Bioinformatics Tools for RNA-seq Gene and Isoform Quantification Article Swipe

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Chi Zhang , Baohong Zhang , Michael S. Vincent , Shanrong Zhao ·

YOU? · · 2016 · Open Access · · DOI: https://doi.org/10.4172/2469-9853.1000140

In recent years, RNA-seq has emerged as a powerful technology in estimation of gene or transcript expression.'Union-exon' and transcript based approaches are widely used in gene quantification.The 'Union-exon' based approach is simple, but it does not distinguish between isoforms when multiple alternatively spliced transcripts are expressed from the same gene.Because a gene is expressed in one or more transcript isoforms, the transcript based approach is more biologically meaningful than the 'union exon'-based approach.However, estimating the expression of individual isoform is intrinsically challenging because different isoforms of a gene usually have a high proportion of genomic overlap.Recently, a number of tools have been developed for RNA-seq isoform quantification.We review those methods and their main features to serve as guidance for users to choose suitable tools for their specific projects.

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Computational Biology

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RNA-Seq Computational biology Gene isoform Gene Biology Bioinformatics Computer science Genetics Gene expression Transcriptome

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Type: article
Language: en
Landing Page: http://doi.org/10.4172/2469-9853.1000140
PDF: https://doi.org/10.4172/2469-9853.1000140
OA Status: diamond
Cited By: 11
References: 62
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DOI: https://doi.org/10.4172/2469-9853.1000140

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Title: Bioinformatics Tools for RNA-seq Gene and Isoform Quantification

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Type: article

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Language: en

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Publication year: 2016

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Publication date: 2016-01-01

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Authors: Chi Zhang, Baohong Zhang, Michael S. Vincent, Shanrong Zhao

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Landing page: https://doi.org/10.4172/2469-9853.1000140

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Concepts: RNA-Seq, Computational biology, Gene isoform, Gene, Biology, Bioinformatics, Computer science, Genetics, Gene expression, Transcriptome

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Cited by: 11

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