http://genetics.bwh.harvard.edu/pph2/dokuwiki/ 2012-05-16T05:53:29-04:00 http://genetics.bwh.harvard.edu/pph2/dokuwiki/ http://genetics.bwh.harvard.edu/pph2/dokuwiki/lib/tpl/dokucms/images/favicon.ico text/html 2010-12-09T18:23:35-04:00 http://genetics.bwh.harvard.edu/pph2/dokuwiki/about?rev=1291937015&do=diff PolyPhen-2 is a new development of the PolyPhen tool for annotating coding nonsynonymous SNPs. Some of the highlights of the new version are: * High quality multiple sequence alignment pipeline * Probabilistic classifier based on machine-learning method * Optimized for high-throughput analysis of the next-generation sequencing data text/html 2012-02-13T11:25:11-04:00 http://genetics.bwh.harvard.edu/pph2/dokuwiki/appendix_a?rev=1329150311&do=diff Following is a description of PolyPhen-2 annotation summary report. Reports in this format are produced by both PolyPhen-2 Batch query web service, as well as by standalone PolyPhen-2 software. It is a plain text tab-separated file with each line annotating single protein variant (amino acid residue substitution).         text/html 2012-02-13T11:31:22-04:00 http://genetics.bwh.harvard.edu/pph2/dokuwiki/appendix_b?rev=1329150682&do=diff Following is a description of MapSNPs annotation summary report. MapSNPs genomic SNP annotation tool is part of the PolyPhen-2 Batch query web service. Whenever you submit genomic SNPs in the form of chromosome coordinates/alleles, a report formatted as described below will appear under SNPs link on the Batch query results web page. It is a plain text tab-separated file with each line annotating a corresponding protein sequence variant (amino acid residue substitution) for each missense allelic … text/html 2010-10-07T22:08:31-04:00 http://genetics.bwh.harvard.edu/pph2/dokuwiki/docs?rev=1286503711&do=diff Overview PolyPhen-2 Web User Guide PolyPhen-2 Standalone User Guide Frequently Asked Questions APPENDIX A: PolyPhen-2 annotation summary report explained APPENDIX B: MapSNPs annotation summary report explained text/html 2012-04-25T22:07:15-04:00 http://genetics.bwh.harvard.edu/pph2/dokuwiki/downloads?rev=1335406035&do=diff Downloadable material. Software Licensing The software provided herein is free for academic instruction and research use only. Commercial licenses are available to legal entities, including companies and organizations (both for-profit and non-profit), requiring the software for general commercial use. To obtain a commercial license please, contact us via e-mail. text/html 2012-02-15T21:18:27-04:00 http://genetics.bwh.harvard.edu/pph2/dokuwiki/faq?rev=1329358707&do=diff Inconsistent predictions * Q: I noticed a substantial degree of variance in the predictions and scores output by PolyPhen-2 Web server as compared to my local PolyPhen-2 installation, how would you explain this? * A: The most common source of discrepancies in PolyPhen-2 output is different versions of the non-redundant protein sequence database (UniRef100) utilized for constructing multiple sequence alignments (MSA). text/html 2012-03-08T14:58:25-04:00 http://genetics.bwh.harvard.edu/pph2/dokuwiki/news?rev=1331236705&do=diff Mar 08, 2012 WHESS.db 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… text/html 2012-02-15T12:20:59-04:00 http://genetics.bwh.harvard.edu/pph2/dokuwiki/overview?rev=1329326459&do=diff Most of human genetic variation is represented by SNPs (Single-Nucleotide Polymorphisms) and many of them are believed to cause phenotypic differences between human individuals. We specifically focus on nonsynonymous SNPs (nsSNPs), i.e., SNPs located in coding regions and resulting in amino acid variation in protein products of genes. It was shown in several studies that impact of amino acid allelic variants on protein structure/function can be reliably predicted via analysis of multiple sequen… text/html 2010-12-09T17:25:26-04:00 http://genetics.bwh.harvard.edu/pph2/dokuwiki/sidebar?rev=1291933526&do=diff    Home    News    About    Overview    Documentation    Downloads text/html 2012-03-08T15:08:37-04:00 http://genetics.bwh.harvard.edu/pph2/dokuwiki/start?rev=1331237317&do=diff PolyPhen-2 (Polymorphism Phenotyping v2) is a software tool which predicts possible impact of amino acid substitutions on the structure and function of human proteins using straightforward physical and evolutionary comparative considerations. Explore navigation menu on the left to find out more About PolyPhen-2, consult the Documentation (work in progress), or Download standalone software, datasets and publications.