novoSNP statistics

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Citations per year

Number of citations per year for the bioinformatics software tool novoSNP
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Tool usage distribution map

This map represents all the scientific publications referring to novoSNP per scientific context
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Associated diseases

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Popular tool citations

chevron_left Variant detection Sequence alignment chevron_right
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Protocols

novoSNP specifications

Information


Unique identifier OMICS_10354
Name novoSNP
Software type Package/Module
Interface Graphical user interface
Restrictions to use Academic or non-commercial use
Input data novoSNP takes a reference sequence and a number of sequencing trace files as input.
Output data It generates a list of possible variations with a quality score.
Operating system Unix/Linux
Computer skills Medium
Stability Stable
Maintained Yes

Versioning


No version available

Publication for novoSNP

novoSNP citations

 (38)
library_books

Detection of mutations in MYOC, OPTN, NTF4, WDR36 and CYP1B1 in Chinese juvenile onset open angle glaucoma using exome sequencing

2018
Sci Rep
PMCID: 5852028
PMID: 29540704
DOI: 10.1038/s41598-018-22337-2

[…] Sanger sequencing, including amplification, sequencing, and analysis of the target fragments, have been previously described. Sequence alignment and analysis of variations were performed by using the NovoSNP program. […]

library_books

Candidate Genes and Molecular Markers Correlated to Physiological Traits for Heat Tolerance in Fine Fescue Cultivars

2018
Int J Mol Sci
PMCID: 5796065
PMID: 29301249
DOI: 10.3390/ijms19010116

[…] under UV light, recovered using GeneJET gel extraction and DNA cleanup micro kit (Thermo Fisher Scientific), and used for Sanger sequencing (GenScript, Piscataway, NJ, USA).SNPs were identified using NovoSNP program [], which could detect heterozygous sequence data based on a cumulative scoring scheme. Multiple alignments were performed by default value, and SNP positions and the heterozygous alle […]

library_books

A missense variant in the coil1A domain of the keratin 25 gene is associated with the dominant curly hair coat trait (Crd) in horse

2017
PMCID: 5686958
PMID: 29141579
DOI: 10.1186/s12711-017-0359-5

[…] ycler pro thermocycler (Eppendorf). The resulting amplicons were purified and bidirectionally sequenced by Eurofins MWG (Germany) using conventional Sanger sequencing. Variants were detected with the NovoSNP software []. Finally, variant g.21891160G>A (KRT25:p.R89H) was genotyped on an extended panel of 150 curly and 203 randomly chosen straight-haired animals from 35 different breeds using Custom […]

call_split

Rapid Discovery of De Novo Deleterious Mutations in Cattle Enhances the Value of Livestock as Model Species

2017
Sci Rep
PMCID: 5597596
PMID: 28904385
DOI: 10.1038/s41598-017-11523-3
call_split See protocol

[…] pro thermocycler (Eppendorf). The resulting amplicons were purified and bidirectionally sequenced by Eurofins MWG (Germany) using conventional Sanger sequencing. Polymorphisms were detected with the NovoSNP software.For BD1, BD2 and OI, the de novo nature of the candidate mutations was confirmed using PCR and Sanger sequencing in a panel of affected and unaffected animals, and DNA samples extract […]

call_split

Association of Candidate Genes With Submergence Response in Perennial Ryegrass

2017
Front Plant Sci
PMCID: 5432546
PMID: 28559908
DOI: 10.3389/fpls.2017.00791
call_split See protocol

[…] cted using an ABI 3730 genetic analyzer according to the manufacturer’s instructions (Applied Biosystems, Carlsbad, CA, USA) in the Genomic Center at Purdue University. SNPs were identified using the NovoSNP program 3.0.1 Microsoft Windows Platform version (). […]

library_books

Deleterious ABCA7 mutations and transcript rescue mechanisms in early onset Alzheimer’s disease

2017
Acta Neuropathol
PMCID: 5563332
PMID: 28447221
DOI: 10.1007/s00401-017-1714-x

[…] with BigDye termination cycle sequencing kit v3.1 (Thermo Fisher), and sequenced with ABI3730 DNA Analyzer (Thermo Fisher). Sanger sequences were analyzed using Seqman (DNAstar, Madison, WI, USA) and NovoSNP software []. Exon 23 (73 bp + 4 bp splice sites) was not duly screened. Of note, this exon contains no known PTC mutations [Exome Aggregation Consortium (ExAC) (accessed April 2017)]. In addit […]


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novoSNP institution(s)
Department of Molecular Genetics, Flanders Interuniversity Institute for Biotechnology, University of Antwerp, Antwerpen, Belgium

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