Uncovering the Complexity of Transcriptomes with RNA-Seq
In recent years, the introduction of massively parallel sequencing platforms for Next Generation Sequencing (NGS) protocols, able to simultaneously sequence hundred thousand DNA fragments, dramatically changed the landscape of the genetics studies. RNA-Seq for transcriptome studies, Chip-Seq for DNA...
Main Authors: | , , , |
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Format: | Article |
Language: | English |
Published: |
Hindawi Limited
2010-01-01
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Series: | Journal of Biomedicine and Biotechnology |
Online Access: | http://dx.doi.org/10.1155/2010/853916 |
Summary: | In recent years, the introduction of massively parallel sequencing platforms for Next Generation Sequencing (NGS) protocols, able to simultaneously sequence hundred thousand
DNA fragments, dramatically changed the landscape of the genetics studies. RNA-Seq for transcriptome studies, Chip-Seq for DNA-proteins interaction,
CNV-Seq for large genome nucleotide variations are only some of the intriguing new
applications supported by these innovative platforms. Among them RNA-Seq
is perhaps the most complex NGS application. Expression levels of specific genes,
differential splicing, allele-specific expression of transcripts can be accurately determined by RNA-Seq experiments to address many biological-related issues. All these attributes are not readily achievable from previously widespread
hybridization-based or tag sequence-based approaches. However, the unprecedented level
of sensitivity and the large amount of available data produced by NGS platforms provide
clear advantages as well as new challenges and issues. This technology brings the
great power to make several new biological observations and discoveries, it also requires
a considerable effort in the development of new bioinformatics tools to deal with these
massive data files. The paper aims to give a survey of the RNA-Seq
methodology, particularly focusing on the challenges that this application presents both
from a biological and a bioinformatics point of view. |
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ISSN: | 1110-7243 1110-7251 |