nsSNPAnalyzer protocols

View nsSNPAnalyzer computational protocol

nsSNPAnalyzer statistics

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nsSNPAnalyzer specifications

Information


Unique identifier OMICS_00156
Name nsSNPAnalyzer
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes

Maintainer


  • person_outline Yan Cui <>

Publication for nsSNPAnalyzer

nsSNPAnalyzer in pipelines

 (2)
2017
PMCID: 5529537
PMID: 28747718
DOI: 10.1038/s41598-017-06575-4

[…] (identified in step 1) using several different in-silico approaches such as stability analysis of mutant proteins using eris (step 2a), identification of disease associated snps using mutpred and nssnpanalyzer (step 2b), association of snps with highly conserved buried (structural) and exposed (functional) amino acid residues in il-8 protein using clustal omega and consurf (step 2c), […]

2017
PMCID: 5529537
PMID: 28747718
DOI: 10.1038/s41598-017-06575-4

[…] snps (identified in step 1) to four different in-silico approaches such as stability analysis of mutant proteins using eris (step 2a), identification of disease associated snps using mutpred and nssnpanalyzer (step 2b), association of snps with highly conserved buried (structural) and exposed (functional) amino acid residues in il-8 protein using clustal omega and consurf (step 2c), […]


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nsSNPAnalyzer in publications

 (17)
PMCID: 5903617
PMID: 29664915
DOI: 10.1371/journal.pone.0195971

[…] was predicted using the default settings of eleven different in silico prediction algorithms, sift [], polyphen-2 [], panther-psep [], mutpred [], mutationtaster [], provean [], pmut [], fathmm [], nssnpanalyzer [], align gv-gd [], and revel []. these programs were used to analyse 18 functionally characterised pitx2 missense variants plus 13 additional, functionally uncharacterized pitx2 […]

PMCID: 5529537
PMID: 28747718
DOI: 10.1038/s41598-017-06575-4

[…] (identified in step 1) using several different in-silico approaches such as stability analysis of mutant proteins using eris (step 2a), identification of disease associated snps using mutpred and nssnpanalyzer (step 2b), association of snps with highly conserved buried (structural) and exposed (functional) amino acid residues in il-8 protein using clustal omega and consurf (step 2c), […]

PMCID: 5470696
PMID: 28614374
DOI: 10.1371/journal.pone.0179314

[…] with scikit-learn [] in this study., to evaluate the performance of the proposed predsav, six existing savs prediction methods, including funsav [], polyphen2 [], suspect [], sift [], snap [] and nssnpanalyzer [], are evaluated on the benchmark dataset., and show the detailed results of comparing our method with the existing methods. overall, our approach shows dominant advantage […]

PMCID: 5363706
PMID: 28272408
DOI: 10.1038/srep43830

[…] be further evaluated for its validity., the complete list of snps for human hoxb13 was retrieved from the dbsnp and ensembl database. those snps were analyzed with sift, polyphen, panther, provean, nssnpanalyzer, phd-snp, etc., to screen the most deleterious nssnp’s affecting the protein structure and function. further, the screened nssnp’s were mapped onto the protein structure […]

PMCID: 5278360
PMID: 28134345
DOI: 10.1038/srep41329

[…] changes, using svms trained on the protherm database, from sequence only or from structural information, and (ii) disease associated variants from sequence only using the phd-snp prediction pipeline.nssnpanalyzer uses a random forest classifier, trained on a curated dataset of variants (modsnp) using (i) variant structural environment, (ii) position conservation within the msa, and (iii) […]


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nsSNPAnalyzer institution(s)
Department of Molecular Sciences, Center of Genomics and Bioinformatics, University of Tennessee Health Science Center, Memphis, TN, USA

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