Investigating extended regulatory regions of genomic DNA sequences.
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MOTIVATION: Despite the growing volume of data on primary nucleotide sequences, the regulatory regions remain a major puzzle with regard to their function. Numerous recognising programs considering a diversity of properties of regulatory regions have been developed. The system proposed here allows the specific contextual, conformational and physico-chemical properties to be revealed based on analysis of extended DNA regions. RESULTS: The Internet-accessible computer system RegScan, designed to analyse the extended regulatory regions of eukaryotic genes, has been developed. The computer system comprises the following software: (i) programs for classification dividing a set of promoters into TATA-containing and TATA-less promoters and promoters with and without CpG islands; (ii) programs for constructing (a) nucleotide frequency profiles, (b) sequence complexity profiles and (c) profiles of conformational and physico-chemical properties; (iii) the program for constructing the sets of degenerate oligonucleotide motifs of a specified length; and (iv) the program searching for and visualising repeats in nucleotide sequences. The system has allowed us to demonstrate the following characteristic patterns of vertebrate promoter regions: the TATA box region is flanked by regions with an increased G+C content and increased bending stiffness, the TATA box content is asymmetric and promoter regions are saturated with both direct and inverted repeats. AVAILABILITY: The computer system RegScan is available via the Internet at http://www.mgs.bionet.nsc. ru/Systems/RegScan, http://www.cbil.upenn.edu/mgs/systems/r egscan/. (+info)
Conformational and physicochemical DNA features specific for transcription factor binding sites.
(58/12469)
MOTIVATION: A reliable recognition of transcription factor binding sites is essential for analysis of regulatory genomic sequences. The experimental data make evident an important role of DNA conformational features for site functioning. However, Internet-available tools for revealing conformational and physicochemical DNA features significant for the site functioning and subsequent use of these features for site recognition have not been developed up to now. RESULTS: We suggest an approach for revealing significant conformational and physicochemical properties of functional sites implemented in the database B-DNA-VIDEO. This database is designed to study the sets of various transcription factor binding sites, providing evidence that transcription factor binding sites are characterized by specific sets of significant conformational and physicochemical DNA properties. For a fixed site, by using the B-DNA features selected for this site recognition, the C-program recognizing this site may be generated, control tested and stored in the database B-DNA-VIDEO. Each B-DNA-VIDEO entry links to the Web-applet recognizing the site, whose significant B-DNA features are stored in this entry as the 'site recognition programs'. The pairwise linked entry-applet pairs are compiled within the B-DNA-VIDEO system, which is simultaneously the database and the program tools package applicable immediately for recognizing the sites stored in the database. Indeed, this is the novelty. Hence, B-DNA-VIDEO is the Web resource of both 'searching for static data' and 'active computation' type, that is why it was called an 'activated database'. AVAILABILITY: B-DNA-VIDEO is available at http://wwwmgs.bionet.nsc.ru/systems/BDNAVideo/ and the mirror site at http://www.cbil.upenn.edu/mgs/systems/c onsfreq/. (+info)
Integrated databases and computer systems for studying eukaryotic gene expression.
(59/12469)
MOTIVATION: The goal of the work was to develop a WWW-oriented computer system providing a maximal integration of informational and software resources on the regulation of gene expression and navigation through them. Rapid growth of the variety and volume of information accumulated in the databases on regulation of gene expression necessarily requires the development of computer systems for automated discovery of the knowledge that can be further used for analysis of regulatory genomic sequences. RESULTS: The GeneExpress system developed includes the following major informational and software modules: (1) Transcription Regulation (TRRD) module, which contains the databases on transcription regulatory regions of eukaryotic genes and TRRD Viewer for data visualization; (2) Site Activity Prediction (ACTIVITY), the module for analysis of functional site activity and its prediction; (3) Site Recognition module, which comprises (a) B-DNA-VIDEO system for detecting the conformational and physicochemical properties of DNA sites significant for their recognition, (b) Consensus and Weight Matrices (ConsFrec) and (c) Transcription Factor Binding Sites Recognition (TFBSR) systems for detecting conservative contextual regions of functional sites and their recognition; (4) Gene Networks (GeneNet), which contains an object-oriented database accumulating the data on gene networks and signal transduction pathways, and the Java-based Viewer for exploration and visualization of the GeneNet information; (5) mRNA Translation (Leader mRNA), designed to analyze structural and contextual properties of mRNA 5'-untranslated regions (5'-UTRs) and predict their translation efficiency; (6) other program modules designed to study the structure-function organization of regulatory genomic sequences and regulatory proteins. AVAILABILITY: GeneExpress is available at http://wwwmgs.bionet.nsc. ru/systems/GeneExpress/ and the links to the mirror site(s) can be found at http://wwwmgs.bionet.nsc.ru/mgs/links/mirrors.html+ ++. (+info)
Information technology outside health care: what does it matter to us?
