Computational Methods for Mapping, Assembly and Quantification for Coding and Non-coding Transcripts
The measurement of gene expression has long provided significant insight into biological functions. The development of high-throughput short-read sequencing technology has revealed transcriptional complexity at an unprecedented scale, and informed almost all areas of biology. However, as researchers...
Main Authors: | , , |
---|---|
Format: | Article |
Language: | English |
Published: |
Elsevier
2019-01-01
|
Series: | Computational and Structural Biotechnology Journal |
Online Access: | http://www.sciencedirect.com/science/article/pii/S2001037019300625 |
id |
doaj-89221ad40e234ada9a598d876f02c13d |
---|---|
record_format |
Article |
spelling |
doaj-89221ad40e234ada9a598d876f02c13d2020-11-25T02:39:20ZengElsevierComputational and Structural Biotechnology Journal2001-03702019-01-0117628637Computational Methods for Mapping, Assembly and Quantification for Coding and Non-coding TranscriptsIsaac A. Babarinde0Yuhao Li1Andrew P. Hutchins2Department of Biology, Southern University of Science and Technology, 1088 Xueyuan Lu, Shenzhen, ChinaDepartment of Biology, Southern University of Science and Technology, 1088 Xueyuan Lu, Shenzhen, ChinaCorresponding author.; Department of Biology, Southern University of Science and Technology, 1088 Xueyuan Lu, Shenzhen, ChinaThe measurement of gene expression has long provided significant insight into biological functions. The development of high-throughput short-read sequencing technology has revealed transcriptional complexity at an unprecedented scale, and informed almost all areas of biology. However, as researchers have sought to gather more insights from the data, these new technologies have also increased the computational analysis burden. In this review, we describe typical computational pipelines for RNA-Seq analysis and discuss their strengths and weaknesses for the assembly, quantification and analysis of coding and non-coding RNAs. We also discuss the assembly of transposable elements into transcripts, and the difficulty these repetitive elements pose. In summary, RNA-Seq is a powerful technology that is likely to remain a key asset in the biologist's toolkit. Keywords: RNA-Seq, Transcript, Genome, Transposable element, Long non-coding RNAhttp://www.sciencedirect.com/science/article/pii/S2001037019300625 |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Isaac A. Babarinde Yuhao Li Andrew P. Hutchins |
spellingShingle |
Isaac A. Babarinde Yuhao Li Andrew P. Hutchins Computational Methods for Mapping, Assembly and Quantification for Coding and Non-coding Transcripts Computational and Structural Biotechnology Journal |
author_facet |
Isaac A. Babarinde Yuhao Li Andrew P. Hutchins |
author_sort |
Isaac A. Babarinde |
title |
Computational Methods for Mapping, Assembly and Quantification for Coding and Non-coding Transcripts |
title_short |
Computational Methods for Mapping, Assembly and Quantification for Coding and Non-coding Transcripts |
title_full |
Computational Methods for Mapping, Assembly and Quantification for Coding and Non-coding Transcripts |
title_fullStr |
Computational Methods for Mapping, Assembly and Quantification for Coding and Non-coding Transcripts |
title_full_unstemmed |
Computational Methods for Mapping, Assembly and Quantification for Coding and Non-coding Transcripts |
title_sort |
computational methods for mapping, assembly and quantification for coding and non-coding transcripts |
publisher |
Elsevier |
series |
Computational and Structural Biotechnology Journal |
issn |
2001-0370 |
publishDate |
2019-01-01 |
description |
The measurement of gene expression has long provided significant insight into biological functions. The development of high-throughput short-read sequencing technology has revealed transcriptional complexity at an unprecedented scale, and informed almost all areas of biology. However, as researchers have sought to gather more insights from the data, these new technologies have also increased the computational analysis burden. In this review, we describe typical computational pipelines for RNA-Seq analysis and discuss their strengths and weaknesses for the assembly, quantification and analysis of coding and non-coding RNAs. We also discuss the assembly of transposable elements into transcripts, and the difficulty these repetitive elements pose. In summary, RNA-Seq is a powerful technology that is likely to remain a key asset in the biologist's toolkit. Keywords: RNA-Seq, Transcript, Genome, Transposable element, Long non-coding RNA |
url |
http://www.sciencedirect.com/science/article/pii/S2001037019300625 |
work_keys_str_mv |
AT isaacababarinde computationalmethodsformappingassemblyandquantificationforcodingandnoncodingtranscripts AT yuhaoli computationalmethodsformappingassemblyandquantificationforcodingandnoncodingtranscripts AT andrewphutchins computationalmethodsformappingassemblyandquantificationforcodingandnoncodingtranscripts |
_version_ |
1724786779821703168 |