1
|
Kiel M, Sagory-Zalkind P, Miganeh C, Stork C, Leimbach A, Sekse C, Mellmann A, Rechenmann F, Dobrindt U. Identification of Novel Biomarkers for Priority Serotypes of Shiga Toxin-Producing Escherichia coli and the Development of Multiplex PCR for Their Detection. Front Microbiol 2018; 9:1321. [PMID: 29997582 PMCID: PMC6028524 DOI: 10.3389/fmicb.2018.01321] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Accepted: 05/30/2018] [Indexed: 12/22/2022] Open
Abstract
It would be desirable to have an unambiguous scheme for the typing of Shiga toxin-producing Escherichia coli (STEC) isolates to subpopulations. Such a scheme should take the high genomic plasticity of E. coli into account and utilize the stratification of STEC into subgroups, based on serotype or phylogeny. Therefore, our goal was to identify specific marker combinations for improved classification of STEC subtypes. We developed and evaluated two bioinformatic pipelines for genomic marker identification from larger sets of bacterial genome sequences. Pipeline A performed all-against-all BLASTp analyses of gene products predicted in STEC genome test sets against a set of control genomes. Pipeline B identified STEC marker genes by comparing the STEC core proteome and the "pan proteome" of a non-STEC control group. Both pipelines defined an overlapping, but not identical set of discriminative markers for different STEC subgroups. Differential marker prediction resulted from differences in genome assembly, ORF finding and inclusion cut-offs in both workflows. Based on the output of the pipelines, we defined new specific markers for STEC serogroups and phylogenetic groups frequently associated with outbreaks and cases of foodborne illnesses. These included STEC serogroups O157, O26, O45, O103, O111, O121, and O145, Shiga toxin-positive enteroaggregative E. coli O104:H4, and HUS-associated sequence type (ST)306. We evaluated these STEC marker genes for their presence in whole genome sequence data sets. Based on the identified discriminative markers, we developed a multiplex PCR (mPCR) approach for detection and typing of the targeted STEC. The specificity of the mPCR primer pairs was verified using well-defined clinical STEC isolates as well as isolates from the ECOR, DEC, and HUSEC collections. The application of the STEC mPCR for food analysis was tested with inoculated milk. In summary, we evaluated two different strategies to screen large genome sequence data sets for discriminative markers and implemented novel marker genes found in this genome-wide approach into a DNA-based typing tool for STEC that can be used for the characterization of STEC from clinical and food samples.
Collapse
Affiliation(s)
- Matthias Kiel
- Institute of Hygiene, University of Münster, Münster, Germany
| | | | - Céline Miganeh
- Genostar Bioinformatics, Montbonnot-Saint-Martin, France
| | - Christoph Stork
- Institute of Hygiene, University of Münster, Münster, Germany
| | | | | | | | | | - Ulrich Dobrindt
- Institute of Hygiene, University of Münster, Münster, Germany
| |
Collapse
|
2
|
Arulandhu AJ, Staats M, Hagelaar R, Voorhuijzen MM, Prins TW, Scholtens I, Costessi A, Duijsings D, Rechenmann F, Gaspar FB, Barreto Crespo MT, Holst-Jensen A, Birck M, Burns M, Haynes E, Hochegger R, Klingl A, Lundberg L, Natale C, Niekamp H, Perri E, Barbante A, Rosec JP, Seyfarth R, Sovová T, Van Moorleghem C, van Ruth S, Peelen T, Kok E. Development and validation of a multi-locus DNA metabarcoding method to identify endangered species in complex samples. Gigascience 2018; 6:1-18. [PMID: 29020743 PMCID: PMC5632295 DOI: 10.1093/gigascience/gix080] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Accepted: 08/15/2017] [Indexed: 11/19/2022] Open
Abstract
DNA metabarcoding provides great potential for species identification in complex samples such as food supplements and traditional medicines. Such a method would aid Convention on International Trade in Endangered Species of Wild Fauna and Flora (CITES) enforcement officers to combat wildlife crime by preventing illegal trade of endangered plant and animal species. The objective of this research was to develop a multi-locus DNA metabarcoding method for forensic wildlife species identification and to evaluate the applicability and reproducibility of this approach across different laboratories. A DNA metabarcoding method was developed that makes use of 12 DNA barcode markers that have demonstrated universal applicability across a wide range of plant and animal taxa and that facilitate the identification of species in samples containing degraded DNA. The DNA metabarcoding method was developed based on Illumina MiSeq amplicon sequencing of well-defined experimental mixtures, for which a bioinformatics pipeline with user-friendly web-interface was developed. The performance of the DNA metabarcoding method was assessed in an international validation trial by 16 laboratories, in which the method was found to be highly reproducible and sensitive enough to identify species present in a mixture at 1% dry weight content. The advanced multi-locus DNA metabarcoding method assessed in this study provides reliable and detailed data on the composition of complex food products, including information on the presence of CITES-listed species. The method can provide improved resolution for species identification, while verifying species with multiple DNA barcodes contributes to an enhanced quality assurance.
