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http://hdl.handle.net/10609/90706
Title: Development of an API for miRNA sequencing data that converts mirGFF3 files to VCF
Author: Espín Garcia, Roderic
Director: Marco Galindo, Maria Jesús
Tutor: Pantano Rubiño, Lorena
Keywords: microRNA
VCF
web applications
Issue Date: 2-Jan-2019
Publisher: Universitat Oberta de Catalunya (UOC)
Abstract: MicroARN (also called miARN) are short RNA molecules with a nucleotides length of 20-25 that regulates gene expressions. miRNAs are essential to all biological processes and its associated with several human diseases. isomiRs are sequence variants from annotated miRNAs. isomiRs can also depend on sex or ethnicity. Currently, a project called mirtop unites research of miRNAs and isomiRs with the aim of promoting the development of downstream analysis tools. In that project a new format called mirGFF3 was originated, for the output of miRNA/isomiR detection and quantification results. The main goal of this project is to add a tool to the mirtop API that converts mirGFF3 format files to VCF (Variant Call Format). In this format, genetic variants respect the reference genome are stored, and is a file format very used in other useful bioinformatics tools. Python was the programming language chosen to implement the conversion tool. Synthetic and real samples will be used (already in mirGFF3 format) to test the functionality. A subsequent analysis (also with python) will be carried out by plotting graphs, although this analysis is independent from the mirtop project.
Language: English
URI: http://hdl.handle.net/10609/90706
Appears in Collections:Bachelor thesis, research projects, etc.

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