TEcandidates: prediction of genomic origin of expressed transposable elements using RNA-seq data | Zendy

Braulio ValdebenitoMaturana | Zendy; Gonzalo Riadi | Zendy

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TEcandidates: prediction of genomic origin of expressed transposable elements using RNA-seq data

Author(s) -

Braulio ValdebenitoMaturana,

Gonzalo Riadi

Publication year - 2018

Publication title -

bioinformatics

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 3.599

H-Index - 390

eISSN - 1367-4811

pISSN - 1367-4803

DOI - 10.1093/bioinformatics/bty423

Subject(s) - rna seq , transposable element , computational biology , pipeline (software) , genome , annotation , reference genome , biology , sequence assembly , gene annotation , genomics , computer science , transcriptome , genetics , gene , gene expression , programming language

In recent years, Transposable Elements (TEs) have been related to gene regulation. However, estimating the origin of expression of TEs through RNA-seq is complicated by multi-mapping reads coming from their repetitive sequences. Current approaches that address multi-mapping reads are focused in expression quantification and not in finding the origin of expression. Addressing the genomic origin of expressed TEs could further aid in understanding the role that TEs might have in the cell.

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