PhD-SNP statistics

Tool stats & trends

Looking to identify usage trends or leading experts?

Protocols

PhD-SNP specifications

Information


Unique identifier OMICS_00158
Name PhD-SNP
Alternative name Predictor of human Deleterious Single Nucleotide Polymorphisms
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Python
Computer skills Advanced
Stability Stable
Maintained Yes

Taxon


  • Primates
    • Homo sapiens

Versioning


No version available

Maintainer


  • person_outline Emidio Capriotti

Information


Unique identifier OMICS_00158
Name PhD-SNP
Alternative name Predictor of human Deleterious Single Nucleotide Polymorphisms
Interface Web user interface
Restrictions to use None
Programming languages Python
Computer skills Basic
Stability Stable
Maintained Yes

Taxon


  • Primates
    • Homo sapiens

Maintainer


  • person_outline Emidio Capriotti

Publication for Predictor of human Deleterious Single Nucleotide Polymorphisms

PhD-SNP citations

 (39)
call_split

Determination of genotypic and clinical characteristics of Colombian patients with mucopolysaccharidosis IVA

2018
PMCID: 5926073
PMID: 29731656
DOI: 10.2147/TACG.S141881
call_split See protocol

[…] many), Mutation Taster (http://www.mutationtaster.org; NCBI 37/Ensembl 69, Schwarz, Cooper, Schuelke, Seelow), PMUT (http://mmb2.pcb.ub.es/PMut/; IRB Barcelona Institute for Research in Biomedicine), PhD-SNP (http://snps.biofold.org/phd-snp/phd-snp.html), and FATHMM (http://fathmm.biocompute.org.uk; University of Bristol Integrative Epidemiology Unit, UK) and taking into account the ACMG recommend […]

library_books

Development of pathogenicity predictors specific for variants that do not comply with clinical guidelines for the use of computational evidence

2017
BMC Genomics
PMCID: 5558188
PMID: 28812538
DOI: 10.1186/s12864-017-3914-0

[…] ty gap has been already mentioned by Capriotti et al. [] who describe how their consensus predictor Meta-SNP performs much better for those cases for which their four constituting predictors PANTHER, PhD-SNP, SIFT and SNAP agreed in their verdict than for those where they disagreed. Here we have shown that developing specific predictors for this hard case benefits our performance for PRDIS and imp […]

library_books

High confidence assessment of functional impact of human mitochondrial non synonymous genome variations by APOGEE

2017
PLoS Comput Biol
PMCID: 5501658
PMID: 28640805
DOI: 10.1371/journal.pcbi.1005628

[…] e, we queried the Meta-SNP server [], but submitting the fasta sequences of the OXPHOS proteins and the corresponding lists of amino acid mutations. It returned categorical predictions and scores for PhD-SNP, SIFT, SNAP and PANTHER [–].MitImpact accounted also for the MtoolBox Disease Scores. We set the pathogenicity threshold to 0.4311, as described in [] (details in S1 File), and considered harm […]

library_books

HOXA7, HOXA9, and HOXA10 are differentially expressed in clival and sacral chordomas

2017
Sci Rep
PMCID: 5435709
PMID: 28515451
DOI: 10.1038/s41598-017-02174-5

[…] Viewer Software (Broad Institute, MA, USA). The impact of confirmed mutations on protein functions were classified using 8 online protein prediction tools (Polyphen-2, FATHMM, SIFT, PANTHER, Provean, PHD-SNP, SNAP, and Meta-SNP) according to the providers’ instructions. […]

library_books

PhD SNPg: a webserver and lightweight tool for scoring single nucleotide variants

2017
Nucleic Acids Res
PMCID: 5570245
PMID: 28482034
DOI: 10.1093/nar/gkx369

[…] de variants (SNVs) on human health, nevertheless only few of them are capable of assessing the effect of SNVs in non-coding regions ().In this paper, we present PhD-SNPg, which is an extension of the PhD-SNP algorithm () for predicting the impact of human SNVs, both in coding and non-coding regions. PhD-SNPg is available both as web server, and standalone software to process large datasets of vari […]

library_books

Computational Modeling of complete HOXB13 protein for predicting the functional effect of SNPs and the associated role in hereditary prostate cancer

2017
Sci Rep
PMCID: 5363706
PMID: 28272408
DOI: 10.1038/srep43830

[…] and function. The nsSNPAnalyzer (http://snpanalyzer.uthsc.edu/) is a tool to predict the phenotypic effect of the missense SNPs based on the data from MSA and three-dimensional protein structure. The PhD-SNP (Predictor of human Deleterious Single Nucleotide Polymorphisms) server (http://SNPs.biofold.org/phd-snp/phd-snp.html) functions with the help of support vector machines based (SVM-based) and […]

Citations

Looking to check out a full list of citations?

PhD-SNP institution(s)
Laboratory of Biocomputing, CIRB/Department of Biology, University of Bolognavia Irnerio, Bologna, Italy

PhD-SNP reviews

star_border star_border star_border star_border star_border
star star star star star

Be the first to review PhD-SNP