DNA-Aligner

Abstract

The DNA-ALIGNER is a novel model designed to align mRNA and gene sequences. In cellular biology, DNA is transcribed into mRNA, which serves as the template for protein synthesis. DNA-ALIGNER addresses the challenge of aligning gene and mRNA sequences by leveraging pre-trained embeddings from the Nucleotide Transformer. The model employs a multi-tower architecture, including mRNATower, GeneTower, and middleTower, to process both gene and mRNA sequences independently and jointly. By performing sequence alignment, DNA-ALIGNER learns meaningful numerical representations of gene data, which can be utilized for downstream tasks in various biological applications. The model uses masked language modeling (MLM) and sequence reconstruction techniques to ensure accurate alignment. Loss functions, including cross-entropy for MLM and DICE loss for sequence reconstruction and Alignment, optimize the alignment and learning process. The DNA-ALIGNER provides a powerful tool for bioinformatics research, enabling a better under- standing of gene sequences, mutation analysis, and application in task-specific networks.