OligoFormer: an accurate and robust prediction method for siRNA design.

ABSTRACT:

Motivation

RNA interference (RNAi) has become a widely used experimental approach for post-transcriptional regulation and is increasingly showing its potential as future targeted drugs. However, the prediction of highly efficient siRNAs (small interfering RNAs) is still hindered by dataset biases, the inadequacy of prediction methods, and the presence of off-target effects. To overcome these limitations, we propose an accurate and robust prediction method, OligoFormer, for siRNA design.

Results

OligoFormer comprises three different modules including thermodynamic calculation, RNA-FM module, and Oligo encoder. Oligo encoder is the core module based on the transformer encoder. Taking siRNA and mRNA sequences as input, OligoFormer can obtain thermodynamic parameters, RNA-FM emb

SUBMITTER: Bai Y 

PROVIDER: S-EPMC11494384 | biostudies-literature | 2024 Oct

REPOSITORIES: biostudies-literature