WHESS.db Quick search option added to the PolyPhen-2 web interface.
PolyPhen-2 build r394 was released which fixes a number of bugs reported since the initial v2.2.2 release.
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
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.
No significant changes to the classifiers performance or prediction accuracy were introduced in this version
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.
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.
Version 2.0.23 (r349) of the standalone PolyPhen-2 software has been released.
INSTALL.mapsnps
file for installation instructions
*.prf
) from your scratch
and precomputed
directories before using new version