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Generation and Bioinformatic Analysis of Synthetic Ago HITS-CLIP Data
Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology.
2013 (English)Independent thesis Advanced level (degree of Master (Two Years)), 30 credits / 45 HE creditsStudent thesis
Abstract [en]

Micro-RNAs (miRNAs) have been discovered to regulate messenger RNA (mRNA) translation and degradation. Various recent studies have been focused on miRNA target prediction, in order to get a better understanding of the rules and nature of miRNA regulation over mRNAs. In this project we aim to create a software module to identify miRNA target sites on mRNAs. As basis to this project, we refer to a study that identified a platform for miRNA-mRNA interaction in protein-RNA complexes in mouse brain (AGO HITS-CLIP study). We propose a probabilistic model of the data from this study, and generate synthetic sample data according to this model, in order to create a test bed for a discovery module. Our discovery module analyzes the sample data to identify peak regions where the interaction density is high. We present results both on synthetic sample data and data from the AGO HITS-CLIP study to evaluate our module.

Place, publisher, year, edition, pages
IT, 13 039
National Category
Engineering and Technology
URN: urn:nbn:se:uu:diva-204891OAI: diva2:640047
Educational program
Master Programme in Computer Science
Available from: 2013-08-12 Created: 2013-08-12 Last updated: 2013-08-12Bibliographically approved

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