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
Please cite:
Adzhubei IA, Schmidt S, Peshkin L, Ramensky VE, Gerasimova A, Bork P, Kondrashov AS, Sunyaev SR. Nat Methods 7(4):248-249 (2010). PubMedPDFSupplemental Information
Other References:
Adzhubei I, Jordan DM, Sunyaev SR. Predicting functional effect of human missense mutations using PolyPhen-2. Curr Protoc Hum Genet, Chapter 7:Unit7.20 (2013). PubMedPDF
Ramensky V, Bork P, Sunyaev S. Human non-synonymous SNPs: server and survey. Nucleic Acids Res 30(17):3894-3900 (2002). PubMedPDF
Sunyaev SR, Eisenhaber F, Rodchenkov IV, Eisenhaber B, Tumanyan VG, Kuznetsov EN. PSIC: profile extraction from sequence alignments with position-specific counts of independent observations. Protein Eng 12(5):387-394 (1999). PubMedPDF