====== 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** [[http://genetics.bwh.harvard.edu/pph2/dbsearch.shtml|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 [[downloads#software|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 ([[downloads#datasets|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 [[downloads|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 [[appendix_b|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 [[downloads|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 {{polyphen2rocs.pdf|ROC curves}} and {{polyphen2thresholds.pdf|FPR/TPR threshold plots}} for version 2.1.0, obtained on updated HumDiv and HumVar datasets, available for download [[downloads#datasets|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 [[downloads|released]]. == ChangeLog: == * Integrated MapSNPs genomic SNP annotation tool now included, see ''INSTALL.mapsnps'' file 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 your ''scratch'' and ''precomputed'' directories 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