nagnag protocols

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nagnag specifications

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Unique identifier OMICS_14621
Name nagnag
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data Genome annotation, genome files and corresponding species RNA-seq
Input format GTF, GFF, BAM
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License GNU General Public License version 3.0
Computer skills Advanced
Version 1.0.3
Stability Stable
Maintained Yes

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  • person_outline Xiaoyong Sun <>

Publication for nagnag

nagnag in pipelines

 (2)
2014
PMCID: 4068082
PMID: 24995327
DOI: 10.1155/2014/736798

[…] tool (samtools) was used to store, sort, and index the binary sam data (bam files) with respect to sequence alignment (http://samtools.sourceforge.net) []., to identify lincrna containing nagnag alternative splicing sites, we screened the lincrna sequences using the classical expression of the “nagnag” motif. alignment of rna-seq reads to the nagnag splicing junctions was used […]

2007
PMCID: 1892095
PMID: 17570866
DOI: 10.1186/1471-2105-8-S5-S7

[…] errors in larger numbers than dense blocks of errors. the program genomeflicer by mielordt et al. [] admits at most 2 errors in a window of length 20 in order to confirm genes and to distinguish nagnag acceptor isoforms []. we also expect that clustdb helps to study highly repetitive genes, a problem described especially challenging by check []. we developed clustdb to play a major role […]


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nagnag in publications

 (44)
PMCID: 5621691
PMID: 28961258
DOI: 10.1371/journal.pone.0185126

[…] more than 50% splicing events. this allows the splicing machinery to skip a stop codon and synthesise the p53 protein with a single amino acid deletion (p53δy126). the 378c>g mutation creates the nagnag motif that contains two 3′ ss in tandem. hiller et al., 2004 [] estimated that the nagnag motif is present in 30% of human genes and suggested that it may play a functional role in about 5% […]

PMCID: 5555464
PMID: 28626003
DOI: 10.1534/g3.117.042622

[…] isoform (see figure s2b). the other four refseq transcripts represent alternatively spliced variants of the long isoform xm_009305336. alternative splicing occurs at tandem splice acceptors with a nagnag motif found at 3′ acceptor splice sites of exon 3 (transcript xm_017358057), exon 8 (transcript xm_017358056), and exon 15 (transcript xm_017358058). alternative tandem splicing of mrna leads […]

PMCID: 5619915
PMID: 28391323
DOI: 10.1093/gbe/evx012

[…] by at least 10 reads). this comparison showed a clear preference for minor slts sites to be located near major slts sites, in particular a separation of exactly three nucleotides (so-called nagnag acceptor sites; ). on the other hand, many other minor splice sites were found dozens or hundreds of nucleotides away from the major site (). notably, though, for the vast majority of genes, […]

PMCID: 5123294
DOI: 10.1186/s12864-016-3103-6

[…] predictor but not by the controller and often reflect a built-in stringency of the controller. in order to distinguish subtle modifications in the regulation of alternative transcription, such as nagnag alternative transcripts [] that add or delete one amino acid next to an exon junction, the controller rejects every pair that contains deletions in near junctions. using the nucleotide […]

PMCID: 5092172
PMID: 27768061
DOI: 10.3791/54473

[…] tandem splice site. acceptor tandem splice sites are more frequent43 and the principles of the outlined protocol could serve as a starting point for developing assays for coincidence detection of nagnag splicing and other splicing events within 200 nucleotides. other potential applications include quantification of coincidence of other subtle sequence differences, like indels or double/triple […]


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nagnag institution(s)
Affiliated Hospital of Shandong University of Traditional Chinese Medicine, Shandong, China; Plant Functional Biology and Climate Change Cluster (C3), University of Technology Sydney, Sydney, NSW, Australia; Preventive Medicine-Health and Biomedical Informatics, Northwestern University, Chicago, IL, USA; Department of Plant Pathology, Nanjing Agricultural University, Nanjing, China; Agricultural Big-Data Research Center, College of Information Science and Engineering, Shandong Agricultural University, Shandong, China

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