0DCC717B19; Tue, 21 Nov 2000 09:41:23 +0000 (GMT) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 60001) id 2ED4917AED; Mon, 20 Nov 2000 15:30:30 +0000 (GMT) To: bionet-software-acedb@net.bio.net From: Eric.Delorme@clermont.in2p3.fr (DELORME Eric) Newsgroups: bionet.software.acedb Subject: ACEDB BALST and kill pid Organization: LPC CNRS Message-ID: <3A195FBB.5CFCB788@clermont.in2p3.fr> MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6024) id 37D4E17AE8; Mon, 20 Nov 2000 15:30:27 +0000 (GMT) X-Received: from clrhp04.in2p3.fr (clrhp04.in2p3.fr [193.48.80.80]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id 103A3415D5 for ; Mon, 20 Nov 2000 15:30:18 +0000 (GMT) X-Received: from clermont.in2p3.fr (IDENT:delorme@clrpc138.in2p3.fr [193.48.80.24]) by clrhp04.in2p3.fr (8.9.3/8.9.3/In2p3) with ESMTP id QAA29654 for ; Mon, 20 Nov 2000 16:30:17 +0100 (MET) X-Mailer: Mozilla 4.72 [fr] (X11; U; Linux 2.2.12-20 i686) X-Accept-Language: en X-To: acedb@net.bio.net Date: Tue, 21 Nov 2000 09:41:23 +0000 (GMT) Sender: owner-acedb@hgmp.mrc.ac.uk Precedence: bulk Hello UNDER LINUX (red-hat 6.1) When i launch acedb and make a blast the application close at the end of the blast. UNDER SUN When i launch acedb and make a blast, only the window who say wait 5 minutes close at the end of the blast. Apparently the reason is the code follow. lines 193 of blast_search # Finally, mv $2.b to $2.out and signal acedb mv $2.b $2.out if ($1 != "0") kill -USR1 $1 My request is UNDER LINUX how to close a window and only a window, not the application Thanks ... 8-) --- From owner-acedb@hgmp.mrc.ac.uk Tue Nov 21 15:58:24 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 0A9FB17B39; Tue, 21 Nov 2000 15:58:21 +0000 (GMT) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6019) id A607E17B35; Tue, 21 Nov 2000 15:58:16 +0000 (GMT) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6024) id 35E2617B33; Tue, 21 Nov 2000 15:14:29 +0000 (GMT) Received: from dns2.nrc.ca (dns2.nrc.ca [132.246.161.200]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id D472A415EB for ; Tue, 21 Nov 2000 15:14:10 +0000 (GMT) Received: (from news@localhost) by dns2.nrc.ca (8.9.3+Sun/8.9.0) id KAA00250; Tue, 21 Nov 2000 10:13:59 -0500 (EST) To: bionet-software-acedb@net.bio.net From: Mark Wilkinson Newsgroups: bionet.software.acedb Subject: quick Y/N question (Ed? Richard? this might be for you...) Organization: PBI-NRC Message-ID: <3A1A8EB9.9A4319B@gene.pbi.nrc.ca> Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 4.72 [en] (X11; U; Linux 2.2.14-5.0 i686) X-Accept-Language: en Date: Tue, 21 Nov 2000 15:58:16 +0000 (GMT) Sender: owner-acedb@hgmp.mrc.ac.uk Precedence: bulk Hi all! does Acedb strictly follow the guidelines for GFF2 as described on the sanger website? I am only asking as I have just modified the BioPerl Feature modules such that they dump and read strictly compliant GFF2... (or at least, as "strictly" as I can understand from my own reading of the format overview...). I am just wondering if this will facilitate movement between Ace and BioPerl, or if Ace uses its own flavour of GFF... Cheers all! M -- --- Dr. Mark Wilkinson Bioinformatics Group National Research Council of Canada Plant Biotechnology Institute 110 Gymnasium Place Saskatoon, SK Canada From owner-acedb@hgmp.mrc.ac.uk Tue Nov 21 15:58:24 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id B667F17B35; Tue, 