NetGene2 protocols

View NetGene2 computational protocol

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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


Add your version

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 in pipelines

 (5)
2014
PMCID: 3880305
PMID: 24404183
DOI: 10.1371/journal.pone.0084692

[…] . promoter region was confirmed using expressed sequence tag (est) database from genbank and prediction of 5′utr (untranslated region) intron was performed at netgene2 website (http://www.cbs.dtu.dk/services/netgene2/) . conserved cis-acting regulatory was carried out using the pattern search from softberry website (http://www.softberry.com/berry.phtml). […]

2013
PMCID: 3688710
PMID: 23840414
DOI: 10.1371/journal.pone.0066146

[…] (sum of the intensities of all bands in the lane) to minimize the variation in the quantity of loaded pcr product., raw sequence data was assembled and checked with dnastar (madison, wi, usa). netgene2 was used to detect possible intron splice sites . the sequences were compared with the genbank database sequences using blastn and blastp for its and amino acid sequences deduced […]

2013
PMCID: 3865592
PMID: 24498620
DOI: 10.1002/mgg3.23

[…] (splicefinder). splicefinder integrates two functional annotation tools for ngs, annovar and mutationtaster and two canonical splice site prediction programs for single mutation analysis, sspnn and netgene2. by splicefinder, we identified somatic mutations affecting rna splicing in a colon cancer sample, in eight atypical chronic myeloid leukemia (acml), and eight cml patients. a novel […]

2012
PMCID: 3567443
PMID: 23023333
DOI: 10.1038/ng.2425

[…] for medical research). all nucleotide numbers are in reference to chmp1a isoform 2 cdna (nm_002768, in which a of the atg start site is +1) from the ucsc genome browser., splice prediction software netgene2 was used to determine the effect of the family 1 allele on chmp1a splicing. ebv-transformed lymphocytes were grown in rpmi-1640 with 15% (v/v) fetal bovine serum and 1% (v/v) […]

2008
PMCID: 2596294
PMID: 18762986
DOI: 10.1007/s00438-008-0376-8

[…] implemented at the biology workbench server (http://workbench.sdsc.edu). multiple sequence comparisons were performed with clustalw (thompson et al. ). splice site analysis was performed at the netgene2 server (hebsgaard et al. ; http://www.cbs.dtu.dk/services/netgene2)., transcription profiles of individual ogre subfamilies were investigated using rt-pcr with subfamily-specific primers […]


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NetGene2 in publications

 (166)
PMCID: 5941635
PMID: 29739340
DOI: 10.1186/s12881-018-0585-x

[…] 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 are a frequent cause of hereditary deafness in brazilian patients, we analyzed 68 families presenting autosomal recessive […]

PMCID: 5919682
PMID: 29659569
DOI: 10.1371/journal.pgen.1007355

[…] 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, […]

PMCID: 5840826
PMID: 29510678
DOI: 10.1186/s12887-018-1060-8

[…] 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.table 1f forward, r reverse, f forward, r reverse, 2 patients in whom gck […]

PMCID: 5841003
PMID: 29531935
DOI: 10.4103/2277-9175.225927

[…] 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., the medical […]

PMCID: 5824380
PMID: 29266775
DOI: 10.1111/jcmm.13425

[…] 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 […]


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NetGene2 institution(s)
Center for Biological Sequence Analysis, Technical University of Denmark, Lyngby, Denmark

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