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comparison polyphen2_web/polyphen2_web.xml @ 2:f8f4ad14f5a6 draft

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author saketkc
date Mon, 14 Apr 2014 17:50:33 -0400
parents b319f980c9e6
children 3c40b02934ad
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1:1cbb0f884e7c 2:f8f4ad14f5a6
63 PolyPhen-2 (Polymorphism Phenotyping v2) is a software tool which predicts possible impact of amino acid substitutions 63 PolyPhen-2 (Polymorphism Phenotyping v2) is a software tool which predicts possible impact of amino acid substitutions
64 on the structure and function of human proteins using straightforward physical and evolutionary comparative considerations. 64 on the structure and function of human proteins using straightforward physical and evolutionary comparative considerations.
65 65
66 .. class:: infomark 66 .. class:: infomark
67 67
68 * HumDiv model uses 5% / 10% FPR thresholds for “probably damaging” / “possibly damaging” predictions 68 *Classifier model* used by the probabilistic predictor:
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70 -HumDiv is preferred for evaluating rare alleles, dense mapping of regions identified by genome-wide association studies,
71 and analysis of natural selection. HumDiv model uses 5% / 10% FPR thresholds for “probably damaging” / “possibly damaging” predictions
72
73
74 -HumVar is better suited for diagnostics of Mendelian diseases which requires distinguishing mutations with drastic effects
75 from all the remaining human variation, including abundant mildly deleterious alleles.
76 HumVar model uses 10% / 20% FPR thresholds for “probably damaging” / “possibly damaging” predictions
69 77
70 .. class:: infomark 78 .. class:: infomark
71 79
72 * HumVar model uses 10% / 20% FPR thresholds for “probably damaging” / “possibly damaging” predictions 80 *Transcripts* A set of Transcripts on which genomic SNPs will be mapped:
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82
83 -*All* includes all UCSC knownGene transcripts (highly redundant)
84
85 -*Canonical* includes UCSC knownCanonical subset
86
87 -*CCDS* further restricts knownCanonical subset to those transcripts which are also annotated as part of NCBI CCDS.
88
89
90 .. class:: infomark
91
92 *Annotations* for the following functional categories of genomic SNPs will be included in the output:
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94
95 -*All*: coding-synon, introns, nonsense missense utr-3, utr-5.
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97
98 -*Coding*: coding-synon, nonsense. missense
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100
101 -*Missense*: missense.
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103
104
105 .. class:: warningmark
106
107 Note that PolyPhen-2 predictions are always produced for missense
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73 109
74 .. class:: infomark 110 .. class:: infomark
75 111
76 112
77 '''Input format''': 113 Input format:
78 114
79 115
80 chr22:30421786 A/T 116 chr22:30421786 A/T
81 117
82 chr22:29446079 A/G 118 chr22:29446079 A/G
83 119
84 chr22:40814500 A/G 120 chr22:40814500 A/G
85 121
86 chr22:40815256 C/T 122 chr22:40815256 C/T
123
87 124
88 125
89 **Citations** 126 **Citations**
90 127
91 If you use this tool please cite: 128 If you use this tool please cite: