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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Mutation distribution in the von Willebrand factor gene related to the different von Willebrand disease (VWD) types in a cohort of VWD patients
Hamideh Yadegari,Julia Driesen,Anna Pavlova,Arijit Biswas,Hans-Jörg Hertfelder,Johannes Oldenburg +5 more
TL;DR: Genotypes and phenotype characteristics of patients with VWD are explored with the aim of dissecting the distribution of mutations in different types of VWD and establishing the relationship between genotype and phenotype.
Journal ArticleDOI
Six years’ experience with LipidSeq: clinical and research learnings from a hybrid, targeted sequencing panel for dyslipidemias
Jacqueline S. Dron,Jian Wang,Adam D. McIntyre,Michael A. Iacocca,Michael A. Iacocca,John F. Robinson,Matthew R. Ban,Henian Cao,Robert A. Hegele +8 more
TL;DR: The LipidSeq design based on ontology of lipid disorders has enabled robust detection of variants underlying monogenic and polygenic dyslipidemias and is demonstrated to have helped in diagnosis and improving treatment options.
Journal ArticleDOI
Multiple common and rare variants of ABCG2 cause gout
Toshihide Higashino,Tappei Takada,Hirofumi Nakaoka,Yu Toyoda,Blanka Stiburkova,Hiroshi Miyata,Yuki Ikebuchi,Hiroshi Nakashima,Seiko Shimizu,Makoto Kawaguchi,Masayuki Sakiyama,Akiyoshi Nakayama,Airi Akashi,Yuki Tanahashi,Yusuke Kawamura,Takahiro Nakamura,Kenji Wakai,Rieko Okada,Ken Yamamoto,Kazuyoshi Hosomichi,Tatsuo Hosoya,Kimiyoshi Ichida,Hiroshi Ooyama,Hiroshi Suzuki,Ituro Inoue,Tony R. Merriman,Nariyoshi Shinomiya,Hirotaka Matsuo +27 more
TL;DR: It is revealed that multiple common and rare variants of ABCG2 are independently associated with gout, which could support both the ‘Common Disease, Common Variant’ and ‘ common Disease, Multiple Rare variant’ hypotheses for the association betweenABCG2 and gout susceptibility.
Posted ContentDOI
Genetic costs of domestication and improvement
TL;DR: The evolutionary forces that may contribute to genetic load during domestication and improvement are described, and the available evidence for ‘the cost of domestication’ in animal and plant genomes is reviewed.
Journal ArticleDOI
The Use of Orthologous Sequences to Predict the Impact of Amino Acid Substitutions on Protein Function
TL;DR: It is proposed that homologous proteins are best used to reconstruct ancestral sequences and infer amino acid conservation among only direct lineal ancestors of a particular protein and shown that such an “ancestral site preservation” measure outperforms other prediction methods.
References
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Journal ArticleDOI
Database resources of the National Center for Biotechnology Information
David L. Wheeler,Deanna M. Church,Ron Edgar,Scott Federhen,Wolfgang Helmberg,Thomas L. Madden,Joan Pontius,Gregory D. Schuler,Lynn M. Schriml,Edwin Sequeira,Tugba O. Suzek,Tatiana Tatusova,Lukas Wagner +12 more
TL;DR: In addition to maintaining the GenBank(R) nucleic acid sequence database, the National Center for Biotechnology Information (NCBI) provides data analysis and retrieval resources for the data in GenBank and other biological data made available through NCBI’s website.
Journal ArticleDOI
dbSNP: the NCBI database of genetic variation
Stephen T. Sherry,Minghong Ward,Michael Kholodov,Jonathan Baker,Lon Phan,Elizabeth M. Smigielski,Karl Sirotkin +6 more
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.
Journal ArticleDOI
The SWISS-PROT protein sequence data bank and its supplement TrEMBL in 1999.
Amos Marc Bairoch,Rolf Apweiler +1 more
TL;DR: The Human Proteomics Initiative (HPI), a major project to annotate all known human sequences according to the quality standards of SWISS-PROT, is described.
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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.