nagnag: Identification and quantification of NAGNAG alternative splicing using RNA-Seq data

Yan, X; Sablok, G; Feng, G; Ma, J; Zhao, H; Sun, X

nagnag: Identification and quantification of NAGNAG alternative splicing using RNA-Seq data

Yan, X Sablok, G

Feng, G Ma, J Zhao, H Sun, X

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Publication Type:: Journal Article
Citation:: FEBS Letters, 2015, 589 (15), pp. 1766 - 1770
Issue Date:: 2015-07-03

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Field	Value	Language
dc.contributor.author	Yan, X	en_US
dc.contributor.author	Sablok, G https://orcid.org/0000-0002-4157-9405	en_US
dc.contributor.author	Feng, G	en_US
dc.contributor.author	Ma, J	en_US
dc.contributor.author	Zhao, H	en_US
dc.contributor.author	Sun, X	en_US
dc.date.available	2020-05-25T19:11:29Z
dc.date.issued	2015-07-03	en_US
dc.identifier.citation	FEBS Letters, 2015, 589 (15), pp. 1766 - 1770	en_US
dc.identifier.issn	0014-5793	en_US
dc.identifier.uri	http://hdl.handle.net/10453/37632
dc.description.abstract	© 2015 Federation of European Biochemical Societies. 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.	en_US
dc.relation.ispartof	FEBS Letters	en_US
dc.relation.isbasedon	10.1016/j.febslet.2015.05.029	en_US
dc.subject.classification	Biochemistry & Molecular Biology	en_US
dc.subject.mesh	Untranslated Regions	en_US
dc.subject.mesh	Sequence Analysis, RNA	en_US
dc.subject.mesh	Alternative Splicing	en_US
dc.subject.mesh	Amino Acid Motifs	en_US
dc.title	nagnag: Identification and quantification of NAGNAG alternative splicing using RNA-Seq data	en_US
dc.type	Journal Article
utslib.citation.volume	15	en_US
utslib.citation.volume	589	en_US
utslib.for	0304 Medicinal and Biomolecular Chemistry	en_US
utslib.for	0601 Biochemistry and Cell Biology	en_US
utslib.for	0603 Evolutionary Biology	en_US
pubs.embargo.period	Not known	en_US
pubs.organisational-group	/University of Technology Sydney
pubs.organisational-group	/University of Technology Sydney/Faculty of Science
pubs.organisational-group	/University of Technology Sydney/Strength - C3 - Climate Change Cluster
utslib.copyright.status	open_access
pubs.issue	15	en_US
pubs.publication-status	Published	en_US
pubs.volume	589	en_US

Abstract:

© 2015 Federation of European Biochemical Societies. 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.

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http://hdl.handle.net/10453/37632