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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A probabilistic classifier for olfactory receptor pseudogenes.
TL;DR: It is demonstrated that the CORP algorithm is capable to distinguish between functional and non-functional OR genes with high precision even when the encoded protein would differ by a single amino acid.
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Genetic Epidemiology of Glucose-6-Phosphate Dehydrogenase Deficiency in the Arab World.
C. George Priya Doss,Dima R. Alasmar,Reem I. Bux,P. Sneha,Fadheela Dad Bakhsh,Iman Al-Azwani,Rajaa El Bekay,Hatem Zayed +7 more
TL;DR: A systematic search was implemented using four literature databases to capture all the causative mutations of Glucose-6-phosphate dehydrogenase (G6PD) deficiency in the 22 Arab countries, yielding 33 mutations that were exposed to structural analysis and molecular dynamics simulation analysis.
Journal ArticleDOI
Genome-wide SNP and microsatellite variation illuminate population-level epidemiology in the Leishmania donovani species complex.
Tim Downing,Olivia Stark,Manu Vanaerschot,Hideo Imamura,Mandy Sanders,Saskia Decuypere,Simonne De Doncker,Ilse Maes,Suman Rijal,Shyam Sundar,Jean-Claude Dujardin,Matthew Berriman,Gabriele Schönian +12 more
TL;DR: Microsatellite typing of Leishmania donovani complex isolates discriminates intercontinental groups and genome-wide SNP profiling reveals diversity in a homogeneous population.
Journal ArticleDOI
Global and Site-Specific Effect of Phosphorylation on Protein Turnover
Chongde Wu,Qian Ba,Dayun Lu,Wenxue Li,Barbora Salovska,Pingfu Hou,Torsten Mueller,George Rosenberger,Erli Gao,Yi Di,Hu Zhou,Eugenio F. Fornasiero,Yansheng Liu +12 more
TL;DR: DeltaSILAC profiling revealed a global, unexpected delaying effect of many phosphosites on protein turnover, and found that phosphorylated sites accelerating protein turnover are functionally selected for cell fitness, enriched in Cyclin-dependent kinase substrates, and evolutionarily conserved.
Journal ArticleDOI
Whole-genome resequencing analyses of five pig breeds, including Korean wild and native, and three European origin breeds
Jung-Woo Choi,Won-Hyong Chung,Kyung-Tai Lee,Eun-Seok Cho,Si-Woo Lee,Bong-Hwan Choi,Sang-Heon Lee,Won-Jun Lim,Dajeong Lim,Yun-Gyeong Lee,Joon-Ki Hong,Doo Wan Kim,Hyeon-Jeong Jeon,Jiwoong Kim,Namshin Kim,Tae-Hun Kim +15 more
TL;DR: In this paper, the authors presented whole-genome resequencing analyses of 55 pigs of five breeds representing Korean native pigs, wild boar and three European origin breeds, covering ∼99.2% of the reference genome, at an average of ∼11.7-fold coverage.
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.
Journal ArticleDOI
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.