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news [2021/06/19 20:13] (current) – created - external edit 127.0.0.1
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 +====== 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
news.txt · Last modified: 2021/06/19 20:13 by 127.0.0.1

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