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Protocols

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 citations

 (247)
library_books

Outlier response to anti PD1 in uveal melanoma reveals germline MBD4 mutations in hypermutated tumors

2018
Nat Commun
PMCID: 5951831
PMID: 29760383
DOI: 10.1038/s41467-018-04322-5

[…] al. 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 m […]

call_split

Next generation sequencing reveals a new mutation in the LTBP2 gene associated with microspherophakia in a Spanish family

2018
BMC Med Genet
PMCID: 5948732
PMID: 29751740
DOI: 10.1186/s12881-018-0590-0
call_split See protocol

[…] l 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 in thi […]

call_split

Incorporating epilepsy genetics into clinical practice: a 360°evaluation

2018
PMCID: 5945675
PMID: 29760947
DOI: 10.1038/s41525-018-0052-9
call_split See protocol

[…] the Genome Aggregation Database (gnomAD) and HGMD Professional. Missense variants were also submitted to prediction softwares such as SIFT and PolyPhen-2, while splice site variants were evaluated by NNSPlice and Splicesite finder. Variants analyzed under a dominant inheritance model that were observed more than 10 times in ExAC were considered too common as monogenic causes. Potentially pathogeni […]

library_books

Case report of a novel homozygous splice site mutation in PLA2G6 gene causing infantile neuroaxonal dystrophy in a Sudanese family

2018
BMC Med Genet
PMCID: 5941609
PMID: 29739362
DOI: 10.1186/s12881-018-0592-y

[…] ed 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 pat […]

library_books

Mutation analysis of SLC26A4 (Pendrin) gene in a Brazilian sample of hearing impaired subjects

2018
BMC Med Genet
PMCID: 5941635
PMID: 29739340
DOI: 10.1186/s12881-018-0585-x

[…] /clinvar/). 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/). […]

library_books

Accurate Classification of NF1 Gene Variants in 84 Italian Patients with Neurofibromatosis Type 1

2018
Genes
PMCID: 5924558
PMID: 29673180
DOI: 10.3390/genes9040216

[…] ons, at positions −7, +3 and +5, respectively. The mutation c.1642–7A>G has never been reported previously, and three of the five Alamut predictors supported an abrogation of the splicing donor site; NNsplice and HSF did not forecast any changes in splicing ().Thus, we decided to perform real time (RT)-PCR with primers encompassing exon 15. The normally-sized PCR product was sequenced to reveal an […]

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