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Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm
This protocol describes the use of the 'Sorting Tolerant From Intolerant' (SIFT) algorithm in predicting whether an AAS affects protein function.
SIFT: predicting amino acid changes that affect protein function
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.
Amino acid substitution matrices from protein blocks.
This work has derived substitution matrices from about 2000 blocks of aligned sequence segments characterizing more than 500 groups of related proteins, leading to marked improvements in alignments and in searches using queries from each of the groups.
Predicting deleterious amino acid substitutions.
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.
SIFT web server: predicting effects of amino acid substitutions on proteins
- Ngak-Leng Sim, Prateek Kumar, Jing Hu, S. Henikoff, Georg Schneider, P. Ng
- Computer Science, BiologyNucleic Acids Res.
- 9 June 2012
This work has updated SIFT’s genome-wide prediction tool since the last publication in 2009, and added new features to the insertion/deletion (indel) tool.
The Centromere Paradox: Stable Inheritance with Rapidly Evolving DNA
Incompatibilities between rapidly evolving Centromeric components may be responsible for both the organization of centromeric regions and the reproductive isolation of emerging species.
Genome-wide analysis of Arabidopsis thaliana DNA methylation uncovers an interdependence between methylation and transcription
DNA methylation is mapped in the entire Arabidopsis thaliana genome at high resolution, indicating that genic transcription and DNA methylation are closely interwoven processes.
The epigenetic progenitor origin of human cancer
This work suggests that non-neoplastic but epigenetically disrupted stem/progenitor cells might be a crucial target for cancer risk assessment and chemoprevention.
Unidirectional digestion with exonuclease III creates targeted breakpoints for DNA sequencing.
- S. Henikoff
- 1 June 1984