Table of Contents
News
Jun 11, 2024
PolyPhen-2 version 2.2.3 (build r408) has been released. It contains a bugfix related to handling of protein structural annotations. PolyPhen-2 web server was also updated with the new software build.
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 protein 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:
- Added missing MultiZ alignments for hg18 UCSC genome assembly version
- Corrected substitution profile scores for hg19 MultiZ alignments, which were calculated with the wrong PSIC parameters
- Updated classifier models to reflect the changes in distribution of PSIC profile scores caused by the MultiZ updates
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:
- Integrated bundled annotation and sequence databases
- Integrated precomputed protein and genomic multiple alignments
- Simplified installation (MySQL server no longer required)
- Improved documentation, see INSTALL and README files included
- Up to 150-fold increase in speed for large-scale surveys
- Improved annotation coverage, especially for non-globular proteins
- Makefile updated to provide automatic downloads of WEKA v3-6-6 and MAFFT v6.864
- Numerous bugs fixed
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:
- Fixed reverse-order flanking nucleotides for transcripts on minus strand
- Fixed incorrect CpG context annotations for transcripts on minus strand
- Fixed BLAST search occasionally missing a valid UniProtKB match (-U option)
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:
- HumDiv model uses 5% / 10% FPR thresholds for “probably damaging” / “possibly damaging” predictions
- HumVar model uses 10% / 20% FPR thresholds for “probably damaging” / “possibly damaging” predictions
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:
- Training sets and classifier models updated; new models show increased sensitivity and specificity
- MSA pipeline configuration settings tuned to improve alignments quality and speed
- Better handling of structural features for proteins with PDB 3D structures available
- Support for Grid Engine and Platform LSF distributed computing environments added
- MapSNPs installation procedure and documentation improved
- Makefile updated to provide automatic downloads of WEKA v3-6-4 and MAFFT v6.853
- A number of (mostly minor) bugs fixed
Dec 9, 2010
Version 2.0.23 (r349) of the standalone PolyPhen-2 software has been released.
ChangeLog:
- Integrated MapSNPs genomic SNP annotation tool now included, see
INSTALL.mapsnpsfile for installation instructions - Experimental species-specific support added for mouse, rat, dog, and zebrafish proteomes
- Classifier models updated.
New models are incompatible with PSIC profiles generated by previous versions of the software. Make sure you removed all old PSIC profile files (*.prf) from yourscratchandprecomputeddirectories before using new version - Several LEON memory allocation errors fixed, stability of the MSA pipeline improved
- MapSNPs bug fixed which caused standard gene symbol missing from the annotations for non-coding SNPs
- Makefile download links updated to WEKA v3-6-3 and MAFFT v6.843
- Version strings for all database sources are now written to XML report files