21 Nov 2000 15:58:22 +0000 (GMT) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6019) id 3256017A73; Tue, 21 Nov 2000 15:58:15 +0000 (GMT) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6024) id 8EA8017B12; Tue, 21 Nov 2000 11:18:25 +0000 (GMT) Received: from chx400.switch.ch (chx400.switch.ch [130.59.10.2]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id D4F07415D5 for ; Tue, 21 Nov 2000 11:18:01 +0000 (GMT) Received: from pat.ccc.nottingham.ac.uk ([128.243.40.194] helo=nottingham.ac.uk) by chx400.switch.ch with esmtp (Exim 3.15 #3) id 13yBR3-0004Kr-00 for bionet-software-acedb@moderators.isc.org; Tue, 21 Nov 2000 12:18:01 +0100 Received: from oyez.ccc.nottingham.ac.uk ([128.243.241.164] helo=news.nottingham.ac.uk) by nottingham.ac.uk with esmtp (Exim 3.16 #1) id 13yBQM-0001o5-00 for bionet-software-acedb@moderators.isc.org; Tue, 21 Nov 2000 11:17:18 +0000 Received: from news by news.nottingham.ac.uk with local (Exim 1.92 #1) for bionet-software-acedb@moderators.isc.org id 13yBQz-0003Ry-00; Tue, 21 Nov 2000 11:17:57 +0000 To: bionet-software-acedb@moderators.isc.org From: Keith Bradnam Newsgroups: bionet.software.acedb Subject: Re: Update sequence? Organization: ACS, The University of Nottingham Message-ID: References: <8v46m2$6du$1@nnrp1.deja.com> Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Trace: oyez.ccc.nottingham.ac.uk 974805477 13264 128.243.116.150 (21 Nov 2000 11:17:57 GMT) X-Complaints-To: usenet@news.nottingham.ac.uk NNTP-Posting-Date: 21 Nov 2000 11:17:57 GMT To: JRSchwartz@lbl.gov X-Sender: keith@thale Date: Tue, 21 Nov 2000 15:58:15 +0000 (GMT) Sender: owner-acedb@hgmp.mrc.ac.uk Precedence: bulk On 20 Nov 2000 JRSchwartz@lbl.gov wrote: > > > Hi all, > > I am using acedb for annotation. I was wondering if there is a way to > update the dna sequence for a clone, to add more to it, while preserving > the existing annotations. I have done it in the past by hand, changing > all the froms and tos, but it is a royal pain. Is there a nice way to > do that? If I just delete the DNA sequence and add the new one, will > the annotation be automatically updated? DNA sequences are usually specified as 'UNIQUE' objects in most acedb databases, so if you try to read a new DNA sequence as part of an existing Sequence object it should just replace the existing DNA sequence but not change anything else. E.g. if your sequence/clone object in your database is something like: Sequence : "EMBL:AB006697" DNA "EMBL:AB006697" 80970 Version "AB006697.1" Database_date "26-OCT-2000" Species "Arabidopsis thaliana" Title "Arabidopsis thaliana genomic DNA, chromosome 5, P1 clone:MAH20." Clone "MAH20" Then all you should have to do is put your new DNA sequence in an ace file with the same name as that which already exists and read this into the database. Keith ~ Keith Bradnam - UK CropNet (http://ukcrop.net) webmaster and ~ Arabidopsis Genome Resource (http://ukcrop.net/agr) developer. ~ ~ Nottingham Arabidopsis Stock Centre, University Park, ~ University of Nottingham, NG7 2RD, UK. Tel: (0115) 951 3091 From owner-acedb@hgmp.mrc.ac.uk Wed Nov 22 09:23:26 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 78BD217AAC; Wed, 22 Nov 2000 09:23:24 +0000 (GMT) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6019) id 04CAD17AA6; Wed, 22 Nov 2000 09:23:20 +0000 (GMT) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 60001) id 