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Construction of the Genomic Promoter Sequence Database and Web Application System

Author: LiZuo
Tutor: ZhouYanHong；LuFeng
School: Huazhong University of Science and Technology
Course: Applied Computer Technology
Keywords: promoter promoter prediction genomic promoter database visualization
CLC: TP311.52
Type: Master's thesis
Year: 2007
Downloads: 108
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Abstract


Identification and collection of genomic promoters and related TSS becomes a crucial problem.Participated in implementing a computational system for predicting promoters and related transcription start sites (TSSs). The biologic methods hardly tackle the whole problem with the explosion of genomic sequences,so the computational prediction of genomic promoters becomes an issue of consequence.A logitlinear model is designed to model the promoters for effectively integrating the proximal promoter information and the different sequence characteristics of promoters with different distances to the TSS. Based on the promoter model, an advanced system called ProKey to locate TSSs and promoters in mammalian genomes was developed. The comparison of the ability to predict TSSs with leading programs, DGSF and Eponine, demonstrated that the prediction accuracy of ProKey is significant higher than that of the well known programs, DGSF and Eponine.Constructed a genomic promoter sequence database. One ,by inspecting international official databases associated with promoter noting, and analysing and processing many of these data resources, Representative of reliable promoter data was extracted. On the other hand,the software ProKey was used on the prediction of the whole human genome. The results of both reliable and predicted data sets was analysed and processed, and the database management system,Mysql,was choosed to store and administrate it.A web application system for the genomic promoter sequence database was constructed based on B/S model,and releasing of the promoter data was provided. By analyzing the current Web database technology, a data textual search system easy for users to understand and operate was designed and realized. The way how to display the data was designed, and the visualization was realized based on a navigation strategy taking chromosome as the focus for the graphic display mode. And a visualization system on the basis of SVG language was constructed.

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CLC: > Industrial Technology > Automation technology,computer technology > Computing technology,computer technology > Computer software > Program design,software engineering > Software Engineering > Software Development
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