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nagnag: Identification and quantification of NAGNAG alternative splicing using RNA‐Seq data
Author(s) -
Yan Xiaoyan,
Sablok Gaurav,
Feng Gang,
Ma Jiaxin,
Zhao Hongwei,
Sun Xiaoyong
Publication year - 2015
Publication title -
febs letters
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.593
H-Index - 257
eISSN - 1873-3468
pISSN - 0014-5793
DOI - 10.1016/j.febslet.2015.05.029
Subject(s) - rna splicing , intron , alternative splicing , proteome , computational biology , biology , rna , gene isoform , identification (biology) , gene , rna seq , genetics , transcriptome , gene expression , botany
Regulation of proteome diversity by alternative splicing has been widely demonstrated in plants and animals. NAGNAG splicing, which was recently defined as a tissue specific event, results in the production of two distinct isoforms that are distinguished by three nucleotides (NAG) as a consequence of the intron proximal or distal to the splice site. Since the NAGNAG mechanism is not well characterized, tools for the identification and quantification of NAGNAG splicing events remain under-developed. Here we report nagnag, an R-based NAGNAG splicing detection tool, which accurately identifies and quantifies NAGNAG splicing events using RNA-Seq. Overall, nagnag produces user-friendly visualization reports and highlights differences between the DNA/RNA/protein across the identified isoforms of the reported gene. The package is available on https://sourceforge.net/projects/nagnag/files/; or http://genome.sdau.edu.cn/research/software/nagnag.html.