From owner-bio-srs@hgmp.mrc.ac.uk Wed Jan 16 10:02:35 2002 Return-Path: Received: from localhost (localhost [127.0.0.1]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id 7FA6617B8A for ; Wed, 16 Jan 2002 10:02:32 +0000 (GMT) Received: from localhost (localhost [127.0.0.1]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id BC2FA17B84 for ; Wed, 16 Jan 2002 10:02:28 +0000 (GMT) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6015) id 2507317B7B; Wed, 16 Jan 2002 10:02:26 +0000 (GMT) Received: from localhost (localhost [127.0.0.1]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id D5D6417B79 for ; Wed, 16 Jan 2002 07:55:51 +0000 (GMT) Received: from saturn.nig.ac.jp (saturn.nig.ac.jp [133.39.3.5]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id E036117B73 for ; Wed, 16 Jan 2002 07:55:48 +0000 (GMT) Received: from gemini.nig.ac.jp (gemini [133.39.192.5]) by saturn.nig.ac.jp (8.9.3+3.2W/3.7Wpl2) with ESMTP id QAA16259 for ; Wed, 16 Jan 2002 16:55:45 +0900 (JST) Received: (from news@localhost) by gemini.nig.ac.jp (8.9.3+3.2W/3.7Wpl2) id QAA04806 for bionet-software-srs@net.bio.net; Wed, 16 Jan 2002 16:55:45 +0900 (JST) To: bionet-software-srs@net.bio.net From: "Tomohiro Koike" Newsgroups: bionet.software.srs Subject: Problem on SRS6.1.3 with GenBank Organization: National Institute of Genetics, Japan. Message-ID: Mime-Version: 1.0 Content-Type: text/plain; charset="iso-2022-jp" Content-Transfer-Encoding: 7bit X-Trace: gemini.nig.ac.jp 1011167744 4804 133.39.201.73 (16 Jan 2002 07:55:44 GMT) X-Complaints-To: news@gemini.nig.ac.jp NNTP-Posting-Date: 16 Jan 2002 07:55:44 GMT X-Newsreader: Microsoft Outlook Express 5.50.4522.1200 X-MimeOLE: Produced By Microsoft MimeOLE V5.50.4522.1200 Date: Wed, 16 Jan 2002 10:02:26 +0000 (GMT) Sender: owner-bio-srs@hgmp.mrc.ac.uk Precedence: bulk Hello all, We are using SRS, and now trying to upgrade our system to version 6.1.3. But unfortunately, we found 6.1.3 always failed to search any keywords with GenBank or DDBJ data as target library. And we also found this problem is not only on our particular environment. There are some public SRS 6.1.3 servers on the net, but as far as we know, several of them have same problem. Following two servers are a part of them. genius.embnet.dkfz-heidelberg.de/menu/cgi-bin/srs/wgetz srs.im.ac.cn/srs6bin/cgi-bin/wgetz When we try to search a keyword, say "1111", with selecting GenBank (or DDBJ) as target library, SRS's cgi returns an error message like this: error library ID does not exist no library with ID "19767" is defined We are investigating this problem, and so far, we found several facts; a) size of data When we index DDBJ dataset, indexing would finish without any error log message, but searches would fail. When we cut DDBJ dataset into half, both half can successfully be indexed and searched. This fact suggests that this problem may depends on size of input data, or index, rather than data quality. b) field to search As far as we tested so far, the only field that can cause the problem is "FtDescription". Other fields look ok, but "Quick Search" includes FtDescription, thus it doesn't. Any work around, suggestions, comments are welcome. Thank you, Tomohiro Koike DNA Databank of Japan From owner-bio-srs@hgmp.mrc.ac.uk Wed Jan 16 10:02:42 2002 Return-Path: Received: from localhost (localhost [127.0.0.1]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id 7526917B88 for ; Wed, 16 Jan 2002 10:02:40 +0000 (GMT) Received: from localhost (localhost [127.0.0.1]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id A847D17B8C for ; Wed, 16 Jan 2002 10:02:32 +0000 (GMT) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6015) id 422CA17B85; Wed, 16 Jan 2002 10:02:31 +0000 (GMT) Received: from localhost (localhost [127.0.0.1]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id B11F917B21 for ; Tue, 15 Jan 2002 14:59:00 +0000 (GMT) Received: from deluge.umist.ac.uk (deluge.umist.ac.uk [130.88.120.66]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id 2541817B18 for ; Tue, 15 Jan 2002 14:58:59 +0000 (GMT) Received: from dailyplanet.umist.ac.uk ([130.88.120.68] helo=news.umist.ac.uk) by