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
Integrative analysis of genomic and transcriptomic characteristics associated with progression of aggressive thyroid cancer
Seong Keun Yoo,Young Shin Song,Eun Kyung Lee,Jinha Hwang,Hwan Hee Kim,Gyeongseo Jung,Young A. Kim,Su Jin Kim,Sun Wook Cho,Jae Kyung Won,Eun Jae Chung,Jong Yeon Shin,Kyu Eun Lee,Kyu Eun Lee,Jong Il Kim,Young Joo Park,Young Joo Park,Jeong-Sun Seo +17 more
TL;DR: The genomic and transcriptomic landscape of ATC and DTC is revealed, highlighting potential therapeutic vulnerabilities and the activation of JAK-STAT signaling pathway could be a potential druggable target in RAS-positive ATC.
Journal ArticleDOI
A novel germline mutation in BAP1 predisposes to familial clear-cell renal cell carcinoma.
Megan N. Farley,Laura S. Schmidt,Laura S. Schmidt,Jessica L. Mester,Samuel Peña-Llopis,Andrea Pavia-Jimenez,Alana Christie,Cathy D. Vocke,Christopher J. Ricketts,James Peterson,Lindsay A. Middelton,Lisa N. Kinch,Nick V. Grishin,Maria J. Merino,Adam R. Metwalli,Chao Xing,Xian Jin Xie,Patricia L. M. Dahia,Charis Eng,W. Marston Linehan,James Brugarolas +20 more
TL;DR: Findings suggest that BAP1 is an early-onset familial RCC predisposing gene, which may drive tumor development in a subset of patients with inherited renal cell cancer.
Journal ArticleDOI
Enrichment of sequencing targets from the human genome by solution hybridization
Ryan Tewhey,Ryan Tewhey,Masakazu Nakano,Masakazu Nakano,Xiaoyun Wang,Xiaoyun Wang,Carlos Pabón-Peña,Barbara Novak,A. Giuffre,Eric Lin,Scott Happe,Doug N Roberts,Emily M LeProust,Eric J. Topol,Olivier Harismendy,Olivier Harismendy,Kelly A. Frazer,Kelly A. Frazer +17 more
TL;DR: It is demonstrated that the tiling probe frequency is important for generating sequence data with high uniform coverage of targets, and 93% sensitivity to detect SNPs, with a calling accuracy greater than 99%.
Journal ArticleDOI
Thiopurine S-methyltransferase pharmacogenetics: variant allele functional and comparative genomics.
TL;DR: In this paper, the authors investigated the functional effects of human TPMT variant alleles that alter the encoded amino acid sequence of the enzyme, and found that the level of enzyme protein was the major factor responsible for variation in activity.
Journal ArticleDOI
Instantaneous Within-Patient Diversity of Pseudomonas aeruginosa Quorum-Sensing Populations from Cystic Fibrosis Lung Infections
TL;DR: The results show that the diversity of QS types is high within and among patients, suggesting diverse selection pressures in the CF lung, and shows that conclusions about the properties of P. aeruginosa QS populations in individual CF infections cannot be drawn from the characterization of one or a few selected isolates.
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.