Collapse
Affiliation(s)
- Alfred J Arulandhu
- RIKILT Wageningen University & Research, P.O. Box 230, 6700 AE Wageningen, The Netherlands.,Food Quality and Design Group, Wageningen University and Research, P.O. Box 8129, 6700 EV Wageningen, The Netherlands
| | - Martijn Staats
- RIKILT Wageningen University & Research, P.O. Box 230, 6700 AE Wageningen, The Netherlands
| | - Rico Hagelaar
- RIKILT Wageningen University & Research, P.O. Box 230, 6700 AE Wageningen, The Netherlands
| | - Marleen M Voorhuijzen
- RIKILT Wageningen University & Research, P.O. Box 230, 6700 AE Wageningen, The Netherlands
| | - Theo W Prins
- RIKILT Wageningen University & Research, P.O. Box 230, 6700 AE Wageningen, The Netherlands
| | - Ingrid Scholtens
- RIKILT Wageningen University & Research, P.O. Box 230, 6700 AE Wageningen, The Netherlands
| | | | - Danny Duijsings
- Baseclear B. V, Einsteinweg 5, 2333 CC Leiden, The Netherlands
| | - François Rechenmann
- GenoStar Bioinformatics Solutions, 60 rue Lavoisier, 38330 Montbonnot Saint Martin, France
| | - Frédéric B Gaspar
- iBET, Instituto de Biologia Experimental e Tecnológica, Apartado 12, 2780-901 Oeiras, Portugal
| | | | - Arne Holst-Jensen
- Norwegian Veterinary Institute, Ullevaalsveien 68, P.O. Box 750 Sentrum, 0106 Oslo, Norway
| | - Matthew Birck
- U.S. Customs and Border Protection Laboratory, 1100 Raymond Blvd Newark, NJ 07102 USA
| | - Malcolm Burns
- LGC, Queens Road, Teddington, Middlesex, TW11 0LY, UK
| | | | - Rupert Hochegger
- Austrian Agency for Health and Food Safety, Spargelfeldstrasse 191, 1220 Vienna, Austria
| | - Alexander Klingl
- Generalzolldirektion, Direktion IX, Bildungs- und Wissenschaftszentrum der Bundesfinanzverwaltung, Dienstort Hamburg, Baumacker 3, D-22523 Hamburg, Germany
| | - Lisa Lundberg
- Livsmedelsverket, Att. Lisa Lundberg, Strandbodgatan 4, SE 75323 Uppsala, Sweden
| | - Chiara Natale
- AGENZIA DELLE DOGANE E DEI MONOPOLI, Laboratori e servizi chimici - Laboratorio Chimico di Genova, 16126 Genova, Via Rubattino n. 6, Italy
| | - Hauke Niekamp
- Eurofins GeneScan GmbH, Engesserstrasse 4 79108 Freiburg, Germany
| | - Elena Perri
- CREA-SCS sede di Tavazzano - Laboratorio via Emilia, Km 307, 26838 Tavazzano, Italy
| | - Alessandra Barbante
- CREA-SCS sede di Tavazzano - Laboratorio via Emilia, Km 307, 26838 Tavazzano, Italy
| | - Jean-Philippe Rosec
- Service Commun des Laboratoires, Laboratoire de Montpellier, Parc Euromédecine, 205 rue de la Croix Verte, 34196 Montpellier Cedex 5, France
| | - Ralf Seyfarth
- Biolytix AG, Benkenstrasse 254, 4108 Witterswil, Switzerland
| | - Tereza Sovová
- Crop Research Institute, Department of Molecular Genetics, Drnovská 507, 161 06 Prague, Czech Republic
| | | | - Saskia van Ruth
