Mercurial > repos > saketkc > polyphen2
changeset 2:f8f4ad14f5a6 draft
Uploaded
| author | saketkc |
|---|---|
| date | Mon, 14 Apr 2014 17:50:33 -0400 |
| parents | 1cbb0f884e7c |
| children | 3c40b02934ad |
| files | polyphen2_web/polyphen2_web.xml |
| diffstat | 1 files changed, 40 insertions(+), 3 deletions(-) [+] |
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--- a/polyphen2_web/polyphen2_web.xml Mon Apr 14 17:30:34 2014 -0400 +++ b/polyphen2_web/polyphen2_web.xml Mon Apr 14 17:50:33 2014 -0400 @@ -65,16 +65,52 @@ .. class:: infomark - * HumDiv model uses 5% / 10% FPR thresholds for “probably damaging” / “possibly damaging” predictions + *Classifier model* used by the probabilistic predictor: + + -HumDiv is preferred for evaluating rare alleles, dense mapping of regions identified by genome-wide association studies, + and analysis of natural selection. HumDiv model uses 5% / 10% FPR thresholds for “probably damaging” / “possibly damaging” predictions + + + -HumVar is better suited for diagnostics of Mendelian diseases which requires distinguishing mutations with drastic effects + from all the remaining human variation, including abundant mildly deleterious alleles. + HumVar model uses 10% / 20% FPR thresholds for “probably damaging” / “possibly damaging” predictions .. class:: infomark - * HumVar model uses 10% / 20% FPR thresholds for “probably damaging” / “possibly damaging” predictions + *Transcripts* A set of Transcripts on which genomic SNPs will be mapped: + + + -*All* includes all UCSC knownGene transcripts (highly redundant) + + -*Canonical* includes UCSC knownCanonical subset + + -*CCDS* further restricts knownCanonical subset to those transcripts which are also annotated as part of NCBI CCDS. + + + .. class:: infomark + + *Annotations* for the following functional categories of genomic SNPs will be included in the output: + + + -*All*: coding-synon, introns, nonsense missense utr-3, utr-5. + + + -*Coding*: coding-synon, nonsense. missense + + + -*Missense*: missense. + + + + .. class:: warningmark + + Note that PolyPhen-2 predictions are always produced for missense + .. class:: infomark - '''Input format''': + Input format: chr22:30421786 A/T @@ -86,6 +122,7 @@ chr22:40815256 C/T + **Citations** If you use this tool please cite: