Affiliation:
1. Biocomputing Group, Department of Pharmacy and Biotechnology, University of Bologna , Bologna 40126, Italy
Abstract
Abstract
Motivation
The advent of massive DNA sequencing technologies is producing a huge number of human single-nucleotide polymorphisms occurring in protein-coding regions and possibly changing their sequences. Discriminating harmful protein variations from neutral ones is one of the crucial challenges in precision medicine. Computational tools based on artificial intelligence provide models for protein sequence encoding, bypassing database searches for evolutionary information. We leverage the new encoding schemes for an efficient annotation of protein variants.
Results
E-SNPs&GO is a novel method that, given an input protein sequence and a single amino acid variation, can predict whether the variation is related to diseases or not. The proposed method adopts an input encoding completely based on protein language models and embedding techniques, specifically devised to encode protein sequences and GO functional annotations. We trained our model on a newly generated dataset of 101 146 human protein single amino acid variants in 13 661 proteins, derived from public resources. When tested on a blind set comprising 10 266 variants, our method well compares to recent approaches released in literature for the same task, reaching a Matthews Correlation Coefficient score of 0.72. We propose E-SNPs&GO as a suitable, efficient and accurate large-scale annotator of protein variant datasets.
Availability and implementation
The method is available as a webserver at https://esnpsandgo.biocomp.unibo.it. Datasets and predictions are available at https://esnpsandgo.biocomp.unibo.it/datasets.
Supplementary information
Supplementary data are available at Bioinformatics online.
Funder
PRIN 2017
Italian Ministry of University and Research
Publisher
Oxford University Press (OUP)
Subject
Computational Mathematics,Computational Theory and Mathematics,Computer Science Applications,Molecular Biology,Biochemistry,Statistics and Probability
Cited by
16 articles.
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