RNA Interference Analyzer

Bc. Michal Škrdla

Master's thesis

Abstract:

This master thesis is focused on RNA Interference (RNAi) effect and its usage in gene silencing. RNAi uses a special very short subsequence of silenced mRNA sequence. It is possible to find usable subsequence on its pursuant biochemical properties and structural characteristics. Specifically, this work studies relationship between mentioned theoretically calculated property of subsequences and their efficiency for RNAi for any input set of experimental data. Furthermore, in this work software RNA Interference Analyzer is designed, implemented, tested and used. The Analyzer computes biochemical or structural property for input sets of experimental data (mRNA sequences, their subsequences and efficiency of subsequences). According to this property the Analyzer makes statistical analyses which are displayed and offers the ability to download results for next usage. By this software, a set of analyses for data from CGB and Sonnhammer databases was realized. In these analyses, factual dependence of property value on subsequence RNAi efficiency was verified. These results fit outcomes presented in literature which validate usability of the Analyzer.

Kľúčové slová

RNA Interference (RNAi), Gene Silencing, Average Accessibility, GC Content, Ui-Tei Rules, Tuschl Rules, Amarzguioui Rules, Reynolds Rules, Breaking Energy, Java

Jazyk práce: Czech

Datum vytvoření / odevzdání či podání práce: 16. 2. 2006

Obhajoba závěrečné práce

• Obhajoba proběhla 16. 2. 2006
• Vedúci: doc. RNDr. Radka Svobodová Vařeková, Ph.D.

Masaryk University

Faculty of Informatics

Master programme / odbor:
Informatics / Informatics