In Silico Biology - Volume 2, issue 3

Authors: Wingender, Edgar

Article Type: Other

Citation: In Silico Biology, vol. 2, no. 3, pp. 165-167, 2002

Authors: Schomburg, Dietmar | Vingron, Martin

Article Type: Other

Citation: In Silico Biology, vol. 2, no. 3, pp. 169-171, 2002

Authors: Luo, Jingchu

Article Type: Other

Citation: In Silico Biology, vol. 2, no. 3, pp. 173-177, 2002

Authors: Schulze-Kremer, Steffen

Article Type: Other

Abstract: About five years ago, ontology was almost unknown in bioinformatics, even more so in molecular biology. Nowadays, many bioinformatics articles mention it in connection with text mining, data integration or as a metaphysical cure for problems in standardisation of nomenclature and other applications. This article attempts to give an account of what concept ontologies in the domain of biology and bioinformatics are; what they are not; how they can be constructed; how they can be …used; and some fallacies and pitfalls creators and users should be aware of. Show more

Keywords: Domain ontology, biology, bioinformatics, bio-ontologies, design, guidelines, semantics, philosophy

Citation: In Silico Biology, vol. 2, no. 3, pp. 179-193, 2002

Authors: Rinner, Oliver | Morgenstern, Burkhard

Article Type: Research Article

Abstract: Comparative sequence analysis is a powerful approach to identify functional elements in genomic sequences. Herein, we describe AGenDA (Alignment-based GENe Detection Algorithm), a novel method for gene prediction that is based on long-range alignment of syntenic regions in eukaryotic genome sequences. Local sequence homologies identified by the DIALIGN program are searched for conserved splice signals to define potential protein-coding exons; these candidate exons are then used to assemble complete gene structures. The …performance of our method was tested on a set of 105 human-mouse sequence pairs. These test runs showed that sensitivity and specificity of AGenDA are comparable with the best gene- prediction program that is currently available. However, since our method is based on a completely different type of input information, it can detect genes that are not detectable by standard methods and vice versa. Thus, our approach seems to be a useful addition to existing gene-prediction programs. Availability: DIALIGN is available through the Bielefeld Bioinformatics Server (BiBiServ) at http://bibiserv.techfak.uni-bielefeld.de/dialign/ The gene-prediction program AGenDA described in this paper will be available through the BiBiServ or MIPS web server at http://mips.gsf.de. Show more

Keywords: gene prediction, sequence alignment, comparative genome analysis, cross-species sequence comparison, phylogenetic footprinting, genome annotation, dynamic programming

Citation: In Silico Biology, vol. 2, no. 3, pp. 195-205, 2002

Authors: Glass, Änne | Gierl, Lothar

Article Type: Short Communication

Abstract: MOTIVATION: Most of diseases are caused by a set of gene defects, which occur in a complex association. The association scheme of expressed genes can be modelled by genetic networks. Genetic networks are efficiently facilities to understand the dynamic of pathogenic processes by modelling molecular reality of cell conditions. In this sense a genetic network consists of first, a set of genes of specified cells, tissues or species and second, causal relations between these genes determining …the functional condition of the biological system, i. e. under disease. A relation between two genes will exist if they both are directly or indirectly associated with disease [8]. Our goal is to characterize diseases (especially autoimmune diseases like chronic pancreatitis CP, multiple sclerosis MS, rheumatoid arthritis RA) by genetic networks generated by a computer system. We want to introduce this practice as a bioinformatic approach for finding targets. Show more

Keywords: genetic networks, model, functional genomics, proteomics, genomic data, expression data, chip data, data mining, analysis , bioinformatics, software system, complex association, causal relation, interaction, targets, artificial intelligence, AI, ART, parser engine

