From owner-genstruc@hgmp.mrc.ac.uk Sat Jul 7 09:04:48 2001 Return-Path: Received: from localhost (localhost [127.0.0.1]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id D399817A5B for ; Sat, 7 Jul 2001 09:04:47 +0100 (BST) Received: from localhost (localhost [127.0.0.1]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id 0425017AB7 for ; Sat, 7 Jul 2001 09:04:45 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 60001) id B1B2317A5B; Sat, 7 Jul 2001 09:04:42 +0100 (BST) To: genstruc@net.bio.net Newsgroups: bionet.genome.gene-structure From: woodss@bcc.orst.edu (Sheri Woods) Subject: Position in Bioinformatics/Biocomputing Date: 4 Jul 2001 01:08:36 +0100 Message-Id: <20010707080442.B1B2317A5B@mercury.hgmp.mrc.ac.uk> Sender: owner-genstruc@hgmp.mrc.ac.uk Precedence: bulk The Center for Gene Research & Biotechnology will hire a Biocomputing Support/Bioinformaticist at either the Ph.D. level or the MS/BS/BA level with research experience (see http://osu.orst.edu/dept/cgrb/positions.html). This is a research and service position in an expanding bioinformatics team. Applicants with backgrounds in either a biological or computer-related field are sought. Required qualifications include strong computer skills across a range of platforms, programming experience (e.g. PERL, C/C++, SQL) for development or application of bioinformatics/biocomputing programs, and broad familiarity with sequence analysis programs, sequence databases and sequence data management. Database and web site development experience is highly desirable. Salary will be commensurate with experience and qualifications. Send letter of interest, curriculum vitae, and names and contact information for three references to: Dr. James Carrington, Director, Center for Gene Research & Biotechnology, Oregon State University, Corvallis, OR 97331-7303. Email (cgrb-info@bcc.orst.edu) or fax (541-737-3045) applications will be accepted. Review of applications will begin on July 15, 2001. OSU is an AA/EOE Employer and has a policy of being responsive to the needs of dual-career couples. --- ===== Moderated bionet.genome.gene-structure ____________________________________________________________ Do You Yahoo!? Get your free @yahoo.co.uk address at http://mail.yahoo.co.uk or your free @yahoo.ie address at http://mail.yahoo.ie From owner-genstruc@hgmp.mrc.ac.uk Thu Jul 26 18:31:31 2001 Return-Path: Received: from localhost (localhost [127.0.0.1]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id 2041B17B01 for ; Thu, 26 Jul 2001 18:31:29 +0100 (BST) Received: from localhost (localhost [127.0.0.1]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id 9854E17AD7 for ; Thu, 26 Jul 2001 18:31:26 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 60001) id 21BA817B01; Thu, 26 Jul 2001 18:31:21 +0100 (BST) To: genstruc@net.bio.net Newsgroups: bionet.genome.gene-structure From: webmaster@softberry.com (" webmaster") Subject: Annotated 20000 Promoters in Human Genome Date: 11 Jul 2001 22:50:48 +0100 Message-Id: <20010726173121.21BA817B01@mercury.hgmp.mrc.ac.uk> Sender: owner-genstruc@hgmp.mrc.ac.uk Precedence: bulk Annotated 20000 Promoters in Human Genome in Genome Explorer Promoters predicted in December draft of human genome are presented in Genome Explorer along with known and predicted genes: http://softberry.com/genomd/chrvis.html Right mouse click on a promoter in Genome Explorer reveals promoter sequence, presented in two blocks for TATA+ promoters and in one block for TATA-less promoters. First block of TATA+ promoter is TATA-box, and the second is a stretch from predicted transcription start site (TSS) to known 5'-end of mRNA or translation start site. Promoters were predicted by Softberry promoter prediction program TSSW in regions up to 3000 from known starts of coding regions (ATG codon) or known mapped 5'-mRNA ends. We found that limiting promoter search to such regions drastically reduces false positive predictions. Also, we have very strong thresholds for prediction of TATA-less promoters to minimize false positive predictions. Our promoter prediction software accurately predicts about 50% promoters accurately with a small average deviation from true start site. Such accuracy makes possible experimental work with found promoter candidates. For 20 experimentally verified promoters on Chromosome 22, TSSW predicted 15, placed 12 of them within (-150,+150) region from true TSS and 6 (30% of all promoters) - within -8,+2 region from true TSS. These results are significantly better than those obtained with PromoterInspector program (Scherf M., Klingenhoff A., Fresch K. et al. (2001) First Pass Annotation of promoters of human chromosome 22. Genome Res., 11,333- 340), where only 50% promoters from the same sample were found, with deviations from true TSS ranging from 200 to 1000 bp. We predicted 17632 TATA+ promoter and 2383 TATA-less promoters overall in human genome draft. For Chromosome 22, we predicted 350 TATA+ promoters and 85 TATA-less promoters. New Fgenesh++ gene predictions for December draft of human genome are presented by Softberry Inc. (www.softberry.com) at http://genome.cse.ucsc.edu/goldenPath/decTracks.html and will be presented in Softberry Genome Explored with some expression data soon (http://softberry.com/genomb/chrvis.html) 44409 genes include 5883 genes correponding to refseq mRNA, 3592 genes corresponding to GenBank mRNAs, 2047 known genes and 302 pseudogenes. Methods of predictions are described at: Solovyev V.V. (2001) Statistical approaches in Eukaryotic gene prediction. In: Handbook of Statistical genetics (eds. Balding D. et al.), John Wiley & Sons, Ltd., p. 83-127.) --- ===== Moderated bionet.genome.gene-structure ____________________________________________________________ Do You Yahoo!? Get your free @yahoo.co.uk address at http://mail.yahoo.co.uk or your free @yahoo.ie address at http://mail.yahoo.ie