Referencing SIFT

Kumar P, Henikoff S, Ng PC. Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm. Nat Protoc. 2009;4(7):1073-81. PubMed PDF

Ng PC, Henikoff S. Predicting the Effects of Amino Acid Substitutions on Protein Function Annu Rev Genomics Hum Genet. 2006;7:61-80. PubMed PDF Supp

Ng PC, Henikoff S. SIFT: predicting amino acid changes that affect protein function. Nucleic Acids Res. 2003 Jul 1;31(13):3812-4. PubMed

Ng PC, Henikoff S. Accounting for Human Polymorphisms Predicted to Affect Protein Function. Genome Res. 2002 Mar;12(3):436-46. PubMed Data

Ng PC, Henikoff S. Predicting Deleterious Amino Acid Substitutions. Genome Res. 2001 May;11(5):863-74. PubMed






SIFT predicts whether an amino acid substitution affects protein function. SIFT prediction is based on the degree of conservation of amino acid residues in sequence alignments derived from closely related sequences, collected through PSI-BLAST. SIFT can be applied to naturally occurring nonsynonymous polymorphisms or laboratory-induced missense mutations.

** PROVEAN project New **

Visit our new PROVEAN project to get functional predictions from multiple tools. We welcome your feedback or questions.

New features in PROVEAN Human Genome Variants DB:

  • Single submission returns functional predictions from SIFT and PROVEAN. PROVEAN is a new prediction tool which works for both SNPs and indels. (Choi et al., 2012, PLOS ONE)
  • Updated versions of Ensembl gene annotation (GRCh37 Ensembl 66) and NCBI dbSNP database (Build 137).
  • New database structure to support fast retrieval for genome-wide analysis.

Human Genome DB

Tool Description

SIFT/PROVEAN Human SNPs

Get SIFT and PROVEAN predictions for SNPs and indels (Ensembl 66) (Sample format)

SIFT Human SNPs

Get SIFT predictions for nonsynonymous SNPs (Ensembl 63) (Sample format)
 

Other human genome tools:

SIFT Human Protein DB

Tool Description (Ensembl 63)

SIFT Human Protein

Get SIFT predictions for nonsynonymous AA substitutions (Ensembl ENSP ID)

SIFT dbSNP DB

Tool Description (dbSNP Build 132)

SIFT dbSNP rs IDs

Get SIFT predictions for dbSNP SNPs including non-human species (NCBI rs ID)

SIFT dbSNP Protein

Get SIFT predictions for dbSNP proteins including non-human species (RefSeq ID or GI number)

SIFT Single Protein Tools

Tool Description

SIFT BLink

Run SIFT analysis on single protein using precomputed BLAST from NCBI BLink (RefSeq ID or GI number)

SIFT Sequence

Run SIFT analysis on single protein through a PSI-BLAST search (fasta)

SIFT Related Sequences

Run SIFT analysis on protein query and a group of related sequences (multi-fasta)

SIFT Aligned Sequences

Run SIFT analysis on protein query already in multi-sequence alignments (MSA)