SIFT: predicting amino acid changes that affect protein function
Pauline C. Ng,Steven Henikoff +1 more
TLDR
SIFT is a program that predicts whether an amino acid substitution affects protein function so that users can prioritize substitutions for further study and can distinguish between functionally neutral and deleterious amino acid changes in mutagenesis studies and on human polymorphisms.Abstract:
Single nucleotide polymorphism (SNP) studies and random mutagenesis projects identify amino acid substitutions in protein-coding regions. Each substitution has the potential to affect protein function. SIFT (Sorting Intolerant From Tolerant) is a program that predicts whether an amino acid substitution affects protein function so that users can prioritize substitutions for further study. We have shown that SIFT can distinguish between functionally neutral and deleterious amino acid changes in mutagenesis studies and on human polymorphisms. SIFT is available at http://blocks.fhcrc.org/sift/SIFT.html.read more
Citations
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Journal Article
Assessment of canine BEST1 variations identifies new mutations and establishes an independent bestrophinopathy model (cmr3).
Barbara Zangerl,Kaisa Wickström,Julianna Slavik,S. J. Lindauer,Saija Ahonen,Claude Schelling,Hannes Lohi,Karina E Guziewicz,Gustavo D. Aguirre +8 more
TL;DR: A third independent canine model for human bestrophinopathies has been established in the LH breed, and results indicate that cmr has a larger impact on the general dog population than was initially suspected.
Journal ArticleDOI
Candidate genes and single nucleotide polymorphisms associated with variation in residual feed intake in beef cattle
B. K. Karisa,Jennifer M. Thomson,Jennifer M. Thomson,Zhiqiang Wang,Paul Stothard,Stephen S. Moore,Stephen S. Moore,Graham Plastow +7 more
TL;DR: The candidate gene approach was used to identify genes associated with residual feed intake (RFI) in beef steers and indicated that the significant genes were involved in biological pathways such as lipid, protein and energy metabolism, electron transport and membrane signaling.
Journal ArticleDOI
OSBPL2 encodes a protein of inner and outer hair cell stereocilia and is mutated in autosomal dominant hearing loss (DFNA67).
Michaela Thoenes,Ulrike Zimmermann,Inga Ebermann,Martin Ptok,Morag A. Lewis,Holger Thiele,Susanne Morlot,Markus Hess,Andreas Gal,Tobias Eisenberger,Carsten Bergmann,Gudrun Nürnberg,Peter Nürnberg,Karen P. Steel,Marlies Knipper,Hanno J. Bolz +15 more
TL;DR: This study and the recent description of another frameshift mutation in a Chinese ADNSHL family identify OSBPL2 as a novel gene for progressive deafness.
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Evaluating our ability to predict the structural disruption of RNA by SNPs
TL;DR: A large-scale meta-analysis of Selective 2'-Hydroxyl Acylation analyzed by Primer Extension data, which probes the structure of RNA found that several single point mutations exist that significantly disrupt RNA secondary structure in the five transcripts the authors analyzed.
Journal ArticleDOI
Exome sequencing explained: a practical guide to its clinical application.
TL;DR: This review provides a practical guide for clinicians and genomic informaticians on the clinical application of whole-exome sequencing, addressing sequencing capture and methodology, quality control parameters at different stages of sequencing analysis and proposing an exome data filtering strategy that includes primary filtering (for the removal of probable benign variants) and secondary filtering for the prioritization of remaining candidates.
References
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TL;DR: The dbSNP database is a general catalog of genome variation to address the large-scale sampling designs required by association studies, gene mapping and evolutionary biology, and is integrated with other sources of information at NCBI such as GenBank, PubMed, LocusLink and the Human Genome Project data.
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Amos Marc Bairoch,Rolf Apweiler +1 more
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Predicting Deleterious Amino Acid Substitutions
Pauline C. Ng,Steven Henikoff +1 more
TL;DR: A tool that uses sequence homology to predict whether a substitution affects protein function is constructed, which may be used to identify plausible disease candidates among the SNPs that cause missense substitutions.
Journal ArticleDOI
Human non‐synonymous SNPs: server and survey
TL;DR: A World Wide Web server is presented to predict the effect of an nsSNP on protein structure and function and the dependence of selective pressure on the structural and functional properties of proteins is studied.