news
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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 '' | ||
+ | |||
+ | **PolyPhen-2 web server** was also updated with the new software and structural databases. | ||
+ | |||
+ | ==== Mar 08, 2012 ==== | ||
+ | |||
+ | **WHESS.db** [[http:// | ||
+ | |||
+ | ==== 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# | ||
+ | |||
+ | The software release is accompanied by a new build of the whole human exome sequence space ([[downloads# | ||
+ | |||
+ | == ChangeLog: == | ||
+ | |||
+ | * Integrated bundled annotation and sequence databases | ||
+ | * Integrated precomputed protein and genomic multiple alignments | ||
+ | * Simplified installation (MySQL server no longer required) | ||
+ | * Improved documentation, | ||
+ | * 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]], | ||
+ | |||
+ | * 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/ | ||
+ | |||
+ | New version improves significantly on the classifiers performance: | ||
+ | |||
+ | ^ | ||
+ | | False Positive Rate | 5% | ||
+ | | True Positive Rate | ||
+ | | Probability Threshold | ||
+ | | Correctly Classified Instances | ||
+ | | Incorrectly Classified Instances | 13.3% ||| 10.1% ||| | ||
+ | | Kappa statistic | ||
+ | |||
+ | ^ | ||
+ | | False Positive Rate | 5% | ||
+ | | True Positive Rate | ||
+ | | Probability Threshold | ||
+ | | Correctly Classified Instances | ||
+ | | Incorrectly Classified Instances | 20.8% ||| 18.8% ||| | ||
+ | | Kappa statistic | ||
+ | |||
+ | Note:\\ | ||
+ | * **HumDiv** model uses 5% / 10% FPR thresholds for " | ||
+ | * **HumVar** model uses 10% / 20% FPR thresholds for " | ||
+ | |||
+ | You can also download fivefold cross-validation {{polyphen2rocs.pdf|ROC curves}} and {{polyphen2thresholds.pdf|FPR/ | ||
+ | |||
+ | == 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 '' | ||
+ | * 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 ('' | ||
+ | * 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