Comparison between relational database and XML in querying motif sequence

Abstract

An enterprise information approach is the process of building models which include with process models, data models and resource models. An enterprise in general is a unit of economic organization or activity which these activities are required to develop and deliver products or services to a customer. An enterprise also includes a number of functions and operations. The aim of this research is to study an enterprise approach and their appropriate model to integrate multiple biological data use by the scientist in protein secondary structure prediction process. This project needs to investigates the data format and database will be use by the scientist at the Bioinformatics Research Lab, FBB, UTM in order to predict protein secondary structure process. The size, complexity and number of database used for predict protein secondary structure process and integrating all the data from the different database into one database is a challenging problem. This project approach have integrated different database such as Prosite, Blast, Prints and PDB and transformed these databases in flat file format and other format into relational form using XML and asp.net. As a result, this project showed some tool can search different data and different sizes of protein secondary structure data stored in the relational database and the result can be retrieved faster and reliable compared to XQuery direct from the XML file. A prototype web based user interface is provided to allow user access and search for protein secondary structure prediction in repository and local relational database.