Citation: In Silico Biology, vol. 2, no. 3, pp. 207-211, 2002

Authors: Barbasiewicz, Anna | Liu, Lin | Lang, B. Franz | Burger, Gertraud

Article Type: Research Article

Abstract: GOBASE is a relational database that integrates data associated with mitochondria and chloro-plasts. The most important data in GOBASE, i. e., molecular sequences and taxonomic information, are obtained from the public sequence data repository at the National Center for Biotechnology Information (NCBI), and are validated by our experts. Maintaining a curated genomic database comes with a towering labor cost, due to the shear volume of available genomic sequences and the plethora of annotation errors and omissions …in records re-trieved from public repositories. Here we describe our approach to increase automation of the database population process, thereby reducing manual intervention. As a first step, we used Unified Modeling Language (UML) to construct a list of potential errors. Each case was evaluated independently, and an expert solution was devised, and represented as a diagram. Subsequently, the UML diagrams were used as templates for writing object-oriented automation programs in the Java programming language. Show more

Keywords: automation, curation, GOBASE, Java, population, UML

Citation: In Silico Biology, vol. 2, no. 3, pp. 213-217, 2002

Authors: Köhler, Jacob | Schulze-Kremer, Steffen

Article Type: Research Article

Abstract: A system for "intelligent" semantic integration and querying of federated databases is being implemented by using three main components: A component which enables SQL access to integrated databases by database federation (MARGBench), an ontology based semantic metadatabase (SEMEDA) and an ontology based query interface (SEMEDA-query). In this publication we explain and demonstrate the principles, architecture and the use of SEMEDA. Since SEMEDA is implemented as 3 tiered web application database providers can enter …all relevant semantic and technical information about their databases by themselves via a web browser. SEMEDA' s collaborative ontology editing feature is not restricted to database integration, and might also be useful for ongoing ontology developments, such as the "Gene Ontology" [2]. SEMEDA can be found at http://www-bm.cs.uni-magdeburg. de/semeda/. We explain how this ontologically structured information can be used for semantic database integration. In addition, requirements to ontologies for molecular biological database integration are discussed and relevant existing ontologies are evaluated. We further discuss how ontologies and structured knowledge sources can be used in SEMEDA and whether they can be merged supplemented or updated to meet the requirements for semantic database integration. Show more

Keywords: Semantic database integration, molecular biology, meta-database, ontology, knowledge representation, controlled vocabulary

Citation: In Silico Biology, vol. 2, no. 3, pp. 219-231, 2002

Authors: Orlov, Yuri L. | Filippov, Vladimir P. | Potapov, Vladimir N. | Kolchanov, Nikolay A.

Article Type: Research Article

Abstract: A method has been developed for constructing a tree source model for genetic text generation. Model visualisation in the form of suffix (context) trees provides a new way of context analysis of symbol sequences. Estimation of the stochastic complexity of the data in the frame of the model serves as a criterion for the model's ascertainment. The model and complexity values are used for analysis of genetic texts. The software realisation of this algorithm enables to …reveal statistical properties of genetic sequences based on an information measure. The program developed is available via Internet at http://wwwmgs.bionet.nsc.ru/mgs/programs/complexity/. Show more

Keywords: complexity, information measure, suffix tree visualisation, variable memory Markov model, genetic texts, statistical modelling

Citation: In Silico Biology, vol. 2, no. 3, pp. 233-247, 2002

Authors: Werner, Thomas

Article Type: Other

Abstract: The combination of full-scale genomic sequencing with high throughput expression analysis provides a new and largely unexploited basis for in silico functional genomics. Recent break through developments in locat-ing and analyzing promoters now allow extending functional genomics in silico far beyond identification of protein sequences into the complex regulatory structures and mechanisms of the genome. However, only first examples of this new type of approach are emerging at present and intensive further developments …of bioinformatics tools will be required before such analysis can become large-scale routine in genomic sequence analysis. Nevertheless, the door to a new dimension of functional analysis of the genomic sequence is open. Finally, only the tight integration of the enormous amount of knowledge gained from proteins sequence analysis with the complementary information about gene regulation will afford us with a more complete picture of the networks than constitute life. Show more

Keywords: genome annotation, gene regulation, promoter prediction, promoter modeling, functional context, transcription factor binding sites, promoter modules , RANTES, chemokine, coexpressed genes

Citation: In Silico Biology, vol. 2, no. 3, pp. 249-255, 2002