VarioWatch protocols

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VarioWatch specifications

Information


Unique identifier OMICS_08692
Name VarioWatch
Interface Web user interface
Restrictions to use None
Programming languages Java
Computer skills Basic
Stability No
Maintained No

Taxon


  • Primates
    • Homo sapiens

Maintainer


This tool is not available anymore.

Publication for VarioWatch

VarioWatch in pipeline

2011
PMCID: 3287847
PMID: 22373437
DOI: 10.1186/1753-6561-5-S9-S13

[…] line models. we identified an additional two variants (in brca2 and mftrr) by searching the literature., by querying data from five databases (ensembl, ucsc blat, rescue-ese, fas-ess, and sift), variowatch provides functional annotation for snps. we used the following criteria, as implemented in the program: (1) whether or not the mutation affects the protein structure, (2) whether the snp […]


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VarioWatch in publications

 (5)
PMCID: 5010694
PMID: 27590274
DOI: 10.1186/s12967-016-1005-7

[…] were two-tailed and statistical significance was defined as p < 0.05., the in silico analysis for possible functional implications of each polymorphism was evaluated by using four web-tools: (a) variowatch (http://genepipe.ncgm.sinica.edu.tw/variowatch/); (b) rsnabase (http://rsnp.psych.ac.cn/); (c) sift (http://sift.bii.a-star.edu.sg/index.html); (d) analysis for possible mirna binding site […]

PMCID: 4850189
PMID: 27038471
DOI: 10.1007/s10142-016-0489-9

[…] the greater the value of the pdeleterious score, the higher the tendency of a variant to have severe impairments in protein function (brunham et al. ). risk associated with aas was determined by variowatch (http://genepipe.ncgm.sinica.edu.tw/variowatch/main.do) by submitting snp id with upstream 5′ and downstream 3′ regions as 50,000 bp. variowatch analyzes aas using integrated databases […]

PMCID: 3738504
PMID: 23951166
DOI: 10.1371/journal.pone.0071450

[…] potentially functional variants, as many as possible, were included in the genotyping multiplexes. these 21 additional snps (8 for cry2, 11 for cry1 and 2 for ttc1) were selected using pupasuite , variowatch , dbsmr and mirnasnp databases. presents all the 48 snps that were successfully genotyped in this study and their selection criteria., bp; base pair position based on ncbi36/hg18 […]

PMCID: 3446884
PMID: 23029076
DOI: 10.1371/journal.pone.0045533

[…] (rs2070850, rs2070852, rs1799867, rs2282687, and rs3136516), were detected ( and ). all snps were analyzed for their functional impact by using four web-based programs (mutation taster, polyphen, variowatch, and sift). the 5 intronic snps were predicted as polymorphisms with no functional effect while the exonic snp was predicted to be possibly damaging. the non-synonymous (ns) snp, rs5896 […]

PMCID: 3287847
PMID: 22373437
DOI: 10.1186/1753-6561-5-S9-S13

[…] and functional data. using data from the pilot3 study of the 1000 genomes project available through genetic analysis workshop 17, we compared the results of four programs (sift, polyphen, mapp, and variowatch) used to predict the functional relevance of variants in 101 genes. analysis was conducted without knowledge of the simulation model. agreement between programs was modest ranging […]


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VarioWatch institution(s)
National Center for Genome Medicine and Institute of Biomedical Sciences, Academia Sinica, Taiwan, China
VarioWatch funding source(s)
Academia Sinica Life Sciences [40-05-GMM]; National Science Council, Taiwan, R.O.C. [NSC100-2319-B-001-001]; National Center for Genomic Medicine

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