deluge.umist.ac.uk with smtp (Exim 3.33 #1) id 16QV37-00074h-00 for bionet-software-srs@net.bio.net; Tue, 15 Jan 2002 14:58:53 +0000 To: bionet-software-srs@net.bio.net From: "iDEAL'02" Newsgroups: bionet.software.srs Subject: CFP: IDEAL'02 3rd International Conference on Intelligent Data Engineering & Automated Learning X-Priority: 3 X-MSMail-Priority: Normal X-Newsreader: Microsoft Outlook Express 6.00.2600.0000 X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2600.0000 Message-ID: <3c444832$1@news.umist.ac.uk> X-Trace: 15 Jan 2002 15:18:10 GMT, llama.ee.umist.ac.uk X-Scanner: exiscan *16QV37-00074h-00*MNw5aaE3HfM* (UMIST, Manchester, UK.) Date: Wed, 16 Jan 2002 10:02:31 +0000 (GMT) Sender: owner-bio-srs@hgmp.mrc.ac.uk Precedence: bulk ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ IDEAL 2002, Third International Conference on Intelligent Data Engineering and Automated Learning ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Call for Papers 12-14 August, 2002 Manchester, UK http://ideal02.ee.umist.ac.uk ideal@umist.ac.uk IDEAL is a biennial conference dedicated to emerging and challenging topics in intelligent data analysis and engineering and their associated learning paradigms. Following the highly successful IDEAL'98 and IDEAL'00 conferences held in Hong Kong, the third conference in this series will bring together researchers, scientists and practitioners from all over the world to present their findings, to exchange ideas, and to share their successes. IDEAL is an ideal forum for revealing and developing the latest theoretical advances and practical applications in intelligent data engineering and automated learning. The main themes of the conference are Document Analysis and Management, Data Mining and Fusion, Financial Engineering, Agents, and Bioinformatics. IDEAL'02 will be held at UMIST (University of Manchester Institute of Science and Technology), Manchester, UK, a university with a reputation of innovation and a long history in leading research and development. Manchester is the birthplace of the industrial revolution, the computer revolution and many developments in artificial intelligence. The conference is organised in collaboration with the IEEE Neural Networks Council. Conference Topics Technical areas include, but are not limited to: DOCUMENT ANALYSIS: * Text and Web Mining * Document Classification and Clustering * Indexing and Retrieval Methods * Knowledge Discovery * Probabilistic and Statistical Learning * Pattern Recognition DATA MINING: * Sequential and Time series Analysis * Multivariate Data Visualisation * Internet and Multimedia Database * Data Warehouse and E-organisations * Multi-model Data Analysis * Medical Diagnosis and Database FINANCIAL ENGINEERING: * Portfolio Management * Risk Analysis and Management * Fraud Detection * Modelling and Forecasting * Electronic Commerce * Statistics and Econometrics LEARNING AND AGENTS: * Neural Networks and Emergent Systems * Evolutionary Computation * Fuzzy Logic * Multi-agents Systems * Autonomous Agents * Agent Architectures and Protocols * Collaborative and Collective learning * Evolution, Learning and Adaptation BIOINFORMATICS: * Protein Structural Prediction * Microarray Informatics * Gene Prediction * Novel Computational Algorithms and Tools Important Dates: *Submission of Paper 1 March 2002 *Notification of Acceptance 20 April 2002 *Final Camera-Ready Paper 1 June 2002 Submission and Publication: Authors are invited to submit manuscripts written in English. Papers should be in one column format and single-spaced format. Text and illustrations should fill, but not extend an area of 122 mm x 193 mm. Please use 10-point Times-Roman font. Each paper should not exceed six pages including figures and references. Authors can either submit four copies of their manuscript to the IDEAL 2002 Secretariat (contact address shown below) or submit a postscript or PDF file of their paper by email (ideal@umist.ac.uk). All submissions will be refereed by experts in the field based on originality, significance, quality and clarity. The accepted papers will be included in IDEAL 2002 