Mejora de la plataforma web de análisis RNA-Seq en S. lycopersicum, TomExpress

Díaz Uzquiano, Marina (2020). Mejora de la plataforma web de análisis RNA-Seq en S. lycopersicum, TomExpress. Proyecto Fin de Carrera / Trabajo Fin de Grado, E.T.S. de Ingeniería Agronómica, Alimentaria y de Biosistemas (UPM), Madrid, España.

Description

Title: Mejora de la plataforma web de análisis RNA-Seq en S. lycopersicum, TomExpress
Author/s:
  • Díaz Uzquiano, Marina
Contributor/s:
  • Rodríguez González, Alejandro
Item Type: Final Project
Degree: Grado en Biotecnología
Date: July 2020
Subjects:
Faculty: E.T.S. de Ingeniería Agronómica, Alimentaria y de Biosistemas (UPM)
Department: Lenguajes y Sistemas Informáticos e Ingeniería del Software
Creative Commons Licenses: Recognition - No derivative works - Non commercial

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Abstract

Over the last few years, new sequencing methods and assembly techniques have allowed researchers to perform faster and easier assemblies of genomes and transcriptomes. This has met with an increase of said assemblies in the public domain. For instance, the new tomato genome of 2010, which brought the interest of the scientific community and the tomato became a plant model for the Solanacea family. Thanks to this resource and the new next-generation sequencing technologies, RNA-Seq (RNA sequencing) became the preferred method for studying the tomato transcriptome and its expression patters. Nonetheless RNA-Seq remained an expensive technique for some laboratories. This where the idea of TomExpress arose: a web platform that holds public RNA-Seq data and allows users to exploit it through different analysis tools. Thanks to TomExpress, researchers are now able to analyze tomato RNA-Seq data as if they had produced the sequencing themselves. The RNA-Seq projects that populate TomExpress’ database, are manually curated in order to select relevant sequencing conditions. The raw data from these projects is then processed and normalized through a common pipeline. Thus, making TomExpress a reliable source of information. TomExpress became a popular tool within the scientific community that studied Solanum lycopersicum L., and had an on-growing community of users. The increase of new users came along with an increased demand of new data analysis tools, and even the demand of new TomExpress-alike platforms. In addition to that, TomExpress needed updates to improve user experience. Also, a new tomato genome was sequenced and used in TomExpress as the reference genome, but it lacked functional annotation, so this new information had to be produced and added to the database. This current project describes the updates that were made in TomExpress from version v.18.0.0 to version v.20.2.0. Including the making of two new correlation networks, and the functional annotation of the SLYMIC tomato genome.

More information

Item ID: 66823
DC Identifier: https://oa.upm.es/66823/
OAI Identifier: oai:oa.upm.es:66823
Deposited by: Biblioteca ETSI Agrónomos
Deposited on: 22 Apr 2021 10:14
Last Modified: 22 Jun 2021 22:30
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