SuSPect: Enhanced Prediction of Single Amino Acid Variant (SAV) Phenotype Using Network Features
By C. Yates, Ioannis Filippis, Lawrence A. Kelley, Michael J.E. Sternberg. 2014
245 citations recorded by the source corpus.
Whole-genome and exome sequencing studies reveal many genetic variants between individuals, some of which are linked to disease. Many of these variants lead to single amino acid variants (SAVs), and accurate prediction of their phenotypic impact is important. Incorporating sequence conservation and network-level features, we have developed a method, SuSPect (Disease-Susceptibility-based SAV Phenotype Prediction), for predicting how likely SAVs are to be associated with disease. SuSPect performs significantly better than other available batch methods on the VariBench benchmarking dataset, with a balanced accuracy of 82%. SuSPect is available at www.sbg.bio.ic.ac.uk/suspect. The Web site has been implemented in Perl and SQLite and is compatible with modern browsers. An SQLite database of possible missense variants in the human proteome is available to download at www.sbg.bio.ic.ac.uk/suspect/download.html.
Subfields: Molecular Biology
How researchers see this paper
The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.
In Molecular Biology
- Michael J.E. Sternberg
- Lawrence A. Kelley
- C. Yates
- Mark N. Wass
- Zsuzsanna Dosztányi
- Stefans Mezulis
- Yang Zhang
- Andrej Sali
Citations in the corpus
- Prediction of protein disorder based on IUPred (2018, background): “73 The list of various approaches that take advantage of the energy estimation approach or directly the output of IUPred predictions is given in Table I.”
- Using deep mutational scanning to benchmark variant effect predictors and identify disease mutations (2020, unknown): “SuSPect (Yates et al , 2014) showed good performance across most groups, ranking 5 th for humans 3 rd for bacteria and 2 nd for viral proteins.”
- The Phyre2 web portal for protein modelling, prediction and analysis (2015, background): “See Steps 25–28 of the PROCEDURE for details on alignment interpretation.”