PolyPhred protocols

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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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Publications for PolyPhred

PolyPhred in pipelines

 (54)
2017
PMCID: 5399367
PMID: 28429786
DOI: 10.1038/srep46490

[…] 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 […]

2017
PMCID: 5519743
PMID: 28729690
DOI: 10.1038/s41598-017-06401-x

[…] 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 […]

2016
PMCID: 4932773
PMID: 27357321
DOI: 10.1038/ijos.2016.1

[…] 3100; applied biosystems, foster city, ca, usa). base calling and contig assembly were done using phred/phrap, and visually inspected with consed. polymorphic sites were automatically identified by polyphred and verified manually., a linear regression was used with a recessive model to investigate the influence of snp status in on enamel thickness, controlling for sex, age, and tooth number […]

2016
PMCID: 5143281
PMID: 27914139
DOI: 10.3346/jkms.2017.32.1.108

[…] sequencer (applied biosystems, foster city, ca, usa). the sequencing primers were the same as those used for the pcr amplification. mutational analyses were performed using phred, phrap, consed, and polyphred 5.04 software (university of washington, seattle, wa, usa)., kiss1r = kisspeptin receptor., the gnrh stimulation test was conducted to evaluate pubertal status in all patients. basal serum […]

2015
PMCID: 4349320
PMID: 25756342
DOI: 10.1186/s13567-015-0162-7

[…] and conditions [,]. the sequences were produced with an abi 3730 capillary sequencer (pe applied biosystems, foster city, ca, usa) and assembled into complete contigs with phred and phrap [,], polyphred (version 6.10), and consed software [], and visually genotyped. by dna and cdna sequence, both ewes were homozygous for tmem154 a4δ53 and had tmem154 “4,4” diplotypes [genbank: kp142216 - […]


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PolyPhred in publications

 (187)
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; […]

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 […]

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 […]

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 […]

PMCID: 5312091
PMID: 28202468
DOI: 10.1242/bio.020040

[…] format making use of automated liquid handling tools. pcr fragments were sequenced by sanger sequencing using the m13 reverse primer aggaaacagctatgaccat and screened for point mutations with the polyphred software tool (; ). all primary hits that were predicted as potentially deleterious mutations upon translation were verified in an independent pcr amplification and sanger sequencing […]


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

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