74E1B17B4C; Tue, 21 Nov 2000 17:01:48 +0000 (GMT) To: bionet-software-acedb@net.bio.net From: mwilkinson@gene.pbi.nrc.ca (Mark Wilkinson) Newsgroups: bionet.software.acedb Subject: Re: quick Y/N question (Ed? Richard? this might be for you...) Organization: PBI-NRC Message-ID: <3A1AA7C2.C83C2723@gene.pbi.nrc.ca> References: <200011211612.QAA28728@griffin.sanger.ac.uk> MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6024) id A4C6617B4B; Tue, 21 Nov 2000 17:01:33 +0000 (GMT) X-Received: from gene.pbi.nrc.ca (gene.pbi.nrc.ca [204.83.147.150]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id 19A8C415EC for ; Tue, 21 Nov 2000 17:01:03 +0000 (GMT) X-Received: from gene.pbi.nrc.ca (bioinfo.pbi.nrc.ca [204.83.147.151]) by gene.pbi.nrc.ca (8.8.7/8.8.7) with ESMTP id KAA23241; Tue, 21 Nov 2000 10:33:36 -0600 X-Mailer: Mozilla 4.72 [en] (X11; U; Linux 2.2.14-5.0 i686) X-Accept-Language: en X-To: Richard Durbin X-Cc: acedb@hgmp.mrc.ac.uk Date: Wed, 22 Nov 2000 09:23:20 +0000 (GMT) Sender: owner-acedb@hgmp.mrc.ac.uk Precedence: bulk could someone send me a few lines of a GFF2 dump from Acedb so that I can test it against my BioPerl GFF2 parser? Please chose something "tricky" if possible as I would like to give it a thorough testing... thanks! M Richard Durbin wrote: > Acedb is meant to generate strict version 2 GFF if you set the -version 2 > flag with seqfeatures. If it does not, we should either clarify the GFF > specification, or fix acedb. > > Richard -- --- Dr. Mark Wilkinson Bioinformatics Group National Research Council of Canada Plant Biotechnology Institute 110 Gymnasium Place Saskatoon, SK Canada --- From owner-acedb@hgmp.mrc.ac.uk Wed Nov 22 09:23:28 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id B8ADE17AB2; Wed, 22 Nov 2000 09:23:26 +0000 (GMT) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6019) id 89C0717AA1; Wed, 22 Nov 2000 09:23:20 +0000 (GMT) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 60001) id 784C217B40; Tue, 21 Nov 2000 16:13:10 +0000 (GMT) To: bionet-software-acedb@net.bio.net From: rd@sanger.ac.uk (Richard Durbin) Newsgroups: bionet.software.acedb Subject: Re: quick Y/N question (Ed? Richard? this might be for you...) Organization: BIOSCI/MRC Human Genome Mapping Project Resource Centre Message-ID: <200011211612.QAA28728@griffin.sanger.ac.uk> X-Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6024) id 6B5C917B39; Tue, 21 Nov 2000 16:13:08 +0000 (GMT) X-Received: from mailsrv1.sanger.ac.uk (mailsrv1.sanger.ac.uk [193.62.207.19]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id DD40D415EA for ; Tue, 21 Nov 2000 16:12:58 +0000 (GMT) X-Received: from griffin.sanger.ac.uk (rd@griffin [193.60.84.177]) by mailsrv1.sanger.ac.uk (8.11.1/8.11.1) with ESMTP id eALGCnB09997; Tue, 21 Nov 2000 16:12:49 GMT X-Received: (from rd@localhost) by griffin.sanger.ac.uk (8.8.7/8.8.7) id QAA28728; Tue, 21 Nov 2000 16:12:48 GMT X-To: mwilkinson@gene.pbi.nrc.ca X-Cc: acedb@hgmp.mrc.ac.uk Date: Wed, 22 Nov 2000 09:23:20 +0000 (GMT) Sender: owner-acedb@hgmp.mrc.ac.uk Precedence: bulk Acedb is meant to generate strict version 2 GFF if you set the -version 2 flag with seqfeatures. If it does not, we should either clarify the GFF specification, or fix acedb. Richard --- From owner-acedb@hgmp.mrc.ac.uk Thu Nov 23 10:24:32 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 272CC17AD9; Thu, 23 Nov 2000 10:24:31 +0000 (GMT) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6019) id 1594817AD3; Thu, 23 Nov 2000 10:24:28 +0000 (GMT) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 60001) id 9D55117B79; Wed, 22 Nov 2000 23:30:20 +0000 (GMT) To: bionet-software-acedb@net.bio.net From: jayoung@fhcrc.org (Janet Young) Newsgroups: bionet.software.acedb Subject: non-native byte order Organization: BIOSCI/MRC Human Genome Mapping Project Resource Centre Message-ID: Mime-version: 1.0 Content-type: text/plain; charset="US-ASCII" Content-transfer-encoding: 7bit X-Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6024) id C996917B5E; Wed, 22 Nov 2000 23:30:17 +0000 (GMT) X-Received: from fhcrc.org (uluc01.fhcrc.org [140.107.52.11]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id 4531E415EB for ; Wed, 22 Nov 2000 23:30:11 +0000 (GMT) X-Received: from snap.fhcrc.org (snap [140.107.52.19]) by fhcrc.org (8.10.2/8.10.2) with ESMTP id eAMNU9v28099 for ; Wed, 22 Nov 2000 15:30:09 -0800 (PST) X-Received: from [140.107.30.186] ([140.107.30.186]) by snap.fhcrc.org (8.10.2/8.10.2) with ESMTP id eAMNU8m17760 for ; Wed, 22 Nov 2000 15:30:08 -0800 (PST) X-User-Agent: Microsoft-Entourage/9.0.2509 X-To: acedb Date: Thu, 23 Nov 2000 10:24:28 +0000 (GMT) Sender: owner-acedb@hgmp.mrc.ac.uk Precedence: bulk Hi We've moved labs recently and have moved our acedb database to a new server (from OSF1 on an alpha to SunOS 5.7). Now when I start the new database I get // Database has non-native byte-order: swapping (I tried editing and saving but that's not enough to fix it) This doesn't seem to be a problem right now but I just wondered if it leaves us more open to crashes or if it will make queries slow? How could I swap the byte order? thanks Janet ------------------------------------------------------------------- Dr. Janet Young Fred Hutchinson Cancer Research Center 1100 Fairview Avenue N. tel: (206) 667 1471 C3-168 fax: (206) 667 6524 P.O. Box 19024 email: jayoung@fhcrc.org Seattle, WA 98109-1024, USA. --- From owner-acedb@hgmp.mrc.ac.uk Mon Nov 27 17:00:11 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id B949A17B13; Mon, 27 Nov 2000 17:00:04 +0000 (GMT) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6019) id 896BD17B13; Mon, 27 Nov 2000 16:59:56 +0000 (GMT) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6024) id 6B75E17AEC; Mon, 27 Nov 2000 16:32:13 +0000 (GMT) Received: from mailbox2.ucsd.edu (mailbox2.ucsd.edu [132.239.1.54]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id 7F2E2415CF for ; Mon, 27 Nov 2000 16:32:03 +0000 (GMT) Received: from nottingham.ac.uk (pat.ccc.nottingham.ac.uk [128.243.40.194]) by mailbox2.ucsd.edu (8.11.0/8.11.0) with ESMTP id eARGYKf12365 for ; Mon, 27 Nov 2000 08:34:22 -0800 (PST) Received: from oyez.ccc.nottingham.ac.uk ([128.243.241.164] helo=news.nottingham.ac.uk) by nottingham.ac.uk with esmtp (Exim 3.16 #1) id 140RBD-0001NF-00 for bionet-software-acedb@moderators.isc.org; Mon, 27 Nov 2000 16:30:59 +0000 Received: from news by news.nottingham.ac.uk with local (Exim 1.92 #1) for bionet-software-acedb@moderators.isc.org id 140RBx-0004j2-00; Mon, 27 Nov 2000 16:31:45 +0000 To: bionet-software-acedb@moderators.isc.org From: Keith Bradnam Newsgroups: bionet.software.acedb Subject: wormbase scripts Organization: ACS, The University of Nottingham Message-ID: Reply-To: Keith Bradnam Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Trace: oyez.ccc.nottingham.ac.uk 975342705 18166 128.243.116.150 (27 Nov 2000 16:31:45 GMT) X-Complaints-To: usenet@news.nottingham.ac.uk NNTP-Posting-Date: 27 Nov 2000 16:31:45 GMT X-Sender: keith@thale Date: Mon, 27 Nov 2000 16:59:56 +0000 (GMT) Sender: owner-acedb@hgmp.mrc.ac.uk Precedence: bulk Hi, Is there any chance of getting access to the AceBrowser scripts used for Wormbase? I noticed that they use the script 'epic' rather than 'pic' (which comes with the default AceBrowser setup) to display graphical views of sequences. The reason I ask is that I would like to see the mechanics of the 'epic' script as it doesn't crash in some situations whereas the standard 'pic' script does. For instance, if I click on a piece of text information in our AceBrowser displays (for our AGR database) (e.g. the contents of a remark tag) it returns an internal server error. It doesn't seem to do this for remark tags in wormbase. I also get problems when clicking on gene name or loci objects where it tries to display the resulting (textual) information as a graphic. I would also like to see how the new graphical depiction of sequences at the top of the Wormbase sequence report pages are generated. Is this stuff publically accessible anywhere? Should it be? As an aside, I've also noticed that www.wormbase.org seems to be running on acedb 4.8 unlike the sanger version. This results in quite a different depiction of colours, e.g. contrast: http://wormbase.sanger.ac.uk/perl/ace/elegans/misc/epic?class=Sequence&name=B0207.4 http://www.wormbase.org/perl/ace/elegans/misc/epic?class=Sequence&name=B0207.4 The colours on the www.wormbase.org site are quite hard on the eyes. Does this mean that 4.8 is nearly ready for a full release??? Hope someone can help, Keith ~ Keith Bradnam - UK CropNet (http://ukcrop.net) webmaster and ~ Arabidopsis Genome Resource (http://ukcrop.net/agr) developer. ~ ~ Nottingham Arabidopsis Stock Centre, University Park, ~ University of Nottingham, NG7 2RD, UK. Tel: (0115) 951 3091 From owner-acedb@hgmp.mrc.ac.uk Wed Nov 29 14:33:08 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id B23B317B90; Wed, 29 Nov 2000 14:33:07 +0000 (GMT) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6019) id 7F48417A9B; Wed, 29 Nov 2000 14:33:05 +0000 (GMT) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6024) id 7397717B90; Wed, 29 Nov 2000 13:46:59 +0000 (GMT) Received: from sjc3-1.relay.mail.uu.net (sjc3-1.relay.mail.uu.net [199.171.54.122]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id 8A6DB415DC for ; Wed, 29 Nov 2000 13:46:50 +0000 (GMT) Received: from pegasus.csx.cam.ac.uk by sjc3sosrv11.alter.net with ESMTP (peer crosschecked as: pegasus.csx.cam.ac.uk [131.111.8.69]) id QQjrkh03064 for ; Wed, 29 Nov 2000 13:46:44 GMT Received: from news by pegasus.csx.cam.ac.uk with local (Exim 2.05 #1) id 1417ZL-0006Y6-00 for bionet-software-acedb@moderators.isc.org; Wed, 29 Nov 2000 13:46:43 +0000 To: bionet-software-acedb@moderators.isc.org From: Lavinia Hyde Newsgroups: bionet.software.acedb Subject: Errors in acedb documentation? Organization: University of Cambridge, England Message-ID: References: <200011211612.QAA28728@griffin.sanger.ac.uk> Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Sender: lavinia@rigging Date: Wed, 29 Nov 2000 14:33:05 +0000 (GMT) Sender: owner-acedb@hgmp.mrc.ac.uk Precedence: bulk I have