Table of Contents

News

Jun 21, 2021

PolyPhen-2 version 2.2.3 (build r406) has been released. It contains various bug fixes and enhancements mostly related to handling of structural annotations.

Bundled databases for this version have been updated to include PDB/DSSP Snapshot 25-May-2021 (178229 Structures). Also included now is UniRef100 non-redundant protein sequence database. See INSTALL file in the source code package for updated installation instructions.

PolyPhen-2 web server was also updated with the new software and structural databases.

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: