TETRA: a web-service and a stand-alone program for the analysis and comparison of tetranucleotide usage patterns in DNA sequences

BACKGROUND: In the emerging field of environmental genomics, direct cloning and sequencing of genomic fragments from complex microbial communities has proven to be a valuable source of new enzymes, expanding the knowledge of basic biological processes. The central problem of this so called metagenome-approach is that the cloned fragments often lack suitable phylogenetic marker genes, rendering the identification of clones that are likely to originate from the same genome difficult or impossible. In such cases, the analysis of intrinsic DNA-signatures like tetranucleotide frequencies can provide valuable hints on fragment affiliation. With this application in mind, the TETRA web-service and the TETRA stand-alone program have been developed, both of which automate the task of comparative tetranucleotide frequency analysis. Availability: RESULTS: TETRA provides a statistical analysis of tetranucleotide usage patterns in genomic fragments, either via a web-service or a stand-alone program. With respect to discriminatory power, such an analysis outperforms the assignment of genomic fragments based on the (G+C)-content, which is a widely-used sequence-based measure for assessing fragment relatedness. While the web-service is restricted to the calculation of correlation coefficients between tetranucleotide usage patterns of submitted DNA sequences, the stand-alone program generates a much more detailed output, comprising all raw data and graphical plots. The stand-alone program is controlled via a graphical user interface and can batch-process a multitude of sequences. Furthermore, it comes with pre-computed tetranucleotide usage patterns for 166 prokaryote chromosomes, providing a useful reference dataset and source for data-mining. CONCLUSIONS: Up to now, the analysis of skewed oligonucleotide distributions within DNA sequences is not a commonly used tool within metagenomics. With the TETRA web-service and stand-alone program, the method is now accessible in an easy to use manner for a broad audience. This will hopefully facilitate the interrelation of genomic fragments from metagenome libraries, ultimately leading to new insights into the genetic potentials of yet uncultured microorganisms

Development of bambangan (Mangifera pajang) carbonated drink

Mangifera pajang Kostermans or bambangan is a popular fruit among Sabahan due to its health and economic values. However, the fruit is not fully commercialized since it is usually been used as traditional cuisine by local people. Thus, development of bambangan fruit into carbonated drink was conducted to produce new product concept. The objectives of this study were to conceptualize, formulate, evaluate consumer acceptance, and determine physicochemical properties and nutritional composition of the accepted product. Method used in conceptualising the product was based on questionnaire. The consumer acceptance was evaluated based on descriptive and affective tests with four product formulations tested. The physicochemical properties on carbon dioxide volume, colour, pH, total acidity, total soluble solid (TSS) and viscosity were highlighted, meanwhile nutritional composition on fat, protein, carbohydrates and energy content were determined. About 77% respondents gave positive feedback, and 69% respondents decided this product is within their budget. The formulation of 5% bambangan pulp, 70% water, 25% sugar and 0.2% citric acid was highly accepted in descriptive and affective tests with 4.4 and 6.39 mean scores, respectively. The physicochemical properties and nutritional composition of the acceptance product were in optimum value except for colour, total acidity and TSS. Overall, this study showed that the product has high potential to be commercialized as new product concept, and heritage of indigenous people can be preserved when this fruit is known regionally

An evaluation of scaffolding for virtual interactive tutorials

Scaffolding refers to a temporary support framework used during construction. Applied to teaching and learning it describes measures to support a learner to become confident and self-reliant in a subject. In a Web environment scaffolding features need to replace the instructor. We discuss our approach to Web-based scaffolding based on the cognitive apprenticeship and activity theories. We suggest a set of four scaffold types that have made our scaffolding-supported virtual interactive tutorial successful. We present a novel evaluation approach for virtual tutorials that is embedded into an iterative, evolutionary instructional design

Combination of web usage, content and structure information for diverse web mining applications in the tourism context and the context of users with disabilities

188 p.This PhD focuses on the application of machine learning techniques for behaviourmodelling in different types of websites. Using data mining techniques two aspects whichare problematic and difficult to solve have been addressed: getting the system todynamically adapt to possible changes of user preferences, and to try to extract theinformation necessary to ensure the adaptation in a transparent manner for the users,without infringing on their privacy. The work in question combines information of differentnature such as usage information, content information and website structure and usesappropriate web mining techniques to extract as much knowledge as possible from thewebsites. The extracted knowledge is used for different purposes such as adaptingwebsites to the users through proposals of interesting links, so that the users can get therelevant information more easily and comfortably; for discovering interests or needs ofusers accessing the website and to inform the service providers about it; or detectingproblems during navigation.Systems have been successfully generated for two completely different fields: thefield of tourism, working with the website of bidasoa turismo (www.bidasoaturismo.com)and, the field of disabled people, working with discapnet website (www.discapnet.com)from ONCE/Tecnosite foundation

Data mining technology for the evaluation of web-based teaching and learning systems

Instructional design for Web-based teaching and learning environments causes problems for two reasons. Firstly, virtual forms of teaching and learning result in little or no direct contact between instructor and learner, making the evaluation of course effectiveness difficult. Secondly, the Web as a relatively new teaching and learning medium still requires more research into learning processes with this technology. We propose data mining – techniques to discover and extract knowledge from a database – as a tool to support the analysis of student learning processes and the evaluation of the effectiveness and usability of Web-based courses. We present and illustrate different data mining techniques for the evaluation of Web-based teaching and learning systems

Evaluation of usage patterns for web-based educational systems using web mining

Virtual courses often separate teacher and student physically from one another, resulting in less direct feedback. The evaluation of virtual courses and other computer-supported educational systems is therefore of major importance in order to monitor student progress, guarantee the quality of the course and enhance the learning experience for the student. We present a technique for the usage evaluation of Web-based educational systems focussing on behavioural analysis, which is based on Web mining technologies. Sequential patterns are extracted from Web access logs and compared to expected behaviour