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 beginners guide to SNP calling from high-throughput DNA-sequencing data
Andre Altmann,Peter Weber,Daniel M. Bader,Michael Preuss,Elisabeth B. Binder,Bertram Müller-Myhsok +5 more
TL;DR: This work reviews the essential building blocks for a pipeline that calls SNPs from raw HTS data and employs several alignment programs and SNP calling routines for highlighting the fact that the choice of the tools significantly affects the final results.
Journal ArticleDOI
Analyzing Effects of Naturally Occurring Missense Mutations
TL;DR: The paper provides several examples of the application of 3D structure-based methods to model the effects of protein stability and protein-protein interactions caused by missense mutations as well.
Journal ArticleDOI
Towards Precision Medicine: Advances in Computational Approaches for the Analysis of Human Variants
TL;DR: A detailed comparison of current human variant resources, including HGMD, OMIM, ClinVar, and UniProt/Swiss-Prot are provided, followed by an overview of the computational methods and techniques used to leverage the available data to predict novel deleterious variants.
Journal ArticleDOI
ARMC5 Mutations Are a Frequent Cause of Primary Macronodular Adrenal Hyperplasia
Guilherme Asmar Alencar,Antonio M. Lerario,Mirian Yumie Nishi,Beatriz Marinho de Paula Mariani,Madson Q. Almeida,Johanne Tremblay,Pavel Hamet,Isabelle Bourdeau,Maria Claudia Nogueira Zerbini,Maria Adelaide Albergaria Pereira,Gilberto Carlos Gomes,Manoel de Souza Rocha,Jose Luis Chambo,André Lacroix,Berenice B. Mendonca,Maria Candida Barisson Villares Fragoso +15 more
TL;DR: Inherited autosomal dominant mutations in the ARMC5 gene are a frequent cause of familial primary macronodular adrenal hyperplasia, and biallelic inactivation of AR MC5 is consistent with its role as a potential tumor suppressor gene.
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Fast implementation of real-time fruit detection in apple orchards using deep learning
Hanwen Kang,Chao Chen +1 more
TL;DR: The experimental results show that LedNet can perform real-time apple detection in orchards robustly and efficiently.
References
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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.
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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.