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Protocols

PupaSuite specifications

Information


Unique identifier OMICS_04396
Name PupaSuite
Interface Web user interface
Restrictions to use None
Computer skills Basic
Version 3.1
Stability No
Maintained No

Taxon


  • Primates
    • Homo sapiens

Publication for PupaSuite

PupaSuite citations

 (54)
library_books

Meta Analysis of Genome Wide Association Studies for Abdominal Aortic Aneurysm Identifies Four New Disease Specific Risk Loci

2017
Circ Res
PMCID: 5253231
PMID: 27899403
DOI: 10.1161/CIRCRESAHA.116.308765

[…] onfirmed AAA-associated loci were manually annotated using the University of California Santa Cruz Genome Browser (http://genome.ucsc.edu/cgi-bin/hgGateway) on the hg19 human genome assembly. For the Pupasuite analyses SNPs in linkage disequilibrium (r2>0.5) and with lead SNPs at the novel AAA risk loci identified were extracted from the 1000 Genomes data and then entered into Pupasuite v3.1. In a […]

call_split

Synergistic association of STX1A and VAMP2 with cryptogenic epilepsy in North Indian population

2016
PMCID: 4951625
PMID: 27458546
DOI: 10.1002/brb3.490
call_split See protocol

[…] egion, exonic, intronic, splice site) of SNPs within gene were taken into consideration. Further, SNPs were also examined for any in‐silico functional role by means of online prediction tools such as PupaSuite and SNPinfo. Additionally, significantly associated SNPs, based on genotype‐phenotype correlation, were later searched for any biological role through HaploReg tool in terms of effect on chr […]

library_books

Angiogenesis genotyping in the selection of first line treatment with either sunitinib or pazopanib for advanced renal cell carcinoma

2016
Oncotarget
PMCID: 5122335
PMID: 27175586
DOI: 10.18632/oncotarget.9229

[…] USA), according to the manufacturer's instructions. DNA from each sample was then eluted in 120 μl of eluting solution.Single nucleotide polymorphisms (SNPs) within each gene were selected using the Pupasuite software (http://bioinfo.cipf.es - version 2.0.0, bioinfo 2008), the CIPF (Centro de Investigacion Principe Felipe) Single Nucleotide Polymorphism database (dbSNP) generated by the National […]

call_split

Angiogenesis genotyping and clinical outcome during regorafenib treatment in metastatic colorectal cancer patients

2016
Sci Rep
PMCID: 4846860
PMID: 27117754
DOI: 10.1038/srep25195
call_split See protocol

[…] evaluated by UV spectrophotometry as the ratio absorbance 260/280 nm; a purity index of 1.5–2.0 was considered optimal.Single nucleotide polymorphisms (SNPs) within each gene were selected using the Pupasuite software (http://pupasuite.bioinfo.cipf.es/index.jsf - version 2.0.0, bioinfo 2008), the CIPF (Centro de Investigacion Principe Felipe) Single Nucleotide Polymorphism database (dbSNP) genera […]

library_books

Genetic Polymorphisms in Vitamin D Metabolism and Signaling Genes and Risk of Breast Cancer: A Nested Case Control Study

2015
PLoS One
PMCID: 4619526
PMID: 26488576
DOI: 10.1371/journal.pone.0140478

[…] ially functional SNPs in these genes identified through literature searches and in silico databases (dbSNP, last accessed in 2014, F-SNP http://compbio.cs.queensu.ca/F-SNP/, last accessed 6/2008, and PupaSuite http://pupasuite.bioinfo.cipf.es/, last accessed 6/2009). SNPs with minor allele frequencies (MAF) <5% in the Hapmap CEU population were excluded. For CYP27B1, we genotyped the only SNP in t […]

library_books

Prevalence of mutations in a panel of breast cancer susceptibility genes in BRCA1/2 negative patients with early onset breast cancer

2014
PMCID: 4465412
PMID: 25503501
DOI: 10.1038/gim.2014.176

[…] s.org/data) databases. Variants were analyzed if found at 0.1–1% allele frequency and previously reported to be a breast cancer susceptibility variant. Splicing variants were analyzed with Skippy and PupaSuite,. All variants were visually inspected in the Integrative Genomics Viewer (IGV, http://www.broadinstitute.org/software/igv/log-in). […]

Citations

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PupaSuite institution(s)
Department of Bioinformatics, Centro de Investigación Príncipe Felipe (CIPF), Valencia, Spain

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