NNSplice protocols

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Associated diseases

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NNSplice specifications

Information


Unique identifier OMICS_09612
Name NNSplice
Interface Web user interface
Restrictions to use None
Input data Single/multiple sequences
Input format FASTA
Computer skills Basic
Version 0.9
Stability Stable
Maintained Yes

Maintainer


  • person_outline NNSplice Team <>

NNSplice in pipelines

 (3)
2017
PMCID: 5520478
PMID: 28487558
DOI: 10.1038/emi.2017.13

[…] from genebank (see for accession numbers and details). splicing sites were determined following what was experimentally demonstrated for amdv, donor and acceptor sites were confirmed using nnsplice, and splicing events were reproduced in silico to determine the complete coding sequences for all viral proteins, which were then translated into amino acid sequences., nucleotide […]

2017
PMCID: 5623842
PMID: 28754744
DOI: 10.15252/emmm.201607376

[…] inframe insertion/deletion, splicing variants (predicted to affect splicing by at least two out three programs including human splice finder (desmet et al, ), maxent (desmet et al, ), and nnsplice (reese et al, ), or missense variants predicted to be damaging by either sift (ng & henikoff, ) and polyphen‐2 (adzhubei et al, ). a putative pathogenic variant is confirmed […]

2014
PMCID: 4061088
PMID: 24937211
DOI: 10.1371/journal.pone.0100176

[…] intron/exon boundaries we combined the putative intron and exon sequences (genbank nos.: jx258913 and jx258914) to obtain a 532 base pair sequence of b. calamita locus b allele ‘buca b2’ and used nnsplice version 0.9 , as implemented on http://www.fruitfly.org/seq_tools/splice.html, to predict splice sites., sequences were aligned and edited manually using bioedit v. 7.0.9 . the relative […]


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NNSplice in publications

 (221)
PMCID: 5951831
PMID: 29760383
DOI: 10.1038/s41467-018-04322-5

[…] effect of splice mutations was predicted on the major transcript with the alamut visual software (interactive software, rouen, france), which contains the algorithms splicesitefinder, maxentscan, nnsplice, genesplicer, human splicing finder, ese-finder, and rescue-ese. mutation data from all tcga series were retrieved from the gdc portal in day 29th of september 2017. frequencies of germline […]

PMCID: 5948732
PMID: 29751740
DOI: 10.1186/s12881-018-0590-0

[…] impact of the genomic variations found in the present study, we used the alamut® visual software. this software uses the following relevant prediction tools: i) splice site finder-like, maxentscan, nnsplice, genesplicer, human splicing finder and ese for splicing prediction ii) align gvgd, sift, mutationtaster, polyphen-2 and kd4v for missense prediction., to check all the variants detected […]

PMCID: 5941609
PMID: 29739362
DOI: 10.1186/s12881-018-0592-y

[…] to disrupt splicing and skipping of exon10 with high (100%) confidence score using three different splice prediction tools: maxent (http://genes.mit.edu/burgelab/maxent/xmaxentscan_scoreseq.html), nnsplice (http://www.fruitfly.org/seq_tools/splice.html) and hsf (http://www.umd.be/hsf3/). the mutation co-segregated with the disease in the family. it was found in a homozygous state in the two […]

PMCID: 5941635
PMID: 29739340
DOI: 10.1186/s12881-018-0585-x

[…] polyphen2 [] sift [] and mutation taster [] were used for in silico pathogenicity prediction of the mutations. to address the effect of the splice site mutations, two softwares were used: nnsplice 0.9 version (http://www.fruitfly.org/seq_tools/splice.html) and netgene 2 server (http://www.cbs.dtu.dk/services/netgene2/)., in order to determine whether mutations in the slc26a4 gene […]

PMCID: 5924558
PMID: 29673180
DOI: 10.3390/genes9040216

[…] biosoftware, rouen, france) with the splicesitefinder (http://www.genet.sickkids.on.ca/~ali/splicesitefinder.html), maxentscan (http://genes.mit.edu/burgelab/maxent/xmaxentscan_scoreseq.html), nnsplice (http://www.fruitfly.org/seq_tools/splice.html) and genesplicer (http://www.cbcb.umd.edu/software/genesplicer/gene_spl.shtml), and humansplicingfinder (http://www.umd.be/hsf/) which combines […]


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