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
More filters
Journal ArticleDOI
Expanding the computational toolbox for mining cancer genomes
TL;DR: Cancer genomics software and the insights that have been gained from their application are reviewed.
Journal ArticleDOI
Mutations in BMP4 Are Associated with Subepithelial, Microform, and Overt Cleft Lip
Satoshi Suzuki,Satoshi Suzuki,Mary L. Marazita,Margaret E. Cooper,Nobutomo Miwa,Anne V. Hing,Astanand Jugessur,Nagato Natsume,Kazuo Shimozato,Naofumi Ohbayashi,Yasushi Suzuki,Teruyuki Niimi,Katsuhiro Minami,Masahiko Yamamoto,Tserendorj J. Altannamar,Tudevdorj Erkhembaatar,Hiroo Furukawa,Sandra Daack-Hirsch,Jamie L'Heureux,Carla A. Brandon,Seth M. Weinberg,Seth M. Weinberg,Katherine Neiswanger,Frederic W.-B. Deleyiannis,Javier Enríquez de Salamanca,Alexandre R. Vieira,Andrew C. Lidral,James F. Martin,Jeffrey C. Murray +28 more
TL;DR: Results provide confirmation that microforms and subepithelial OOM defects are part of the spectrum of CL/P and should be considered during clinical evaluation of families with clefts and suggest a role for BMP4 in wound healing.
Journal ArticleDOI
Low-density lipoprotein receptor gene familial hypercholesterolemia variant database: update and pathological assessment.
Ebele Usifo,Sarah Leigh,Ros Whittall,Nicholas Lench,Alison Taylor,Corin Yeats,Christine A. Orengo,Andrew J. Martin,Jacopo Celli,Steve E. Humphries +9 more
TL;DR: An update of the UCL LDLR variant database to include variants reported in the literature and in‐house between 2008 and 2010, transfer of the database to LOVDv.2.0 platform and pathogenicity analysis, which concludes that 79% of the reported variants are likely to be disease causing.
Journal ArticleDOI
Exome sequencing and disease-network analysis of a single family implicate a mutation in KIF1A in hereditary spastic paraparesis
Yaniv Erlich,Simon Edvardson,Emily Hodges,Shamir Zenvirt,Pramod Thekkat,Avraham Shaag,Talya Dor,Gregory J. Hannon,Orly Elpeleg +8 more
TL;DR: It is demonstrated that disease-network analysis provides an additional layer of information to stratify variations even in the presence of incomplete sequencing coverage, a known limitation of exome sequencing.
Journal ArticleDOI
Real-Time Targeted Genome Profile Analysis of Pancreatic Ductal Adenocarcinomas Identifies Genetic Alterations That Might Be Targeted With Existing Drugs or Used as Biomarkers
Aatur D. Singhi,Ben George,Joel R. Greenbowe,Jon Chung,James Suh,Anirban Maitra,Samuel J. Klempner,Andrew Eugene Hendifar,Javle Milind,Talia Golan,Randall E. Brand,Amer H. Zureikat,Somak Roy,Alexa B. Schrock,Vincent A. Miller,Jeffrey S. Ross,Siraj M. Ali,Nathan Bahary +17 more
TL;DR: In targeted genomic profile analyses of 3594 PDACs, 17% were found to contain genomic alterations that might make the tumor cells susceptible to currently used anticancer agents and these alterations might be used as biomarkers for early detection.
References
More filters
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.