| 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. |
| Genome Tools | Single Protein Tools |
1.
 Restrict to coding variants |
SIFT BLink Updated 11 April 2013
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| 2a.
SIFT nonsynonymous single nucleotide variants (genome-scale)
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SIFT Sequence
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| 2b.
Classify coding indels (Insertion/Deletions)
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SIFT Related Sequence
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| SIFT Aligned Sequences |
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| Batch Tools | SIFT WebServices |
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SIFT Batch Protein
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SIFT Web Services
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SIFT dbSNP 135
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SIFT for in-house use (version 5.0.3, released February 04, 2013, compatible with database for SIFT version 5.0.*)
Source code & executables (Sun, Linux) [SIFT version 5.0.3]
04 Feb 2013
MD5 Checksum for SIFT standalone
Script to download SIFT database [released: Jan 14/2013]
Please download the following database as well if you are using SIFT frameshifting indel tool
SIFT Coding Info database for SIFT version 5.0.*
Test sets for initial training of SIFT algorithm
Literature
Referencing SIFT
Referencing SIFT
- Predicting Deleterious Amino Acid Substitutions, Genome Res. 2001 May; 11(5): 863.874.
(Link)
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Accounting for Human Polymorphisms Predicted to Affect Protein Function, Genome Res. 2002 December; 436-446
(Link)
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SIFT: predicting amino acid changes that affect protein function, Nucleic Acids Research, 2003, Vol. 31, No. 13 3812-3814
(Link)
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Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm, Nature Protocols 4, - 1073 - 1081 (2009)
(Link)
Other 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.
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
15 May 2013
31 December 2012
November/December 2012
October 2012
June 2011
- Minor bug fixed on SIFT indels website for indels spanning exon boundaries
- 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.
- 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
- 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
- Get SIFT predictions for genomic SNVs and SIFT BLink by commandline here
- 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
- SIFT v5.0.0 standalone + database released, includes frameshifting indel prediction algorithm.
- SIFT Batch Protein allows more input types (various protein ids and positions) and updated to dbSNP 135
- SIFT nsSNVs tool updated to dbSNP 135
- Fixed strand issues for some dbSNP rs ids
- Reference allele predictions provided
- New SIFT frameshifting indel prediction tool
- Analysis of JCVI Aug 2011 databases available
- SIFT tool for nsSNVs in genome now includes RefSeq, UCSC, and CCDS annotations in addition to Ensemble
June 2011
- Made SIFT available on AWS cloud. Please see instructions.
- 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.
- 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.