- RIKILT Wageningen University & Research, P.O. Box 230, 6700 AE Wageningen, The Netherlands.,Food Quality and Design Group, Wageningen University and Research, P.O. Box 8129, 6700 EV Wageningen, The Netherlands
| | - Tamara Peelen
- Dutch Customs Laboratory, Kingsfordweg 1, 1043 GN, Amsterdam, The Netherlands
| | - Esther Kok
- RIKILT Wageningen University & Research, P.O. Box 230, 6700 AE Wageningen, The Netherlands
| |
Collapse
|
3
|
Lucchetti-Miganeh C, Redelberger D, Chambonnier G, Rechenmann F, Elsen S, Bordi C, Jeannot K, Attrée I, Plésiat P, de Bentzmann S. Pseudomonas aeruginosa Genome Evolution in Patients and under the Hospital Environment. Pathogens 2014; 3:309-40. [PMID: 25437802 PMCID: PMC4243448 DOI: 10.3390/pathogens3020309] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2013] [Revised: 03/26/2014] [Accepted: 03/28/2014] [Indexed: 11/21/2022] Open
Abstract
Pseudomonas aeruginosa is a Gram-negative environmental species and an opportunistic microorganism, establishing itself in vulnerable patients, such as those with cystic fibrosis (CF) or those hospitalized in intensive care units (ICU). It has become a major cause of nosocomial infections worldwide and a serious threat to Public Health because of overuse and misuse of antibiotics that have selected highly resistant strains against which very few therapeutic options exist. Herein is illustrated the intraclonal evolution of the genome of sequential isolates collected in a single CF patient from the early phase of pulmonary colonization to the fatal outcome. We also examined at the whole genome scale a pair of genotypically-related strains made of a drug susceptible, environmental isolate recovered from an ICU sink and of its multidrug resistant counterpart found to infect an ICU patient. Multiple genetic changes accumulated in the CF isolates over the disease time course including SNPs, deletion events and reduction of whole genome size. The strain isolated from the ICU patient displayed an increase in the genome size of 4.8% with major genetic rearrangements as compared to the initial environmental strain. The annotated genomes are given in free access in an interactive web application WallGene designed to facilitate large-scale comparative analysis and thus allowing investigators to explore homologies and syntenies between P. aeruginosa strains, here PAO1 and the five clinical strains described.
Collapse
Affiliation(s)
| | - David Redelberger
- UMR7255-Laboratoire d'Ingénierie des Systèmes Macromoléculaires, CNRS-Aix Marseille University, Marseille 13402, France.
| | - Gaël Chambonnier
- UMR7255-Laboratoire d'Ingénierie des Systèmes Macromoléculaires, CNRS-Aix Marseille University, Marseille 13402, France.
| | | | - Sylvie Elsen
- INSERM, UMR-S 1036, Biology of Cancer and Infection, Grenoble 38054, France.
| | - Christophe Bordi
- UMR7255-Laboratoire d'Ingénierie des Systèmes Macromoléculaires, CNRS-Aix Marseille University, Marseille 13402, France.
| | - Katy Jeannot
- Laboratoire de Bactériologie, Faculté de Médecine-Pharmacie, Université de Franche-Comté, Besançon 25030, France.
| | - Ina Attrée
- INSERM, UMR-S 1036, Biology of Cancer and Infection, Grenoble 38054, France.
| | - Patrick Plésiat
- Laboratoire de Bactériologie, Faculté de Médecine-Pharmacie, Université de Franche-Comté, Besançon 25030, France.
| | - Sophie de Bentzmann
- UMR7255-Laboratoire d'Ingénierie des Systèmes Macromoléculaires, CNRS-Aix Marseille University, Marseille 13402, France.
| |
Collapse
|
4
|
Masseroli M, Mons B, Bongcam-Rudloff E, Ceri S, Kel A, Rechenmann F, Lisacek F, Romano P. Integrated Bio-Search: challenges and trends for the integration, search and comprehensive processing of biological information. BMC Bioinformatics 2014; 15 Suppl 1:S2. [PMID: 24564249 PMCID: PMC4015876 DOI: 10.1186/1471-2105-15-s1-s2] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Many efforts exist to design and implement approaches and tools for data capture, integration and analysis in the life sciences. Challenges are not only the heterogeneity, size and distribution of information sources, but also the danger of producing too many solutions for the same problem. Methodological, technological, infrastructural and social aspects appear to be essential for the development of a new generation of best practices and tools. In this paper, we analyse and discuss these aspects from different perspectives, by extending some of the ideas that arose during the NETTAB 2012 Workshop, making reference especially to the European context. First, relevance of using data and software models for the management and analysis of biological data is stressed. Second, some of the most relevant community achievements of the recent years, which should be taken as a starting point for future efforts in this research domain, are presented. Third, some of the main outstanding issues, challenges and trends are analysed. The challenges related to the tendency to fund and create large scale international research infrastructures and public-private partnerships in order to address the complex challenges of data intensive science are especially discussed. The needs and opportunities of Genomic Computing (the integration, search and display of genomic information at a very specific level, e.g. at the level of a single DNA region) are then considered. In the current data and network-driven era, social aspects can become crucial bottlenecks. How these may best be tackled to unleash the technical abilities for effective data integration and validation efforts is then discussed. Especially the apparent lack of incentives for already overwhelmed researchers appears to be a limitation for sharing information and knowledge with other scientists. We point out as well how the bioinformatics market is growing at an unprecedented speed due to the impact that new powerful in silico analysis promises to have on better diagnosis, prognosis, drug discovery and treatment, towards personalized medicine. An open business model for bioinformatics, which appears to be able to reduce undue duplication of efforts and support the increased reuse of valuable data sets, tools and platforms, is finally discussed.
Collapse
Affiliation(s)
- Marco Masseroli
- Dipartimento di Elettronica, Informazione e Bioingegneria, Politecnico di Milano, Milano, 20133, Italy
| | - Barend Mons
- Leiden University Medical Center, Leiden, 2333 ZA, The Netherlands
- Netherlands Bioinformatics Center, Nijmegen, 6500 HB, The Netherlands
| | - Erik Bongcam-Rudloff
- Department of Animal Breeding and Genetics, SLU-Global Bioinformatics Centre, Swedish University of Agricultural Sciences, Uppsala, 75124, Sweden
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, 75108, Sweden
| | - Stefano Ceri
- Dipartimento di Elettronica, Informazione e Bioingegneria, Politecnico di Milano, Milano, 20133, Italy
| | - Alexander Kel
- GeneXplain GmbH, Wolfenbüttel, 38302, Germany
- Institute of Chemical Biology and Fundamental Medicine SBRAS, Novosibirsk, 630090, Russia
| | | | - Frederique Lisacek
- Proteome Informatics Group, SIB Swiss Institute of Bioinformatics, 1211 Geneva 4, Switzerland
- Section of Biology, University of Geneva, 1211 Geneva 4, Switzerland
| | - Paolo Romano
- Biopolymers and Proteomics, IRCCS AOU San Martino IST, Genoa, 16132, Italy
| |
Collapse
|
5
|
|
6
|
Batt G, Besson B, Ciron PE, de Jong H, Dumas E, Geiselmann J, Monte R, Monteiro PT, Page M, Rechenmann F, Ropers D. Genetic network analyzer: a tool for the qualitative modeling and simulation of bacterial regulatory networks. Methods Mol Biol 2012; 804:439-462. [PMID: 22144166 DOI: 10.1007/978-1-61779-361-5_22] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Genetic Network Analyzer (GNA) is a tool for the qualitative modeling and simulation of gene regulatory networks, based on so-called piecewise-linear differential equation models. We describe the use of this tool in the context of the modeling of bacterial regulatory networks, notably the network of global regulators controlling the adaptation of Escherichia coli to carbon starvation conditions. We show how the modeler, by means of GNA, can define a regulatory network, build a model of the network, determine the steady states of the system, perform a qualitative simulation of the network dynamics, and analyze the simulation results using model-checking tools. The example illustrates the interest of qualitative approaches for the analysis of the dynamics of bacterial regulatory networks.
Collapse
Affiliation(s)
- Grégory Batt
- INRIA Paris - Rocquencourt, Domaine de Voluceau, Le Chesnay, France
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
7
|
Descorps-Declère S, Ziébelin D, Rechenmann F, Viari A. Genepi: a blackboard framework for genome annotation. BMC Bioinformatics 2006; 7:450. [PMID: 17038181 PMCID: PMC1626490 DOI: 10.1186/1471-2105-7-450] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2006] [Accepted: 10/12/2006] [Indexed: 11/12/2022] Open
Abstract
Background Genome annotation can be viewed as an incremental, cooperative, data-driven, knowledge-based process that involves multiple methods to predict gene locations and structures. This process might have to be executed more than once and might be subjected to several revisions as the biological (new data) or methodological (new methods) knowledge evolves. In this context, although a lot of annotation platforms already exist, there is still a strong need for computer systems which take in charge, not only the primary annotation, but also the update and advance of the associated knowledge. In this paper, we propose to adopt a blackboard architecture for designing such a system Results We have implemented a blackboard framework (called Genepi) for developing automatic annotation systems. The system is not bound to any specific annotation strategy. Instead, the user will specify a blackboard structure in a configuration file and the system will instantiate and run this particular annotation strategy. The characteristics of this framework are presented and discussed. Specific adaptations to the classical blackboard architecture have been required, such as the description of the activation patterns of the knowledge sources by using an extended set of Allen's temporal relations. Although the system is robust enough to be used on real-size applications, it is of primary use to bioinformatics researchers who want to experiment with blackboard architectures. Conclusion In the context of genome annotation, blackboards have several interesting features related to the way methodological and biological knowledge can be updated. They can readily handle the cooperative (several methods are implied) and opportunistic (the flow of execution depends on the state of our knowledge) aspects of the annotation process.
