PLM-BLAST: distant homology detection based on direct comparison of sequence representations from protein language models.

ABSTRACT:

Motivation

The detection of homology through sequence comparison is a typical first step in the study of protein function and evolution. In this work, we explore the applicability of protein language models to this task.

Results

We introduce pLM-BLAST, a tool inspired by BLAST, that detects distant homology by comparing single-sequence representations (embeddings) derived from a protein language model, ProtT5. Our benchmarks reveal that pLM-BLAST maintains a level of accuracy on par with HHsearch for both highly similar sequences (with >50% identity) and markedly divergent sequences (with <30% identity), while being significantly faster. Additionally, pLM-BLAST stands out among other embedding-based tools due to its ability to compute local alignments. We show that these loc

SUBMITTER: Kaminski K 

PROVIDER: S-EPMC10576641 | biostudies-literature | 2023 Oct

REPOSITORIES: biostudies-literature