just downloaded and installed acedb_4.71. The README that accompanies it states that the acedb distribution directory should contain at least INSTALL, ace4_7x, celegans, and doc directories - however none of these are present. The README also states that there is a further README inside each subdirectory - which there isn't. The documentation archive at http://probe.nalusda.gov:8000/acedocs/index.html no longer exists. Please could someone update the README? regards Lavinia Hyde Department of Medical Genetics Wellcome Trust Centre for Molecular Mechanisms in Disease Wellcome Trust/MRC Building Addenbrooke's Hospital Site Hills Road, Cambridge CB2 2XY Tel. 01223 762671 Fax. 01223 726102 Website: http://www-gene.cimr.cam.ac.uk/todd/ From owner-acedb@hgmp.mrc.ac.uk Thu Nov 30 13:18:40 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 363F717B9C; Thu, 30 Nov 2000 13:18:40 +0000 (GMT) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6019) id A1E9B17B98; Thu, 30 Nov 2000 13:18:38 +0000 (GMT) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6024) id 474F817ACC; Thu, 30 Nov 2000 09:31:03 +0000 (GMT) Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id 170C2415DC for ; Thu, 30 Nov 2000 09:30:58 +0000 (GMT) Received: (from news@localhost) by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id JAA26733 for bionet-software-acedb@net.bio.net; Thu, 30 Nov 2000 09:30:57 GMT To: bionet-software-acedb@net.bio.net From: Ed Griffiths Newsgroups: bionet.software.acedb Subject: Re: Errors in acedb documentation? Organization: Sanger Centre Message-ID: <3A261E50.E8895974@sanger.ac.uk> References: <200011211612.QAA28728@griffin.sanger.ac.uk> Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Trace: niobium.hgmp.mrc.ac.uk 975576656 26731 193.60.84.177 (30 Nov 2000 09:30:56 GMT) X-Complaints-To: news@net.bio.net NNTP-Posting-Date: 30 Nov 2000 09:30:56 GMT X-Mailer: Mozilla 4.7 [en] (X11; I; OSF1 V4.0 alpha) X-Accept-Language: en Date: Thu, 30 Nov 2000 13:18:38 +0000 (GMT) Sender: owner-acedb@hgmp.mrc.ac.uk Precedence: bulk Lavinia, > I have just downloaded and installed acedb_4.71. The README that > accompanies it states that the acedb distribution directory should contain > at least INSTALL, ace4_7x, celegans, and doc directories - however none of > these are present. The README also states that there is a further README > inside each subdirectory - which there isn't. The documentation archive > at http://probe.nalusda.gov:8000/acedocs/index.html no longer exists. > Please could someone update the README? uuuggghhh, a fair cop on all counts. You are not the first to discover that acedb documentation is not brilliant. OK, I'll make a rash promise... the next release level of acedb (4_9) is soon to be released and I'll make sure all README's are up to date for that new release. Really sorry about the state of the docs.... If you have any questions do post them to this newsgroup or mail acedb developers direct at acedb@sanger.ac.uk. cheers Ed ------------------------------------------------------------------------ | Ed Griffiths, Acedb development, Informatics Group, | | The Sanger Centre, Wellcome Trust Genome Campus, | | Hinxton, Cambridge CB10 1SA, UK | | | | email: edgrif@sanger.ac.uk URL: http://www.sanger.ac.uk/Users/edgrif | | Tel: +44-1223-494780 Fax: +44 1223 494919 | ------------------------------------------------------------------------