Collapse
Affiliation(s)
| | - Danielle Ziébelin
- Université Joseph Fourier, Grenoble, France
- INRIA Rhône-Alpes, Helix group, Montbonnot, France
| | | | - Alain Viari
- INRIA Rhône-Alpes, Helix group, Montbonnot, France
| |
Collapse
|
8
|
Dufayard JF, Duret L, Penel S, Gouy M, Rechenmann F, Perrière G. Tree pattern matching in phylogenetic trees: automatic search for orthologs or paralogs in homologous gene sequence databases. Bioinformatics 2005; 21:2596-603. [PMID: 15713731 DOI: 10.1093/bioinformatics/bti325] [Citation(s) in RCA: 132] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
MOTIVATION Comparative sequence analysis is widely used to study genome function and evolution. This approach first requires the identification of homologous genes and then the interpretation of their homology relationships (orthology or paralogy). To provide help in this complex task, we developed three databases of homologous genes containing sequences, multiple alignments and phylogenetic trees: HOBACGEN, HOVERGEN and HOGENOM. In this paper, we present two new tools for automating the search for orthologs or paralogs in these databases. RESULTS First, we have developed and implemented an algorithm to infer speciation and duplication events by comparison of gene and species trees (tree reconciliation). Second, we have developed a general method to search in our databases the gene families for which the tree topology matches a peculiar tree pattern. This algorithm of unordered tree pattern matching has been implemented in the FamFetch graphical interface. With the help of a graphical editor, the user can specify the topology of the tree pattern, and set constraints on its nodes and leaves. Then, this pattern is compared with all the phylogenetic trees of the database, to retrieve the families in which one or several occurrences of this pattern are found. By specifying ad hoc patterns, it is therefore possible to identify orthologs in our databases.
Collapse
|
9
|
Durand P, Médigue C, Morgat A, Vandenbrouck Y, Viari A, Rechenmann F. Integration of data and methods for genome analysis. Curr Opin Drug Discov Devel 2003; 6:346-52. [PMID: 12833667] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 03/03/2023]
Abstract
The development of genomic and post-genomic technologies has created an explosion in the quantity, diversity and availability of both biological data and methods of analysis. Biologists are currently facing the problem of using all these resources to convert raw data into new valuable knowledge. This review presents software platforms designed to handle data and/or methods in the context of genome analysis.
Collapse
|
10
|
Abstract
Spatial information on genome organization is essential for both gene prediction and annotation among species and a better understanding of genomes functioning and evolution. We propose in this article an object-association model to formalize comparative genomic mapping. This model is being implemented in the GeMCore knowledge base, for which some original capabilities are described. GeMCore associated to the GeMME graphical interface for molecular evolution was used to spatially characterize the minor shift phenomenon between human and mouse.
Collapse
Affiliation(s)
- G Bronner
- Laboratoire de Biométrie et Biologie Evolutive, UMR CNRS 5558 Lyon I Bât Grégoire Mendel, Villeurbanne, France.
| | | | | | | | | |
Collapse
|
11
|
|
12
|
Proux D, Rechenmann F, Julliard L. A pragmatic information extraction strategy for gathering data on genetic interactions. Proc Int Conf Intell Syst Mol Biol 2001; 8:279-85. [PMID: 10977089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/17/2023]
Abstract
We present in this paper a pragmatic strategy to perform information extraction from biologic texts. Since the emergence of the information extraction field, techniques have evolved, become more robust and proved their efficiency on specific domains. We are using a combination of existing linguistic and knowledge processing tools to automatically extract information about gene interactions in the literature. Our ultimate goal is to build a network of gene interactions. The methodologies used and the current results are discussed in this paper.
Collapse
Affiliation(s)
- D Proux
- Xerox Research Centre Europe, Meylan, France.
| | | | | |
Collapse
|
13
|
|
14
|
Sanchez C, Lachaize C, Janody F, Bellon B, Röder L, Euzenat J, Rechenmann F, Jacq B. Grasping at molecular interactions and genetic networks in Drosophila melanogaster using FlyNets, an Internet database. Nucleic Acids Res 1999; 27:89-94. [PMID: 9847149 PMCID: PMC148104 DOI: 10.1093/nar/27.1.89] [Citation(s) in RCA: 104] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
FlyNets (http://gifts.univ-mrs.fr/FlyNets/FlyNets_home_page.++ +html) is a WWW database describing molecular interactions (protein-DNA, protein-RNA and protein-protein) in the fly Drosophila melanogaster. It is composed of two parts, as follows. (i) FlyNets-base is a specialized database which focuses on molecular interactions involved in Drosophila development. The information content of FlyNets-base is distributed among several specific lines arranged according to a GenBank-like format and grouped into five thematic zones to improve human readability. The FlyNets database achieves a high level of integration with other databases such as FlyBase, EMBL, GenBank and SWISS-PROT through numerous hyperlinks. (ii) FlyNets-list is a very simple and more general databank, the long-term goal of which is to report on any published molecular interaction occuring in the fly, giving direct web access to corresponding s in Medline and in FlyBase. In the context of genome projects, databases describing molecular interactions and genetic networks will provide a link at the functional level between the genome, the proteome and the transcriptome worlds of different organisms. Interaction databases therefore aim at describing the contents, structure, function and behaviour of what we herein define as the interactome world.
