DeepCDS: Ab initio coding sequence prediction in prokaryotic short nucleotide sequences

Abstract

Accurate coding sequence prediction in short prokaryotic metagenomic sequences, such as Illumina reads, remains challenging due to sequence fragmentation, unknown sequence origins, and sequencing errors. Here we introduce DeepCDS, a deep learning-based ab initio coding sequence predictor trained on short prokaryotic sequences with and without simulated Illumina-like sequencing errors. DeepCDS integrates ESM-2 protein language model embeddings with nucleotide-level information to predict complete and fragmented coding sequence regions. Benchmarking on 215 phylogenetically diverse prokaryotic organisms demonstrates that DeepCDS consistently outperforms current state-of-the-art methods in coding sequence detection across sequence lengths from 75bp to 1000bp, including improved identification of both canonical and non-canonical start codons as well as stop codons, and greater robustness to different sequencing error profiles. DeepCDS also remains operational on sequences shorter than existing tools support. We additionally evaluate DeepCDS on a simulated metagenomic dataset from the Critical Assessment of Metagenome Interpretation initiative, where it likewise achieves the strongest performance among tested tools. These findings demonstrate that protein language models capture distinct signals relevant for nucleotide-level coding sequence detection, especially at very short lengths. Ultimately, DeepCDS may help uncover the functional potential of the vast microbial diversity that remains genomically uncharacterized.