Visualization enhancement of bioinformatics software for genetic recombination via UCSC genome browser

• Main Author: Wong, Ryan Wei Jiat
• Other Authors: Zheng Jie
• Format: Final Year Project
• Language: English
• Published: 2014
• Subjects: DRNTU::Engineering::Computer science and engineering::Information systems::Information systems applications
• Online Access: http://hdl.handle.net/10356/59903
• Institution: Nanyang Technological University

The objective of the project is to enhance the visualization aspect of the Bioinformatics software, LDsplit. Its ability to estimate recombination hotspot-SNP associations is remarkable for future research. However the results, recombination profiles, cannot be visualized and utilized as well as many would like to. To address this issue, UCSC Genome browser has been identified with the required visualization tool that will aid in more precise and detailed analytical study. UCSC Genome browser has been widely used in the biology research community and its huge databases will further any studies to a large extent. The visualization improvement of LDsplit is paramount of significance. Recombination is a fundamental cellular process, and the understanding of its mechanism has impactful applications in different areas of biology. For instance, it plays key role in devastating diseases such as Down syndrome and cancer; recently, IBM and National Geographic launched a project to reconstruct the history of human ethnic groups around the world by estimating ancestral recombination events. In short, the enhancement of LDsplit, using UCSC Genome browser, will bring about momentous breakthrough in research. In this project the development environment - local UCSC Genome browser - and the incorporation of LDsplit into the local Genome browser through a java program ‘retrieved.java’ was successfully developed. Users of LDsplit will now be able to fully utilize the Local UCSC Genome browser. It is web-based, allowing collaborators to take advantage of the upgraded functionalities like extensive visualization features and services e.g. zooming/analysis of tracks across Genome-wide level. This report will also present to users the methodologies to re-create such development as described above using graphical instructions which will be helpful to overcome technical difficulties.