PredictSNP statistics

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PredictSNP specifications

Information


Unique identifier OMICS_02218
Name PredictSNP
Interface Web user interface
Restrictions to use Academic or non-commercial use
Input data PredictSNP1: protein sequence; PredictSNP2: list of variants
Input format PredictSNP1: FASTA; PredictSNP2: VCF, GVF, HGVS
Computer skills Basic
Version 2.0
Stability Stable
Maintained Yes

Taxon


  • Primates
    • Homo sapiens

Documentation


Maintainer


  • person_outline PredictSNP Team <>

Publications for PredictSNP

PredictSNP in publications

 (35)
PMCID: 5910821
PMID: 29610305
DOI: 10.1073/pnas.1715896115

[…] which have been manually curated to minimize possible overlaps and proposed to serve as a benchmarking set (). the latter three, indicated by the suffix “selected”, are subsets of varibench (), predictsnp (), and swissvar (), respectively, obtained upon clearing entries already represented in the former two most populated datasets (i.e., humvar and exovar). such preliminary filtering […]

PMCID: 5842716
PMID: 29682366
DOI: 10.1155/2018/6968395

[…] it may be more common in latino populations. the arg22 residue is conserved across species down to zebrafish (danio rerio), and in silico prediction algorithms predict the variant to be deleterious (predictsnp2 deleterious score: 1.0000; cadd deleterious score: 22.6000; fathmm deleterious score: 0.9806) []. this variant results in a semiconservative amino acid substitution that may impact […]

PMCID: 5862610
PMID: 29568389
DOI: 10.18632/oncotarget.24459

[…] panther (http://www.pantherdb.org/tools/csnpscoreform.jsp), phd-snp (http://snps.biofold.org/phd-snp/phd-snp.html), snap (https://www.rostlab.org/services/snap/) and predictsnp (https://loschmidt.chemi.muni.cz/predictsnp1/). these tools predict whether an amino acid substitution or indel has an impact on the biological function of a protein or not., the outcome […]

PMCID: 5754511
PMID: 29298844
DOI: 10.1530/EC-17-0261

[…] was applied independently to both samples (columns) and genes (rows) by pearson’s correlation (r). the prediction of the effects of the newly reported amino acid substitution was performed using the predictsnp tool ()., a total of 38 samples were eligible for inclusion in the study: 18 fas, 14 mi-ftcs and 6 wi-ftcs. every case had a complete follicular growth pattern and a total absence […]

PMCID: 5667839
PMID: 29095929
DOI: 10.1371/journal.pone.0187365

[…] was below 10) and shown as their p-values, assumed significant if <0.05. the prediction of the effect of aminoacid and nucleotide substitution on protein function or gene were evaluated with the predictsnp tool []., out of 5,877 analyzed subjects, 36 (0.61%) were carriers of variants of the hadha gene. we did not find individuals with abnormal homozygous cc genotype and 5,841 (99.39%) […]


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PredictSNP institution(s)
Loschmidt Laboratories, Department of Experimental Biology and Research Centre for Toxic Compounds in the Environment RECETOX, Masaryk University, Brno, Czech Republic; Department of Information Systems, Faculty of Information Technology, Brno University of Technology, Brno, Czech Republic; International Clinical Research Center, St. Anne’s University Hospital Brno, Brno, Czech Republic
PredictSNP funding source(s)
The Czech Ministry of Education of the Czech Republic (LO1214 and LQ1605); European Commission within the Research Infrastructures programme of Horizon 2020 (ELIXIR-EXCELERATE 676559;ec.europa.eu/research) and the European Union Framework Programme (REGPOT 316345;ec.europa.eu/research); the project Research and Application of Advanced Methods in ICT

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