SIFT pipeline

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


  • Animals
    • Homo sapiens

Download


Versioning


Add your version

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


  • Animals
    • Homo sapiens

Maintainer


  • person_outline Pauline Ng <>

Additional information


http://sift.jcvi.org/

Publications for Sorting Intolerant From Tolerant

SIFT citations

 (3)
2018
PMCID: 5844295

[…] positions, and likely ems-induced homozygous snps. we tabulated and compared the blast results for the three data sets., we followed the recommended steps for the setup and application of the sift program to predict the effect of missense mutations on protein function (kumar et al. 2009; version 5.2.2). we downloaded the uniref90 protein database (uniprot consortium 2014; suzek et al. […]

2014
PMCID: 4289236

[…] using the most recent approximate likelihood ratio test (alrt) as an alternative to bootstrap., putative impact of selected compensatory mutations on protein function was assessed through the use of sift scores (available at http://sift.jcvi.org/) [31] computed from the query alignment against uniref90 database hits (with less than 90% identity, with a median sequence conservation equal […]

2013
PMCID: 3751836

[…] to analyze splice sites and splicing silencers and enhancers., to determine the potential deleterious effect of amino acid changes on protein function we used the sift (http://blocks.fhcrc.org/sift/sift.html) software. this software uses the protein sequence similarity of different species and the characteristics of amino acids (structure, polar/no polar, basic/acid) to calculate […]

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

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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.