Embed-Search-Align: DNA sequence alignment using Transformer models.

ABSTRACT:

Motivation

DNA sequence alignment, an important genomic task, involves assigning short DNA reads to the most probable locations on an extensive reference genome. Conventional methods tackle this challenge in two steps: genome indexing followed by efficient search to locate likely positions for given reads. Building on the success of Large Language Models in encoding text into embeddings, where the distance metric captures semantic similarity, recent efforts have encoded DNA sequences into vectors using Transformers and have shown promising results in tasks involving classification of short DNA sequences. Performance at sequence classification tasks does not, however, guarantee sequence alignment, where it is necessary to conduct a genome-wide search to align every read successfully

SUBMITTER: Holur P 

PROVIDER: S-EPMC11919449 | biostudies-literature | 2025 Mar

REPOSITORIES: biostudies-literature