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Protocols

SIFT specifications

Information


Unique identifier OMICS_00137
Name SIFT
Alternative names Sorting Intolerant From Tolerant, SIFT for genomes, SIFT 4G
Software type Application/Script
Interface Command line interface
Restrictions to use None
Input data Some sequence conservation and amino acid properties.
Input format VCF,FASTA,GTF,GFF
Output format VCF,XLS
Operating system Unix/Linux
License GNU General Public License version 3.0
Computer skills Advanced
Version 2.0.0
Stability Stable
Requirements
g++, GNU make, nvcc
Maintained Yes

Taxon


  • Primates
    • Homo sapiens

Download


download.png
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Versioning


No version available

Maintainer


  • person_outline Pauline Ng

Additional information


http://sift.jcvi.org/

Information


Unique identifier OMICS_00137
Name SIFT
Alternative names Sorting Intolerant From Tolerant, SIFT for genomes, SIFT 4G
Interface Web user interface
Restrictions to use None
Input data Some sequence conservation and amino acid properties.
Input format VCF
Output format VCF,XLS
Computer skills Basic
Stability Stable
Maintained Yes

Taxon


  • Primates
    • Homo sapiens

Download


debian.png

Maintainer


  • person_outline Pauline Ng

Additional information


http://sift.jcvi.org/

Publications for Sorting Intolerant From Tolerant

SIFT citations

 (1659)
library_books

Association of IL17RC and COL6A1 genetic polymorphisms with susceptibility to ossification of the thoracic posterior longitudinal ligament in Chinese patients

2018
PMCID: 5952594
PMID: 29764467
DOI: 10.1186/s13018-018-0817-y

[…] addition, no genetic studies have assessed the causes of T-OPLL.In our previous whole-genome sequencing (WGS) study of 30 unrelated northern Chinese Han patients, four different algorithms [including SIFT(http://sift.jcvi.org/) [], PolyPhen-2 (http://genetics.bwh.harvard.edu/pph2/) [], MutationTaster (http://www.mutationtaster.org/) [], and GERP++ (http://mendel.stanford.edu/SidowLab/downloads/ger […]

call_split

Case Report: Identification of an HNF1B p.Arg527Gln mutation in a Maltese patient with atypical early onset diabetes and diabetic nephropathy

2018
PMCID: 5952643
PMID: 29764441
DOI: 10.1186/s12902-018-0257-z
call_split See protocol

[…] o be pathogenic. Non-exonic and synonymous variants were excluded from further analysis. Missense variants were evaluated for functional impact using a variety of in-silico prediction tools including SIFT [], Polyphen2 [], MelaLR [], MetaSVN [], fathmm-MKL [], DANN [], CADD [], MutationTaster [], Mutation Assesser [] and LRT []. […]

library_books

Discovering novel SNPs that are correlated with patient outcome in a Singaporean cancer patient cohort treated with gemcitabine based chemotherapy

2018
BMC Cancer
PMCID: 5948914
PMID: 29751792
DOI: 10.1186/s12885-018-4471-x

[…] ce the majority of our patients are Singaporean Chinese. 23 out of the 77 nsSNPs were found to match this criterion. The second and third criteria were based on prediction results from PolyPhen-2 and SIFT, respectively, both of which are evolutionary sequence conservation-based approaches. We used the batch-query tool of PolyPhen-2 to parse pre-calculated results of all common nsSNPs. For those SN […]

library_books

Cancer driver mutation prediction through Bayesian integration of multi omic data

2018
PLoS One
PMCID: 5940219
PMID: 29738578
DOI: 10.1371/journal.pone.0196939

[…] nd its oncogenic function. Unfortunately, the majority of mutations in tumors occur rather infrequently, making frequency-based approaches marginally effective. In a separate vein, approaches such as SIFT [] and PolyPhen [] compute a phenomenological score for each mutation based on the physical-chemical properties or the extent of evolutionary conservation of the amino acid sequences affected by […]

library_books

Mutation analysis of SLC26A4 (Pendrin) gene in a Brazilian sample of hearing impaired subjects

2018
BMC Med Genet
PMCID: 5941635
PMID: 29739340
DOI: 10.1186/s12881-018-0585-x

[…] eq_tools/splice.htmlOMIM: https://www.omim.org/entry/274600Picard: http://broadinstitute.github.io/picard/PolyPhen2: http://genetics.bwh.harvard.edu/pph2/PRIMER 3: http://bioinfo.ut.ee/primer3-0.4.0/.SIFT: http://sift.jcvi.org/.UCSC: http://genome.ucsc.edu/ and.1000 genomes: http://www.1000genomes.org65000 exomes: http://exac.broadinstitute.org/. […]

library_books

Endothelial nitric oxide synthase genotype is associated with pulmonary hypertension severity in left heart failure patients

2018
PMCID: 5946646
PMID: 29718770
DOI: 10.1177/2045894018773049

[…] ene expression was chosen for both NOS2 and NOS3, the genes that encode iNOS and eNOS, respectively. For NOS2, the non-synonymous SNP rs3730017 (Arg221Trp) was chosen because in silico analyses using SIFT and Polyphen-214 predict that the variant is damaging to the protein structure. For NOS3, the well-studied non-synonymous SNP rs1799983 was chosen, which has been previously associated with alter […]

Citations

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SIFT institution(s)
Faculty of Electrical Engineering and Computing, University of Zagreb, Zagreb, Croatia; Computational and Systems Biology Group, Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore; Bioinformatics Institute, Agency for Science, Technology and Research, Singapore, Singapore
SIFT funding source(s)
Supported in part by A*STAR and the Croatian Science Foundation (project no. 7353, Algorithms for Genome Sequence Analysis).

SIFT review

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Julio Diaz Caballero's avatar image

Julio Diaz Caballero

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Web
The web interface of this software runs smoothly and relatively fast. The output is simple to understand and it is summarized In a single value (SIFT score). Nonetheless, I wanted to run a batch of predictions and tried to download and install SIFT in my computer, but that turned out to be a very difficult process. The dependencies are old and difficult to install. I emailed the author in order to get some assistance, but no reply. I think they stopped supporting SIFT in favour of PROVEAN.