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Non-health-care uses of information technology (IT) provide important lessons for health care informatics that are often overlooked because of the focus on the ways in which health care is different from other domains. Eight examples of IT use outside health care provide a context in which to examine the content and potential relevance of these lessons. Drawn from personal experience, five books, and two interviews, the examples deal with the role of leadership, academia, the private sector, the government, and individuals working in large organizations. The interviews focus on the need to manage technologic change. The lessons shed light on how to manage complexity, create and deploy standards, empower individuals, and overcome the occasional "wrongness" of conventional wisdom. One conclusion is that any health care informatics self-examination should be outward-looking and focus on the role of health care IT in the larger context of the evolving uses of IT in all domains. (+info)
Use of meta-analytic results to facilitate shared decision making.
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OBJECTIVES: Describe and evaluate an Internet-based approach to patient decision support using mathematical models that predict the probability of successful treatment on the basis of meta-analytic summaries of the mean and standard deviation of symptom response. DESIGN: An Internet-based decision support tool was developed to help patients with benign prostatic hypertrophy (BPH) determine whether they wanted to use alpha blockers. The Internet site incorporates a meta-analytic model of the results of randomized trials of the alpha blocker terazosin. The site describes alternative treatments for BPH and potential adverse effects of alpha blockers. The site then measures patients' current symptoms and desired level of symptom reduction. In response, the site computes and displays the probability of a patient's achieving his objective by means of terazosin or placebo treatment. SETTING: Self-identified BPH patients accessing the site over the Internet. MAIN OUTCOME MEASURES: Patients' perceptions of the usefulness of information. RESULTS: Over a three-month period, 191 patients who were over 50 years of age and who reported that they have BPH used the decision support tool. Respondents had a mean American Urological Association (AUA) score of 18.8 and a desired drop in symptoms of 10.1 AUA points. Patients had a 40 percent chance of achieving treatment goals with terazosin and a 20 percent chance with placebo. Patients found the information useful (93 percent), and most (71 percent) believed this type of information should be discussed before prescribing medications. CONCLUSIONS: Interactive meta-analytic summary models of the effects of pharmacologic treatments can help patients determine whether a treatment offers sufficient benefits to offset its risks. (+info)
Financing a future for public biological data.
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MOTIVATION: The public web-based biological database infrastructure is a source of both wonder and worry. Users delight in the ever increasing amounts of information available; database administrators and curators worry about long-term financial support. An earlier study of 153 biological databases (Ellis and Kalumbi, Nature Biotechnol., 16, 1323-1324, 1998) determined that near future (1-5 year) funding for over two-thirds of them was uncertain. More detailed data are required to determine the magnitude of the problem and offer possible solutions. METHODS: This study examines the finances and use statistics of a few of these organizations in more depth, and reviews several economic models that may help sustain them. RESULTS: Six organizations were studied. Their administrative overhead is fairly low; non-administrative personnel and computer-related costs account for 77% of expenses. One smaller, more specialized US database, in 1997, had 60% of total access from US domains; a majority (56%) of its US accesses came from commercial domains, although only 2% of the 153 databases originally studied received any industrial support. The most popular model used to gain industrial support is asymmetric pricing: preferentially charging the commercial users of a database. At least five biological databases have recently begun using this model. Advertising is another model which may be useful for the more general, more heavily used sites. Microcommerce has promise, especially for databases that do not attract advertisers, but needs further testing. The least income reported for any of the databases studied was $50,000/year; applying this rate to 400 biological databases (a lower limit of the number of such databases, many of which require far larger resources) would mean annual support need of at least $20 million. To obtain this level of support is challenging, yet failure to accept the challenge could be catastrophic. CONTACT: [email protected]. edu (+info)
SWEET - WWW-based rapid 3D construction of oligo- and polysaccharides.
(63/12469)
SWEET is a WWW-based tool which rapidly converts the commonly used carbohydrate sequence information directly into a preliminary but reliable 3D model which can be visualised and written to files in several ways. AVAILABILITY: SWEET is accessible via the Internet at http://www.dkfz-heidelberg.de/spec/. CONTACT: a. [email protected] or w.vonderlieth@ dkfz-heidelberg.de SUPPLEMENTARY INFORMATION: The current version of SWEET generates only one conformation out of a manifold. Several authors have analysed possible conformations of high-mannose N-linked glycans using a combination of NMR methods and computational approaches showing that such molecules are rather flexible populating normally several conformations for each glycosidic linkage. The displayed model exhibits for all glycosidic linkages a conformation which is in accordance with the reported variations of Phi, psi and omega values for specific linkage (see http://www.dkfz-heidelberg. de/spec/sweet2/doc/input/sba_example.html). (+info)
Genomes OnLine Database (GOLD 1.0): a monitor of complete and ongoing genome projects world-wide.
(64/12469)
GOLD (Genomes On Line Database) is a World Wide Web resource for comprehensive access to information regarding complete and ongoing genome projects around the world. AVAILABILITY: GOLD is based at the University of Illinois at Urbana-Champaign and is available at http://geta.life.uiuc.edu/ approximately nikos/genomes. html. It is also mirrored at the European Bioinformatics Institute at http://www.ebi.ac.uk/research/cgg/genomes.html. CONTACT: [email protected] (+info)