Alexsys : Alexsys

    Responsible : Julie Thompson
    Participants : Julie Thompson
    Description : The last decade has provided access to a large amount of data resulting from high throughput genomic technologies, such as transcriptomics, proteomics or interactomics. However, this large scale accumulation of data is only a necessary preliminary in the understanding of the principles and fundamental mechanisms of life. Comparative sequence analyses and phylogenetic inferences play an essential role in the biological systems studies aimed at understanding this new data.
In this context, we are developing an expert system, AlexSys, for the construction, refinement, analysis and exploitation of multiple sequence alignments, combining diverse, complementary algorithms and incorporating additional information (structural, functional and evolutionary). A prototype platform is now available, built on the Unstructured Information Management Architecture (UIMA). The alignment methodology is based on ClustalW, but integrates several more powerful algorithms that significantly increase the efficiency and the quality of the multiple alignment. AlexSys also includes a number of diagnostic tests that allow us to automatically select the most suitable alignment algorithm, depending on the set of sequences to be aligned and the biological application.
The modular design of AlexSys facilitates the incorporation of new algorithms and will allow its continued evolution. In the future, we will incorporate more diverse components, covering aspects of genomic and protein data mining, validation and integration of structural/functional data, integrated with a set of different algorithms.