SIFT Sequence protocols

View SIFT Sequence computational protocol

SIFT Sequence statistics

To access cutting-edge analytics on consensus tools, life science contexts and associated fields, you will need to subscribe to our premium service.

Subscribe
info

Citations per year

Citations chart
info

Popular tool citations

chevron_left Variant effect prediction chevron_right
Popular tools chart
info

Tool usage distribution map

Tool usage distribution map
info

Associated diseases

Associated diseases

SIFT Sequence specifications

Information


Unique identifier OMICS_26255
Name SIFT Sequence
Alternative name Sorting Intolerant From Tolerant Sequence
Interface Web user interface
Restrictions to use None
Input data A protein sequence or substitutions of interest.
Input format FASTA
Computer skills Basic
Stability Stable
Maintained Yes

Maintainer


  • person_outline Pauline Ng <>

Publications for Sorting Intolerant From Tolerant Sequence

SIFT Sequence in pipeline

2013
PMCID: 3877046
PMID: 24391785
DOI: 10.1371/journal.pone.0083542

[…] (http://snp.istech21.com/snpanalyzer/2.0/). the effect of amino acid changes in the proteins encoded by the transcripts was predicted in the online sift platform (http://sift.jcvi.org/) using the sift sequence option ., evolutionary divergence (p-distance) between nucleotide sequences was computed from pairwise analysis using the maximum composite likelihood method implemented in mega v5.0 […]


To access a full list of citations, you will need to upgrade to our premium service.

SIFT Sequence in publications

 (7)
PMCID: 5559773
PMID: 28814288
DOI: 10.1186/s12881-017-0448-x

[…] by guanine at position 3474 (haplotype), and the corresponding amino acid change was n1083d. this variant was predicted to alter normal protein features in both function and structure -as shown by sift sequence and project hope. also it was predicted to decrease protein stability -by i-mutant. however, it was expected to probably harmless by mutationtaster2 and benign by polyphen-2. […]

PMCID: 5411961
PMID: 28462921
DOI: 10.1038/srep46428

[…] in-silico tools. azathioprine was then replaced with mycophenolate mofetil., the tpmt protein sequence (p51580) was used in sift, polyphen-2 and align gvgd pathogenicity prediction tools. the sift sequence algorithm was used to search database uniref90 2011 april (swiss-prot/trembl), using a median sequence conservation of 3.00 and the removal of sequences with more than 90% identity […]

PMCID: 4218959
PMID: 25329095
DOI: 10.1038/ncomms6307

[…] does not account for the possibility that the variant classified as ‘derived’ in cavefish is actually present in the standing genetic variation of the surface fish which was not sampled in our data. sift sequence was used to predict the functional impact of nonsynonymous substitutions., all pathway analyses were performed with the ipa suite of tools available […]

PMCID: 4117472
PMID: 25079074
DOI: 10.1371/journal.pone.0102549

[…] geneticists., pathogenicity of identified mutations was predicted using bioinformatics software as previously described by our laboratory , . missense mutations were assessed by sift (sift.jcvi.org, sift sequence, uniprot-trembl 2009 mar) and polyphen2 (http://genetics.bwh.harvard.edu/pph2/) whereas intronic sequence variants were evaluated by the human splicing finder program, version 2.4.1 […]

PMCID: 3855963
PMID: 24348198
DOI: 10.1155/2013/948617

[…] with a mutation and 0.88 that of with an associated snp were this way transformed into 0.99 and 0.12, making the higher score related to mutation and lower to snp. we used single protein tool sift sequence, with default values of median conservation of sequences (3.0). the psi-blast search was applied on uniref90 database, and sequences with the similarity level of 90% […]


To access a full list of publications, you will need to upgrade to our premium service.

SIFT Sequence 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 Sequence funding source(s)
Supported in part by A*STAR and the Croatian Science Foundation (project no. 7353, Algorithms for Genome Sequence Analysis).

SIFT Sequence reviews

star_border star_border star_border star_border star_border
star star star star star

Be the first to review SIFT Sequence