Multimodal Interface for DNA Alignment of Sequences

Major research efforts in Bioinformatics include sequence alignment, gene finding, genome assembly, protein structure alignment, protein structure prediction, prediction of gene expression and protein-protein interactions, and the modeling of evolution. To perform these specific tasks different tools are used. Using these tools separately is a time consuming, inefficient and expensive process. MIDAS is a tool that integrates sequence alignment, genome annotation, and spectral clustering and alignment under the same application. The challenge in this project is in representing the knowledge and analyzing the genome data. The DNA data is first transformed into Fourier domain and clustered in MATLAB based on Euclidean distances between the sequences. Our tool allows visualizing the DNA spectra together with a hierarchical tree in a multimodal interface. This in turn enables a bioinformatician to analyze patterns of a group of sequences. MIDAS is a standalone application which provides an interface around standard sequence alignment tools such as BLAT, ClustalW, as well as newer alignment tools such as Spectrogram analysis via integrating MATLAB code, server connections and data visualizations. JAVA is used as the main programming language during the development of MIDAS. The Spectrogram Analysis script-files in MATLAB are converted into JAVA classes. These classes are used to run standalone MATLAB applications from within JAVA.Media and Knowledge EngineeringElectrical Engineering, Mathematics and Computer Scienc