Collapse
Affiliation(s)
- C Sanchez
- Laboratoire de Génétique et Physiologie du Développement, IBDM, Parc Scientifique de Luminy, CNRS Case 907, 13288 Marseille Cedex 09, France
| | | | | | | | | | | | | | | |
Collapse
|
15
|
Abstract
MOTIVATION To be fully and efficiently exploited, data coming from sequencing projects together with specific sequence analysis tools need to be integrated within reliable data management systems. Systems designed to manage genome data and analysis tend to give a greater importance either to the data storage or to the methodological aspect, but lack a complete integration of both components. RESULTS This paper presents a co-operative computer environment (called Imagenetrade mark) dedicated to genomic sequence analysis and annotation. Imagene has been developed by using an object-based model. Thanks to this representation, the user can directly manipulate familiar data objects through icons or lists. Imagene also incorporates a solving engine in order to manage analysis tasks. A global task is solved by successive divisions into smaller sub-tasks. During program execution, these sub-tasks are graphically displayed to the user and may be further re-started at any point after task completion. In this sense, Imagene is more transparent to the user than a traditional menu-driven package. Imagene also provides a user interface to display, on the same screen, the results produced by several tasks, together with the capability to annotate these results easily. In its current form, Imagene has been designed particularly for use in microbial sequencing projects. AVAILABILITY Imagene best runs on SGI (Irix 6.3 or higher) workstations. It is distributed free of charge on a CD-ROM, but requires some Ilog licensed software to run. Some modules also require separate license agreements. Please contact the authors for specific academic conditions and other Unix platforms. CONTACT imagene home page: http://wwwabi.snv.jussieu.fr/imagene
Collapse
Affiliation(s)
- C Médigue
- Institut Pasteur, REG, 28 rue du Docteur Roux, 75724 Paris Cedex 15,
| | | | | | | |
Collapse
|
16
|
Schmeltzer O, Médigue C, Uvietta P, Rechenmann F, Dorkeld F, Perrière G, Gautier C. Building large knowledge bases in molecular biology. Proc Int Conf Intell Syst Mol Biol 1993; 1:345-353. [PMID: 7584356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Large scale genome sequencing projects are now producing hugh amounts of data which can be readily stored and managed within data base management systems, and analyzed using dedicated software packages. The results of these analyzes should also be stored with the input DNA sequences. The increasing complexity and size of the objects to be described and managed have led biologists to rely on advanced data models such as the object-oriented model. As a joint effort between our computer science and molecular biology research projects, the knowledge bases we have developed in molecular genetics have shown however that the basic object-oriented model is not fully adapted to the complexity of some biological situations encountered. Advanced descriptive capabilities, provided only by knowledge models originated from the AI field, are required. Composite or evolving objects, multiple viewpoints, constraints, tasks and methods, textual annotations are some examples of such capabilities. They are illustrated by biological situations for which they appeared to be necessary. Supporting powerful reasoning mechanisms (e.g. object classification, constraint propagation or qualitative simulators), they allow the development of large knowledge bases in molecular biology. These knowledge bases are expected to become the adequate support for co-operative distributed research efforts.
Collapse
|