Proceedings to be published by Springer-Verlag in the prestigious Lecture Notes in Computer Science series. Camera-Ready papers must comply with the format of LNCS/LNAI proceedings (). Contact Information: IDEAL 2002 Secretariat Dept. of Electrical Engineering and Electronics UMIST PO Box 88 Manchester, M60 1QD, England Fax: +44 (0) 161 200 4784 Email: ideal@umist.ac.uk IDEAL 2002 People International Advisory Committee: Lei Xu, Chinese University of Hong Kong (Chair) Yaser Abu-Mostafa, CALTECH, USA Shun-ichi Amari, RIKEN, Japan Michael Dempster, University of Cambridge, UK Nick Jennings, University of Southampton, UK Erkki Oja, Helsinki University of Technology, Finland Burkhard Rost, Columbia University, USA Programme Committee: Nigel Allinson, UMIST, UK (Chair) Jim Austin, University of York, UK Hamid Bolouri, University of Hertfordshire, UK Max Bramer, University of Portsmouth, UK Laiwan Chan, Chinese University of Hong Kong Tom Downs, University of Queensland, Australia Colin Fyfe, University of Paisley, UK Joydeep Ghosh, University of Texas, USA Tony Holden, University of Cambridge, UK Simon Hubbard, UMIST, UK David Jones, University College London (UCL), UK Samuel Kaski, Helsinki University of Technology, Finland John Keane, UMIST, UK Martin Kersten, CWI Amstedam, Netherlands Irwin King, Chinese University of Hong Kong Chris Kirkham, AXEON Ltd, Scotland, UK Jimmy Lee, Chinese University of Hong Kong Kwong S. Leung, Chinese University of Hong Kong Malik Magdon-Ismail, Rensselaer Polytechnic Institute, USA Luc Moreau, University of Southampton, UK Jose Principe, University of Florida, USA Omer Rana, University of Wales, Cardiff, UK Vic Rayward-Smith, University of East Anglia, UK Jennie Si, Arizona State University, USA Ben Stapley, UMIST, UK Atsuhiro Takasu, National Institute of Informatics, Japan Marc van Hulle, K. U. Leuven, Belgium Lipo Wang, Nanyan Technological University, Singapore Olaf Wolkenhauer, UMIST, UK Andy Wright, BAE Systems, UK Xin Yao, University of Birmingham, UK Xinfeng Ye, University of Auckland, New Zealand Hujun Yin, UMIST, UK Hans-Georg Zimmermann, Siemens, Germany Organising Committee: Hujun Yin, UMIST (Chair) Nigel Allinson, UMIST Richard Freeman, UMIST Simon Hubbard, UMIST John Keane, UMIST Asia Liaison: Yiu-ming Cheung, Hong Kong Baptist University America Liaison: Malik Magdon-Ismail, Rensselaer Polytechnic Institute, USA From owner-bio-srs@hgmp.mrc.ac.uk Tue Jan 22 12:38:57 2002 Return-Path: Received: from localhost (localhost [127.0.0.1]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id 8689717B36 for ; Tue, 22 Jan 2002 12:38:55 +0000 (GMT) Received: from localhost (localhost [127.0.0.1]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id 05C1F17B37 for ; Tue, 22 Jan 2002 12:38:49 +0000 (GMT) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6015) id B626517B2A; Tue, 22 Jan 2002 12:38:46 +0000 (GMT) Received: from localhost (localhost [127.0.0.1]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id 1D6C417ABE for ; Mon, 21 Jan 2002 17:02:11 +0000 (GMT) Received: from rutgers.rutgers.edu (rutgers.edu [165.230.4.76]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id AE35A17ADB for ; Mon, 21 Jan 2002 17:01:53 +0000 (GMT) Received: from resu1.ulb.ac.be (resu1.ulb.ac.be [164.15.59.200]) by rutgers.rutgers.edu (8.8.8/8.8.8) with ESMTP id MAA09800 for ; Mon, 21 Jan 2002 12:01:51 -0500 (EST) Received: from snic.vub.ac.be (snic.ulb.ac.be [164.15.128.20]) by resu1.ulb.ac.be (8.8.8/3.17.1.ap (resu)) id RAA08917; Mon, 21 Jan 2002 17:58:51 +0100 (MET) for Received: (news@localhost) by snic.vub.ac.be (8.9.3/%I%.0.ap (snic.test)) id SAA23138; Mon, 21 Jan 2002 18:01:38 +0100 (MET) for bionet-software-srs@moderators.isc.org To: bionet-software-srs@moderators.isc.org From: Guy Bottu Newsgroups: bionet.software.srs Subject: Re: Problem on SRS6.1.3 with GenBank Organization: Belgian EMBnet Node Message-ID: References: X-Trace: snic.vub.ac.be 1011632498 22378 134.184.15.23 (21 Jan 2002 17:01:38 GMT) X-Complaints-To: usenet@snic.vub.ac.be NNTP-Posting-Date: 21 Jan 2002 17:01:38 GMT User-Agent: tin/1.4.3-20000502 ("Marian") (UNIX) (SunOS/5.7 (sun4u)) Date: Tue, 22 Jan 2002 12:38:46 +0000 (GMT) Sender: owner-bio-srs@hgmp.mrc.ac.uk Precedence: bulk I remember we had similar problems with EMBL under SRS 6.0. The cause being that the FtDescription index file grows beyond the limit of 2Gbyte. SRS 6.1.3 however should be able to manage big index files without problem. Is there maybe a problem with your operating system ? Guy Bottu From owner-bio-srs@hgmp.mrc.ac.uk Thu Jan 24 11:05:59 2002 Return-Path: Received: from localhost (localhost [127.0.0.1]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id C43D317A86 for ; Thu, 24 Jan 2002 11:05:58 +0000 (GMT) Received: from localhost (localhost [127.0.0.1]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id F30A017ACB for ; Thu, 24 Jan 2002 11:05:53 +0000 (GMT) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6015) id 648AF17AB6; Thu, 24 Jan 2002 11:05:52 +0000 (GMT) Received: from localhost (localhost [127.0.0.1]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id AF6E617B4F for ; Wed, 23 Jan 2002 12:21:24 +0000 (GMT) Received: from chx400.switch.ch (chx400.switch.ch [130.59.10.2]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id CB67A17B43 for ; Wed, 23 Jan 2002 12:21:21 +0000 (GMT) Received: from vivaldi.belnet.be ([193.190.198.2]) by chx400.switch.ch with esmtp (Exim 3.20 #1) id 16TMP2-0000Gq-00 for bionet-software-srs@moderators.isc.org; Wed, 23 Jan 2002 13:21:21 +0100 Received: from naxos.belnet.be (naxos6.ipv6.belnet.be [3ffe:80b0:0:1:a00:20ff:fe95:e088]) by vivaldi.belnet.be (8.10.2/8.10.2) with ESMTP id g0NCLJt18634 for ; Wed, 23 Jan 2002 13:21:20 +0100 (MET) Received: (from news@localhost) by naxos.belnet.be (8.9.3+Sun/8.9.3) id NAA10643 for bionet-software-srs@moderators.isc.org; Wed, 23 Jan 2002 13:21:19 +0100 (MET) To: bionet-software-srs@moderators.isc.org From: Przemko Tylzanowski Newsgroups: bionet.software.srs,bionet.software Subject: Complex query retrieval question Organization: KULeuvenNet Message-ID: <3C4EAA7E.2842EADA@med.kuleuven.ac.be> Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Trace: naxos.belnet.be 1011788479 10640 134.58.127.12 (23 Jan 2002 12:21:19 GMT) X-Complaints-To: abuse@belnet.be NNTP-Posting-Date: Wed, 23 Jan 2002 12:21:19 +0000 (UTC) X-Mailer: Mozilla 4.78 [en] (WinNT; U) X-Accept-Language: en Cache-Post-Path: seven.kulnet.kuleuven.ac.be!unknown@joint.med.kuleuven.ac.be X-Cache: nntpcache 2.4.0b5 (see http://www.nntpcache.org/) Date: Thu, 24 Jan 2002 11:05:52 +0000 (GMT) Sender: owner-bio-srs@hgmp.mrc.ac.uk Precedence: bulk Hi! Long time ago existed a program called TargetFinder- it was used to identify sequences of interest (e.g. targets for transcription factors) in promoters. The superiority of that program over EPD was that it was not limited to 600bp of the promoter. Anyway, italians took it offline (after publishing it!). So, I am stuck now. What I would like to do is the following. Identify in the GenBank (or EMBL- does not matter) all sequences containing promoters, enhancers and/or sequences upstream of TATA of mouse or human origin (at this point forget about TATA-less). This bit is easy. I can do it using SRS (funny part is- it will work on the server in England but not Brussels...). But here problems start. What I get as an output is the Feature Sequence (I ask for it) but also the rest of the gene. In cases of large genomic sequences this is VERY PAINFUL... What I would like to do is yo extract from these initial hits (between 2000-4500 depending on the selection of databases) ONLY the sequences containing the promoter part (IT WAS POSSIBLE IN SRS4- command line). There I could say- get me the feature and all sequences that are -2000 and +100 from it. Then I would like to build a database and then run Findpatterns or something like that. So, I guess I need a combination of SRS and GCG/EMBOSS. So, HOW DO I DO IT IN SRS6? I know that I could probably write something in PERL, the problem is I don't really know it. Any suggestions, solutions are welcome! Przemko -- Przemko Tylzanowski Ph.D. LSD & Joint O & N University of Leuven Herestraat 49 3000 Leuven Belgium phone: (32-16)34-61-96 fax : (32-16)34-62-00