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Professors of the Master’s Degree in Bioinformatics develop the first tool for sequencing nanopores on a large-scale

Seqüenciació de nanoporos

Joaquín Dopazo, member of the Academic Coordinating Committee and professor of the Master’s Degree in Bioinformatics has developed in his genomics laboratory of the Príncipe Felipe Research Centre (CIPF) the first tool for sequencing nanopores on a large-scale. This project has also had the collaboration of Vicente Arnau, director of the Master’s Degree, recently graduated in Computer Engineering and awarded with the prize for the best Undergraduate Degree Final Project of his promotion. The developed bioinformatics solution supposes a new tool for the analysis of sequencing of DNA data obtained with Nanopore technology.

18 april 2016

The Genomics Systems Laboratory of the CIPF Centre directed by Dopazo has published in the journal BMC Bioinformatics the article “HPG pore: an efficient and scalable framework for nanopore sequencing data” on its new tool. HPG Pore arises in front of the unlimited rise of data generated by sequencing technology in real time that is expected for the future. This tool aims to solve saturation of information problems, allowing for an efficient management and analysis of great large volumes of genomic data. Ultimately, the objective is easily exploring and analysing the growing volume of sequencing information that generate nanopores technologies.

The recent sequencing technologies present important innovation that allow for advancing in the data processing related to DNA. Among them we find the novel nanopores technology , which allows for obtaining the DNA sequence with a very low cost, therefore in the future the DNA tests could be more frequent in the detection and treatment of diseases. The sequencing technology Nanopore has shown being clinically efficient in the pathogens surveillance in real time, since it allows for quickly identifying the strain and detecting resistance genes or even the structural variation in cancer.

When passing the deoxyribonucleic acid sequence through these little pores, their nucleotides components cause characteristic distortions, which are traduced in measurable electric changes. So that we can virtually “read” the nucleotide sequencing in real time.

With this new technology the DNA is forced to go through an artificial structure that remembers the pores there are in the surface of the bacteria. The device in charge of carrying out the reading is of the size of a mobile phone and it can be connected through a USB port to the computer. According the experts, the indiscriminate use of this technology could collapse in the future the current data processing systems, so this work is presented as the first solution for the control of this information in a scalable way, aiming to process the growing sequencing volume that is generated.

“It is possible that the nanopores sequencing spreads in the future due to its portability and its capacity of sequencing large DNA molecules fragments without previous amplification.”

The project HPG Pore is the first scalable bioinformatics tool that studies the nanopores sequencing data and that can be executed in individual teams, as well as in modern systems of distributed storage, which work with an open technology called Hadoop, which allows for virtually data limitless scale.

According to Dopazo, it is possible that the sequencing of nanopores spreads in the future due to its portability and its capacity of sequencing large DNA molecules without previous amplification. Nowadays, the existing tools for the analysis of this information are just prepared to administrate small projects and they are not scalable.

For this reason, HPG Pore supposes a great advance, since it allows for an effective management of these massive data and constitutes a solution to the needs of the analysis in a near future, as well as a model for the creation of new tools with which treating big volumes of genomic data.

 
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