NetGene2 statistics

info info

Citations per year

Number of citations per year for the bioinformatics software tool NetGene2
info

Tool usage distribution map

This map represents all the scientific publications referring to NetGene2 per scientific context
info info

Associated diseases

This word cloud represents NetGene2 usage per disease context
info

Popular tool citations

chevron_left Splicing defect prediction chevron_right
Want to access the full stats & trends on this tool?

Protocols

NetGene2 specifications

Information


Unique identifier OMICS_09618
Name NetGene2
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data Single sequence
Input format FASTA
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes

Taxon


  • Invertebrates
    • Caenorhabditis elegans
  • Plants and Fungi
    • Arabidopsis thaliana
  • Primates
    • Homo sapiens

Versioning


No version available

Maintainer


  • person_outline Soren Bruk

Information


Unique identifier OMICS_09618
Name NetGene2
Interface Web user interface
Restrictions to use None
Input data Single sequence
Input format FASTA
Computer skills Basic
Stability Stable
Maintained Yes

Taxon


  • Invertebrates
    • Caenorhabditis elegans
  • Plants and Fungi
    • Arabidopsis thaliana
  • Primates
    • Homo sapiens

Maintainer


  • person_outline Soren Bruk

Publications for NetGene2

NetGene2 citations

 (196)
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

[…] Genomes and 6500 Exomes. The IVS19 + 2 T > C is a splice site mutation, never reported before. NNSsplice 0.9 version (Lawrence Berkeley National Laboratory, Genomic Informatic Groups, 2012 link) and Netgene2 Server (Center for Biological sequence analysis, 2012 link) predict that the mutation abolishes the splicing donor site of exon 19. After detection of variants c.84C > A and (IVS19 + 2 T > C) […]

call_split

Targeted next generation sequencing identifies functionally deleterious germline mutations in novel genes in early onset/familial prostate cancer

2018
PLoS Genet
PMCID: 5919682
PMID: 29659569
DOI: 10.1371/journal.pgen.1007355
call_split See protocol

[…] /deleterious variants, MutationTaster [] and Uniprot [] were queried. To infer the putative impact on splicing, the splice site predictors Human Splicing Finder 3.0 [], MaxEntScan [], NNSPLICE [] and NetGene2 [] were used. To predict the biological impact of missense mutations, we looked at data from the predictor tools embedded in the NGS Interpretative Workbench from GeneticistAssistant, which i […]

call_split

Genetic and clinical characteristics of Chinese children with Glucokinase maturity onset diabetes of the young (GCK MODY)

2018
PMCID: 5840826
PMID: 29510678
DOI: 10.1186/s12887-018-1060-8
call_split See protocol

[…] nd the Human Gene Mutation Database (HGMD). The pathogenicity of the mutation occurring in flanking intronic regions resulted in abnormal splicing was predicted by the online tools of MutationTaster, NetGene2, and Human Splicing Finder V3.0, while only MutationTaster was used for frame shift or deletion type mutations.2 patients in whom GCK mutations were not detected, were screened by targeted ne […]

call_split

A Rare Missense Mutation and a Polymorphism with High Frequency in LDLR Gene among Iranian Patients with Familial Hypercholesterolemia

2018
PMCID: 5841003
PMID: 29531935
DOI: 10.4103/2277-9175.225927
call_split See protocol

[…] anipulating multiple alignments of protein sequences and structures.[] The possible effects of nucleotide changes (in intronic conserved site) on splicing process were investigated using Splice Port, NetGene2 Server and Human Splicing Finder software programs.[] These programs provide predictive scores for splicing site and branch point sequence for wild and modified sequence types. […]

call_split

Functional assessment of the BMPR2 gene in lymphoblastoid cell lines from Graves’ disease patients

2017
J Cell Mol Med
PMCID: 5824380
PMID: 29266775
DOI: 10.1111/jcmm.13425
call_split See protocol

[…] or eliminate donor/acceptor splice sites were used Neural Network SPLICE (NNSplice) 0.9 version from the Berkeley Drosophila Genome Project (Lawrence Berkeley National Laboratory, Berkeley, CA, USA), NetGene2 (Technical University of Denmark, Kongens Lyngby, Denmark), Splice View, Human Splicing Finder 2.4.1 version (Aix Marseille Université, Marseille, France) and Automated Splice Site Exon Defin […]

library_books

Fibrinogen as a Pleiotropic Protein Causing Human Diseases: The Mutational Burden of Aα, Bβ, and γ Chains

2017
Int J Mol Sci
PMCID: 5751312
PMID: 29240685
DOI: 10.3390/ijms18122711

[…] e splicing site;(iii)splice-site variants located at intronic positions −3 and +3/+6 predicted as deleterious by three out of three prediction programs. These software were: Human Splicing Finder [], NetGene2 [], and Splice Site Prediction by Neural Network []. We considered as deleterious sequence variations predicted either to completely abolish the wild-type splicing site or to determine a decr […]


Want to access the full list of citations?
NetGene2 institution(s)
Center for Biological Sequence Analysis, Technical University of Denmark, Lyngby, Denmark

NetGene2 reviews

star_border star_border star_border star_border star_border
star star star star star

Be the first to review NetGene2