# HG changeset patch
# User saketkc
# Date 1397512233 14400
# Node ID f8f4ad14f5a6719c8c99ff3785f39ccc4260ce6e
# Parent  1cbb0f884e7c92c04ae3ccfead527a3ed22a81a9
Uploaded

diff -r 1cbb0f884e7c -r f8f4ad14f5a6 polyphen2_web/polyphen2_web.xml
--- 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: