SIFT predicts whether an amino acid substitution affects protein function based on sequence homology and the physical properties of amino acids. SIFT can be applied to naturally occurring nonsynonymous polymorphisms and laboratory-induced missense mutations.

LATEST UPDATES

04 February 2014
  • Fix 1000 Genomes allele frequencies. Updated database available in Code & Data Section.
17 January 2014
  • SIFT Standalone v5.1.1 release - Minor bug fixed for SIFT indels tool
For all updates, please click on History tab.
Genome Tools Single Protein Tools
1.   genome coding variants filter tool Restrict to coding variants
BLink toolSIFT BLink
2a. SIFT missense / nonsynonymous SNV toolSIFT nonsynonymous single nucleotide variants (genome-scale) New! Feb 3,2014 protein sequence toolSIFT Sequence
2b. coding indels toolClassify coding indels (Insertion/Deletions)
protein homologues toolSIFT Related Sequence
protein aligned sequences toolSIFT Aligned Sequences
Batch Tools SIFT WebServices
protein batch toolSIFT Batch Protein
protein homologues toolSIFT Web Services
SIFT dbSNP toolSIFT dbSNP 135
SIFT for in-house use (version 5.1.1, released January 17, 2014, compatible with database for SIFT version 5.0.*)


Run SIFT on the Amazon Cloud


Copyright

Source code & executables (Sun, Linux) [SIFT version 5.1.1]Download SIFT exe 17 January 2014
MD5 Checksum for SIFT standalone

Script to download SIFT database v.5.0.1Download SIFT database [released: February 03/2014]

To install SIFT indel for standalone, please download and unzip the following file
and follow the instructions provided in the README_INDEL file
For downloading indel database

Report bugs

Test sets for initial training of SIFT algorithm

Literature


Our review "Predicting the Effects of Amino Acid Substitutions on Protein Function" in Annual Review of Genomics and Human Genetics

Chapter

Supplementary Table 1



Referencing SIFT
Other Similar ToolsOther Similar Prediction Tools

This website is maintained by the group of Pauline Ng, creator of SIFT. Pauline developed and maintained the SIFT website
at Fred Hutchinson Cancer Researcher Center from 2001-2008, then the J. Craig Venter Institute from 2008-2010, and she is
now at the Genome Institute of Singapore.

Server support is provided by Georg Schneider, creator of protein function prediction tool ANNIE.

Recent changes to SIFT

04 February 2014
  • Fix 1000 Genomes allele frequencies. Updated database available in Code & Data Section.
17 January 2014
  • SIFT Standalone v5.1.1 release - Minor bug fixed for SIFT indels tool
19 Aug 2013
  • BLink tool
      Include "complete genomes" database as a search option
      Web service and standalone are now updated to match the website change in Apr 2013
  • SIFT Indel tool now includes predictions for 3n indels
  • New SIFT 5.1 standalone program with 3n indel predictions and BLink complete genomes options
    See Code & Data section for details
15 May 2013
  • Minor bug fixed on SIFT indels website for indels spanning exon boundaries
11 April 2013
  • SIFT BLink web server updated to parse NCBI's new BLink format. Source code for SIFT BLink will be released in the next standalone version of SIFT. Please contact us if you would like early access to this script.
04 February 2013
  • SIFT 5.0.3 standalone released.
    • nsSNVs now displays all transcripts instead of transcripts with the same amino acid. This is pertinent to a very small percentage of proteins that have alternative reading frames, please see the following document for a brief explanation.
    • indel tool default option values are now consistent with that of SIFT webserver.
    • indel tool now handles cases where input file and directory names are too long
  • SIFT Web Service Tool
    • Longer unique filenames used for increased security
    • Users will receive announcements of impending maintenance via web services tool
14 January 2013
  • New Transcript_DB for Classfy coding indels tool released. This increases annotation of indel location and transcript visualization.
    If you are using standalone indels tool, please download new database from SIFT database for SIFT version 5.0.*

31 December 2012
  • SIFT standalone version 5.0.2 released. nsSNVs tool selects consistent set of transcripts from pre-computed database.
    Script modified: snv_db_engine.pl. SQL query now returns the results in a consistent order.

November/December 2012
  • SIFT standalone version 5.0.1 released. Fixes issue pertaining to multiple transcript display for nsSNVs tool. Predictions have not changed.
  • SIFT commandline for SNVs has been updated to match web interface and SIFT 5.0.1 on 05 Dec 2012.

October 2012

Updated SIFT by commandline:

  • Added error checking of intermediate file.
  • Added process feedback for user to track which step they are at.
  • Fix bug which user may encounter a long wait time before getting a timeout. This was usually due to errors in the config file.
  • Added checking of jobs in SIFT queue and dynamic wait time before job gets processed.
  • New scripts can be downloaded from SIFT Web Services
July 2012
  • Get SIFT predictions for genomic SNVs and SIFT BLink by commandline here
June 2012
  • Fixes to HapMap allele frequencies in SIFT v5.0.0 database
    and update of 1000 Genome allele frequency information to dbSNP135
  • dbSNP tool updated to dbSNP version 135
March 2012
February 2012
  • SIFT nsSNVs tool updated to dbSNP 135
  • Fixed strand issues for some dbSNP rs ids
  • Reference allele predictions provided
January 2012
November 2011
  • SIFT tool for nsSNVs in genome now includes RefSeq, UCSC, and CCDS annotations in addition to Ensemble

June 2011
March 2011
  • Restrict coding tool now accepts the following formats: PileUp, VCF4.0, MAQ, SOAP, GFF3, CASAVA, cg as well as SIFT' own comma-delimited format.
  • Optimized SIFT Indel tool for speed.
  • SIFT Indel tool provides option to check presence in 1000 genome.
February 2011
  • Upgraded database to dbSNP build 132
  • Added HCB, JPT and YRI allele frequencies
  • Included presence in 1000 Genomes (1000 Genome July 2010 data release)
  • Fixed issues pertaining to inexact dbSNP matches. Previously, only checked coordinate positions. Now, also checking allele.
  • Fixed issues pertaining to wrong coordinates in Y chromosome, data regenerated from using information from UCSC.