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Protocols

PolyPhred specifications

Information


Unique identifier OMICS_01815
Name PolyPhred
Software type Package/Module
Interface Command line interface
Restrictions to use Academic or non-commercial use
Operating system Unix/Linux, Mac OS
Computer skills Advanced
Version 6.18
Stability Stable
Maintained Yes

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No version available

Publications for PolyPhred

PolyPhred citations

 (202)
library_books

Two novel variants of the PHEX gene in patients with X linked dominant hypophosphatemic rickets and prenatal diagnosis for fetuses in these families

2018
PMCID: 5810233
PMID: 29393334
DOI: 10.3892/ijmm.2018.3402

[…] to predict the outcomes of variants, the sib bioinformatics resource portal database (http://www.expasy.org/), the human gene variant database (http://www.hgmd.cf.ac.uk) and the polyphred database (http://droog.gs.washington.edu/polyphred/) were used. additionally, to search for the suspected aberrant splicing variants, alamut® alamut interactive biosoftware (version 2.9.0; […]

library_books

ITPKC and SLC11A1 Gene Polymorphisms and Gene Gene Interactions in South Korean Patients with Kawasaki Disease

2017
PMCID: 5725348
PMID: 29214786
DOI: 10.3349/ymj.2018.59.1.119

[…] biosystems, foster city, ca, usa) according to the manufacturer's protocol. the results were then expanded to include all kd patients and controls. dna polymorphisms were identified using the polyphred program (http://droog.gs.washington.edu/polyphred/). tagging snps were selected using haploview version 4.2. among snps selected according to whole-gene sequencing of slc11a1 and itpkc […]

library_books

Bevacizumab and gefitinib enhanced whole brain radiation therapy for brain metastases due to non small cell lung cancer

2017
Braz J Med Biol Res
PMCID: 5685055
PMID: 29185589
DOI: 10.1590/1414-431X20176073

[…] and final 72°c (2 min) for extension. after pcr products were purified, the dna sequencer (abi 3130xl, applied biosystems, usa) was employed for sequential analysis. the results were analyzed by polyphred software (university of washington, usa), and differences were drawn after comparing the sequencing results and egfr gene sequences in the genebank (nm_005225.3)., tumor response […]

library_books

CYP2A6 Polymorphisms Associate with Outcomes of S 1 Plus Oxaliplatin Chemotherapy in Chinese Gastric Cancer Patients

2017
PMCID: 5582793
PMID: 28811232
DOI: 10.1016/j.gpb.2016.11.004

[…] for 10 min., snp calling, quality control, and polymorphism confirmation from dna sequencing were processed using programs developed by university of california, usa (http://elcapitan.ucsd.edu/hyper/polyphred.usage.html)., correlations between polymorphisms/genotypes and toxicity were analyzed using 2-tailed fisher’s exact test and were considered significant with 2-sided p < 0.05 […]

call_split

Functional variation of SHP 2 promoter is associated with preterm birth and delayed myelination and motor development in preterm infants

2017
Sci Rep
PMCID: 5519743
PMID: 28729690
DOI: 10.1038/s41598-017-06401-x
call_split See protocol

[…] using a bigdye terminator cycle sequencing kit and an abi 3730xl automated sequencer (applied biosystems, foster city, ca, usa). mutation analyses were performed using phred, phrap, consed, polyphred 5.04 software (http://droog.mbt.washington.edu/polyphred.html)., to construct a luciferase reporter vector containing the promoter region of the shp-2 wild-type sequence, a 448-bp region […]

call_split

Comprehensive assessment showed no associations of variants at the SLC10A1 locus with susceptibility to persistent HBV infection among Southern Chinese

2017
Sci Rep
PMCID: 5399367
PMID: 28429786
DOI: 10.1038/srep46490
call_split See protocol

[…] and splicing regions of slc10a1 for 40 unrelated pi samples (). each fragment amplified by pcr from genomic dna was sequenced on both strands with an abi prism 3700 sequencer. the phred-phrap-consed-polyphred package (http://www.genome.washington.edu/) was used to assemble the sequences and identify variants., to test for differentiation between populations, three measures of diversity […]


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PolyPhred institution(s)
Department of Molecular Biotechnology, University of Washington, Seattle, WA, USA

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