Thesis

"ChIP-Seq Analyzer": an efficient tool to manage, analyze and present mapped sequence data

Next Generation Sequencing (NGS) ChIP-Seq and RNA-Seq allow systematic study of genome wide protein-DNA binding and gene expression, respectively, and generation of hypotheses regarding gene regulation. NGS experiments generate vast amounts of data in the form of short sequences representing the locations of protein binding regions or transcribed genes across the genome under study. These datasets pose several challenges to a laboratory with limited bioinformatics support. I have developed a "ChIP-Seq Analyzer" application, a set of 3 core components for the automated processing of experimentally-determined binding regions. Components 1 and 3 combined provide a Graphical User Interface for uploading datasets, analyzing, and visualizing results from a single browser. Component 2 includes the core data analysis algorithms that calculate Nearest Distance Gene, perform Transcription Start Site analysis, and determine Overlapping Regions. The user can also analyze RNA-Seq data by itself, based on expression level and clustering by a k-means algorithm.

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