title: nagnag: Identification and quantification of NAGNAG alternative splicing using RNA-Seq data.
abstract: 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.
authors.affiliation: Affiliated Hospital of Shandong University of Traditional Chinese Medicine, No. 42 Wenhua West Road, Jinan, Shandong 250011, China.
authors.forename: Xiaoyan
authors.initials: X
authors.lastname: Yan
authors.affiliation: Plant Functional Biology and Climate Change Cluster (C3), University of Technology Sydney, PO Box 123, Broadway, NSW 2007, Australia.
authors.forename: Gaurav
authors.initials: G
authors.lastname: Sablok
authors.affiliation: Preventive Medicine-Health and Biomedical Informatics, Northwestern University, Chicago, IL 60611, United States.
authors.forename: Gang
authors.initials: G
authors.lastname: Feng
authors.affiliation: Department of Plant Pathology, Nanjing Agricultural University, Weigang Road, Nanjing 210095, China.
authors.forename: Jiaxin
authors.initials: J
authors.lastname: Ma
authors.affiliation: Department of Plant Pathology, Nanjing Agricultural University, Weigang Road, Nanjing 210095, China.
authors.forename: Hongwei
authors.initials: H
authors.lastname: Zhao
authors.affiliation: Agricultural Big-Data Research Center, College of Information Science and Engineering, Shandong Agricultural University, Taian, Shandong 271018, China. Electronic address: johnsunx1@gmail.com.
authors.forename: Xiaoyong
authors.initials: X
authors.lastname: Sun
mesh_terms: D017398:Alternative Splicing; D020816:Amino Acid Motifs; D017423:Sequence Analysis, RNA; D020506:Untranslated Regions
chemical_list: D020506:Untranslated Regions
keywords: Alternative splicing; Differential splicing; Expression quantification; NAGNAG motif