Table of Contents

News

Mar 08, 2012

WHESS.db quick search option added to the PolyPhen-2 web interface.

Feb 23, 2012

PolyPhen-2 build r394 was released which fixes a number of bugs reported since the initial v2.2.2 release.

ChangeLog:

To upgrade from the previous version, download the following two files and extract their contents over your existing installation:

polyphen-2.2.2r394.tar.gz
polyphen-2.2.2-alignments-multiz-2009_10.tar.bz2

Feb 15, 2012

PolyPhen-2 v2.2.2 (r393) has been released. Web server was also brought up to date with the new software release, which includes UniProtKB/UniRef100 Release 2011_12 (14-Dec-2011), PDB/DSSP Snapshot 03-Jan-2012 (78,304 entries) and UCSC GRCh37/hg19 (08-Oct-2009) databases.

The software release is accompanied by a new build of the whole human exome sequence space (WHESS) dataset of precomputed PolyPhen-2 annotations.

ChangeLog:

No significant changes to the classifiers performance or prediction accuracy were introduced in this version

Aug 9, 2011

Interim update of MapSNPs tool released, with fixes for a number of earlier reported bugs:

Please see MapSNPs annotation summary description for the CpG context annotations changes.

May 8, 2011

Version 2.1.0 (r367) of the standalone PolyPhen-2 software has been released. Web server is now updated to utilize new software release, as well as the protein sequences from UniProtKB/UniRef100 Release 2011_04 (05-Apr-2011) and structures from PDB/DSSP Snapshot 06-Apr-2011 (72,244 entries).

New version improves significantly on the classifiers performance:

HumDiv classifier v2.0.23r349 v2.1.0r367
False Positive Rate 5% 10% 20% 5% 10% 20%
True Positive Rate 66% 80% 93% 78% 89% 96%
Probability Threshold 0.987 0.841 0.067 0.953 0.432 0.024
Correctly Classified Instances 86.7% 89.8%
Incorrectly Classified Instances 13.3% 10.1%
Kappa statistic 0.711 0.793
HumVar classifier v2.0.23r349 v2.1.0r367
False Positive Rate 5% 10% 20% 5% 10% 20%
True Positive Rate 40% 58% 76% 53% 68% 83%
Probability Threshold 0.991 0.964 0.746 0.981 0.902 0.493
Correctly Classified Instances 79.2% 81.2%
Incorrectly Classified Instances 20.8% 18.8%
Kappa statistic 0.568 0.625

Note:

You can also download fivefold cross-validation ROC curves and FPR/TPR threshold plots for version 2.1.0, obtained on updated HumDiv and HumVar datasets, available for download here.

ChangeLog:

Dec 9, 2010

Version 2.0.23 (r349) of the standalone PolyPhen-2 software has been released.

ChangeLog: