Bilardi, Alessandra (2008) Regolatori di RNA e loro sequenze bersaglio. [Tesi di dottorato]
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Bioinformatics is an interdisciplinary subject which integrates fields like biology, chemistry, biophysics, biostatist ics and computer science to solve biological problems. Its goal is to enable the discovery of new biological insights as well as to create global perspective from which unifying principles in biology can be discerned. The first and foremost biological problem is the annotation of functional genes hidden in sequenced genomes which can be effectively scanned by computational approaches. The other problems include protein structure prediction, drug discovery, metabolic pathway manipulation and much more. These problems can be consolved
in a faster way by using bioinformatics as a catalyst.
In these four years I have been involved in the annotation of structural and functional genes. In prokariotes I study Rho dependent terminator (RDT) as attenuator and/or terminator of
transcriptional unit (TU). In gram negative bacteria, RDT study is important to understand alternative TUs inside each operon so as it is weighty to identify Rho independent terminator (RIT). If we know where terminators (RDT and RIT) are located then we could cluster genes in operons and so we could contribute in annotating structural and functional genes. In the literature, documented RDT are less than 40 and there are 18 only in Escherichia coli. There is not a RDT prediction program and not even a RDT consensus sequence but only some features that they describe RDT shares. I designed first algorithm about RDT prediction and I suggested first RDT consensus sequence with a weighed matrix. I designed oligos and conditions about microarray experiments in order to confirm our RDT predictions and to understand about Rho functional correlation with genes that they have got a RDT. Microarray results confirmed that I can use intensity of oligos to calculate if one putative RDT exits. But to confirm putative RDTs we do other microarray experiments.
In eukariotes I study plants microRNA and their targets as genes annotated hardly and their function. Standard automatic gene annotation identifies and/or predicts genes that they will be translate. There are programs that they identify and/or predict genes about transfer, ribosomal and microRNA but there is little about microRNA and their targets in plants. I am involved in the annotation of microRNA genes and their targets in Vitis vinifira sequencing genome project. I implemented and tested more finder and predictor programs about microRNA genes and their targets for plants and animals. I proposted an integrated method with which I obtain positive results. Results about microRNA gene prediction could be validate with highthroughput sequencing approach. Results about microRNA target prediction protocol could be the starting point for lab experiments necessary for the validation of microRNA targets.
Beyond, I contributed to visualize data and to do advanced queries with databases about lab projects. I gained through experience and manage a generic genome browser and a advanced query tool about GMOD project. GMOD is the Generic Model Organism Database Toolkit, a collection of software tools for creating and managing genome-scale biological databases. I
realized new versions of some scripts about GMOD tool that they will be proposed in the next GBrowse release. I implemented and tested scripts more fast than real GBrowse scripts and without some bugs. Results of configuration and design about visualization and querying of databases are important since our genomics research group will be the responsible for the development of the Vitis vinifera annotation platform.
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