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
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Book ChapterDOI
Analysis of HGD Gene Mutations in Patients with Alkaptonuria from the United Kingdom: Identification of Novel Mutations.
J. Usher,David B. Ascher,Douglas E. V. Pires,Anna M. Milan,Tom L. Blundell,Lakshminarayan R. Ranganath +5 more
TL;DR: Using computational approaches based on the 3D structure, these novel mutations are predicted to affect the activity of the protein complex through destabilisation of the individual protomer structure or through disruption of protomer-protomer interactions.
Journal ArticleDOI
The potential influence of genetic variants in genes along bile acid and bile metabolic pathway on blood cholesterol levels in the population.
TL;DR: The current state of knowledge about genetic variations in bile acid and bile metabolic pathway is summarized, their impact on blood cholesterol levels and cholesterol metabolic kinetics in the population is assessed, and common genetic variants also play a role in the genetic architecture of plasma lipid traits.
Journal ArticleDOI
High-Throughput Discovery of Mutations in Tef Semi-Dwarfing Genes by Next-Generation Sequencing Analysis
Qihui Zhu,Shavannor M. Smith,Mulu Ayele,Mulu Ayele,Lixing Yang,Ansuya Jogi,Srinivasa R. Chaluvadi,Jeffrey L. Bennetzen +7 more
TL;DR: It is demonstrated that high-throughput sequencing can identify potentially valuable mutations in under-studied plant species like tef and has provided mutant lines that can now be combined and tested in breeding programs for improved lodging resistance.
Journal ArticleDOI
SNooPer: a machine learning-based method for somatic variant identification from low-pass next-generation sequencing
Jean-François Spinella,Pamela Mehanna,Ramon Vidal,Virginie Saillour,Pauline Cassart,Chantal Richer,Manon Ouimet,Jasmine Healy,Daniel Sinnett +8 more
TL;DR: SNooPer is shown how the SNooPer algorithm is not affected by low coverage or low VAFs, and can be used to reduce overall sequencing costs while maintaining high specificity and sensitivity to somatic variant calling.
Journal ArticleDOI
A Comprehensive In Silico Analysis of the Functional and Structural Impact of SNPs in the IGF1R Gene
TL;DR: A comprehensive analysis of the functional and structural impact of all known SNPs in this gene using publicly available computational prediction tools shows that a mutation from arginine to cysteine at position 1216 on the surface of the protein caused the greatest impact on stability.
References
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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
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