SNPeffect statistics

Tool stats & trends

Looking to identify usage trends or leading experts?

Protocols

SNPeffect specifications

Information


Unique identifier OMICS_00187
Name SNPeffect
Restrictions to use None
Database management system MySQL
Community driven No
Data access File download, Browse
User data submission Not allowed
Version 4.0
Maintained Yes

Taxon


  • Primates
    • Homo sapiens

Documentation


Maintainers


  • person_outline Frederic Rousseau
  • person_outline Joost Schymkowitz

Publication for SNPeffect

SNPeffect citations

 (38)
library_books

Phylogenetic and CRISPR/Cas9 Studies in Deciphering the Evolutionary Trajectory and Phenotypic Impacts of Rice ERECTA Genes

2018
Front Plant Sci
PMCID: 5902711
PMID: 29692796
DOI: 10.3389/fpls.2018.00473

[…] iversities within different rice subspecies were calculated using public available PERL script “calc_vcf_diversity.pl” as described in .Putative effects of variants in rice ERfs were predicted using SNPeffect 4.0 () against MSU Rice Genome Annotation Project (RGAP) Release 7 database (). The results for OsER2 were further examined manually based on NCBI model. Tajima’s D-value was estimated using […]

library_books

Genetic dissection of Sharka disease tolerance in peach (P. persica L. Batsch)

2017
BMC Plant Biol
PMCID: 5670703
PMID: 29100531
DOI: 10.1186/s12870-017-1117-0

[…] sing RealignerTargetCreator and IndelRealigner tools, then filtered and merged, generating a single multi-sample file. Mapped reads were visualized in Tablet []. Variants were then annotated by using SNPEffect v2.0 [] and peach reference genes annotations. For the prediction of candidate genes, the following priorities were considered: i) identification of variants from WGS; ii) genes with functio […]

library_books

Spatial distribution of disease associated variants in three dimensional structures of protein complexes

2017
Oncogenesis
PMCID: 5623905
PMID: 28945216
DOI: 10.1038/oncsis.2017.79

[…] ution of structural parameters to the prediction performance has been a long-discussed issue., Numerous tools have been constructed to assess potential changes caused by SNVs in protein 3D structure: SNPeffect database, for example, ignores the conservation profiles of SNVs and relies on predicted structural features (aggregation, amyloidogenicity, stability) and domain and catalytic site annotati […]

call_split

Divergent and convergent modes of interaction between wheat and Puccinia graminis f. sp. tritici isolates revealed by the comparative gene co expression network and genome analyses

2017
BMC Genomics
PMCID: 5389088
PMID: 28403814
DOI: 10.1186/s12864-017-3678-6
call_split See protocol

[…] ighly duplicated genomic regions, a maximum read coverage depth for each variable site was set to be two times the mean coverage depth for entire genome. The filtered VCF files were used as input for SNPeffect [] to predict the functional effect of each DNA sequence variant. De novo genome assembly of genomic reads from individual isolates was performed using CLC bio assembly software (QIAGEN). Th […]

library_books

Genetic Profiles of South Korean Patients With Glucose 6 Phosphate Dehydrogenase Deficiency

2016
PMCID: 5203987
PMID: 28028996
DOI: 10.3343/alm.2017.37.2.108

[…] tabase at an extremely low frequency, i.e., 1.141×10-5 (, ). For the Class IV mutation, G6PD São Paulo, an in silico analysis using SIFT, PROVEAN, PolyPhen-2, Align-GVGD, and the FoldX implemented in SNPeffect 4.0 predicted a relatively mild effect, consistent with the observed enzyme activity levels. […]

call_split

Filaggrin gene mutations and new SNPs in asthmatic patients: a cross sectional study in a Spanish population

2016
PMCID: 4960762
PMID: 27462351
DOI: 10.1186/s13223-016-0137-x
call_split See protocol

[…] h.gov/omim), dbSNP of the NCBI (http://www.ncbi.nlm.nih.gov/snp).The prediction analysis of polymorphisms functional effect was carried out by online platforms ExPASyProSite (http://www.expasy.org/), SNPeffect 4.0 (http://snpeffect.switchlab.org/) and PolyPhen-2 prediction of functional effects of human nsSNPs (http://genetics.bwh.harvard.edu). […]

Citations

Looking to check out a full list of citations?

SNPeffect institution(s)
VIB Switch Laboratory, Leuven, Belgium ; Department of Molecular Cell Biology, University of Leuven, Leuven, Belgium ; Vrije Universiteit Brussel, Brussel, Belgium; Vesalius Research Center, VIB, Leuven, Belgium; Vesalius Research Center, University of Leuven, Leuven, Belgium; Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore; Department of Bioinformatics, Centro de Investigacion Principe Felipe (CIPF), Valencia, Spain; Functional Genomics Node (INB) at CIPF, Valencia, Spain
SNPeffect funding source(s)
Supported by Interuniversity Attraction Poles (IAP Network 6/43) of the Belgian Federal Science Policy Office (BelSPo) (VIB Switch laboratory); Flanders Institute for Science and Technology (IWT), Fund for Scientific Research (FWO), Flanders, MICINN projects BIO2008-04212, and RD06/0020/1019 (RTICC, ISCIII) (Dopazo lab, partial) GVA-FEDER (PROMETEO/2010/001, partial).

SNPeffect reviews

star_border star_border star_border star_border star_border
star star star star star

Be the first to review SNPeffect